Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 99090824
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: 99090824
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 317 characters in sequence are not A, C, G, or T
File 11 of 318
Found at i:2800362 original size:14 final size:15
Alignment explanation
Indices: 2800339--2800371 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
2800329 CGCTGAGGTA
2800339 TTTT-CAATTTCTG-
1 TTTTCCAATTTCTGC
2800352 TTTTCCAATTTCTGC
1 TTTTCCAATTTCTGC
2800367 TTTTC
1 TTTTC
2800372 AAAAAAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.22
14 9 0.50
15 5 0.28
ACGTcount: A:0.12, C:0.21, G:0.06, T:0.61
Consensus pattern (15 bp):
TTTTCCAATTTCTGC
Found at i:2800537 original size:14 final size:14
Alignment explanation
Indices: 2800518--2800552 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
2800508 CGCTGAGGTA
* *
2800518 TTTTCAATTTCTGT
1 TTTTCAATTTATGC
2800532 TTTTCAATTTATGC
1 TTTTCAATTTATGC
2800546 TTTTCAA
1 TTTTCAA
2800553 AAACCAACCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.20, C:0.14, G:0.06, T:0.60
Consensus pattern (14 bp):
TTTTCAATTTATGC
Found at i:2801278 original size:22 final size:24
Alignment explanation
Indices: 2801237--2801294 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 24
2801227 CAAAAACCCC
2801237 AAAACCCAATCAC-AGAAG-CCAA-
1 AAAACCCAATC-CTAGAAGCCCAAT
2801259 AAAACCCAATACCTAG-AGCCCAAT
1 AAAACCCAAT-CCTAGAAGCCCAAT
*
2801283 TAAACCCAATCC
1 AAAACCCAATCC
2801295 CTAAACCCAT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
22 13 0.42
23 9 0.29
24 9 0.29
ACGTcount: A:0.48, C:0.34, G:0.07, T:0.10
Consensus pattern (24 bp):
AAAACCCAATCCTAGAAGCCCAAT
Found at i:2801787 original size:24 final size:25
Alignment explanation
Indices: 2801760--2801812 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
2801750 TTTGAATCGG
*
2801760 TTTCATC-TATTATTTTGTTTTTTT
1 TTTCATCTTATTATTTTGTTCTTTT
* * *
2801784 TTTCTTCTTCTTCTTTTGTTCTTTT
1 TTTCATCTTATTATTTTGTTCTTTT
2801809 TTTC
1 TTTC
2801813 TACTCATAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 6 0.25
25 18 0.75
ACGTcount: A:0.06, C:0.15, G:0.04, T:0.75
Consensus pattern (25 bp):
TTTCATCTTATTATTTTGTTCTTTT
Found at i:2802480 original size:22 final size:22
Alignment explanation
Indices: 2802452--2802498 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
2802442 TTTTTGTTTC
*
2802452 ATTATTAAA-ATTTGTTATTATT
1 ATTATTAAATA-TTGTCATTATT
2802474 ATTATTAAATATTGTCATTATT
1 ATTATTAAATATTGTCATTATT
2802496 ATT
1 ATT
2802499 CTAATATTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.57
Consensus pattern (22 bp):
ATTATTAAATATTGTCATTATT
Found at i:2802506 original size:20 final size:19
Alignment explanation
Indices: 2802471--2802508 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
2802461 ATTTGTTATT
2802471 ATTATTATTAAATATTGTC
1 ATTATTATTAAATATTGTC
*
2802490 ATTATTATTCTAATATTGT
1 ATTATTATT-AAATATTGT
2802509 TAATGTTATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.55
Consensus pattern (19 bp):
ATTATTATTAAATATTGTC
Found at i:2802890 original size:20 final size:20
Alignment explanation
Indices: 2802867--2802932 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
2802857 TTTTAAATAC
2802867 TCTTATATTATGTATATTAT
1 TCTTATATTATGTATATTAT
* *
2802887 TCTTTTAAATAT-TATATT-T
1 TCTTAT-ATTATGTATATTAT
*
2802906 TCTATATATCATGTATA-TAT
1 TCT-TATATTATGTATATTAT
2802926 T-TTATAT
1 TCTTATAT
2802933 ATTACGTACA
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
18 5 0.14
19 9 0.24
20 19 0.51
21 4 0.11
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (20 bp):
TCTTATATTATGTATATTAT
Found at i:2803175 original size:21 final size:22
Alignment explanation
Indices: 2803151--2803194 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
2803141 ATTATGTAGG
*
2803151 TATATATA-TATATATATTTTT
1 TATATATATTATATACATTTTT
2803172 TATATATATTATATACATTTTT
1 TATATATATTATATACATTTTT
2803194 T
1 T
2803195 CTAAGAAAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (22 bp):
TATATATATTATATACATTTTT
Found at i:2815458 original size:19 final size:18
Alignment explanation
Indices: 2815436--2815481 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 18
2815426 CTTTATGTTG
2815436 TTTATTATTCTATTTATTA
1 TTTATTATTCTA-TTATTA
2815455 TTTATTATATTCTATTATTA
1 TTTA-T-TATTCTATTATTA
2815475 -TTATTAT
1 TTTATTAT
2815482 CATTCTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 3 0.12
18 1 0.04
19 7 0.28
20 7 0.28
21 7 0.28
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTATTATTCTATTATTA
Found at i:2815465 original size:16 final size:16
Alignment explanation
Indices: 2815437--2815478 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
2815427 TTTATGTTGT
*
2815437 TTATTATTCTATT-TA
1 TTATTATTATATTCTA
2815452 TTATTTATTATATTCTA
1 TTA-TTATTATATTCTA
2815469 TTATTATTAT
1 TTATTATTAT
2815479 TATCATTCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 3 0.12
16 16 0.67
17 5 0.21
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (16 bp):
TTATTATTATATTCTA
Found at i:2815662 original size:21 final size:23
Alignment explanation
Indices: 2815638--2815679 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
2815628 GTATGCATGC
2815638 ATATGTT-T-ATATATATATATT
1 ATATGTTCTAATATATATATATT
*
2815659 ATATTTTCTAATATATATATA
1 ATATGTTCTAATATATATATA
2815680 GATATATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 1 0.06
23 11 0.61
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (23 bp):
ATATGTTCTAATATATATATATT
Found at i:2832743 original size:89 final size:85
Alignment explanation
Indices: 2832579--2832828 Score: 247
Period size: 89 Copynumber: 2.9 Consensus size: 85
2832569 AGAATCAGTA
* * * *
2832579 AATTCACAGGTCTT-ACCCCCATAAGCAGTAGGGGAATAGATCGAAG-GTAACGAGCTTTAACCC
1 AATT-ACAGATCTTAACCCCC-TAAGCAGTAGGGAAACAGATCGAAGAG-AA-GAGCTTTAAACC
* *
2832642 CCTAAGCAGTAGGGTAACAGGCTG
62 CCTAAGCAGTAGGGTAACAGACCG
* *
2832666 AAGATTTACAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGACGAAGGGTTTTAAACC
1 -A-A-TTACAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGA-GAAGAGCTTTAAACC
* *
2832731 CCTAATCGGTAGGGTAACAGACCG
62 CCTAAGCAGTAGGGTAACAGACCG
* * * * *
2832755 AATTGCAAATCTTATCTCCCTAAGCAGTAGGGAAACAGATCGAAGATGAAGATC-TT-AACTCCC
1 AATTACAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGA-GAAGAGCTTTAAAC-CCC
2832818 TAAGCAGTAGG
64 TAAGCAGTAGG
2832829 AAAACAGATC
Statistics
Matches: 136, Mismatches: 20, Indels: 15
0.80 0.12 0.09
Matches are distributed among these distances:
84 3 0.02
85 14 0.10
86 44 0.32
87 1 0.01
88 2 0.01
89 61 0.45
90 10 0.07
91 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.20
Consensus pattern (85 bp):
AATTACAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGAGAAGAGCTTTAAACCCCTA
AGCAGTAGGGTAACAGACCG
Found at i:2832786 original size:42 final size:43
Alignment explanation
Indices: 2832600--2832878 Score: 197
Period size: 44 Copynumber: 6.4 Consensus size: 43
2832590 CTTACCCCCA
* * * * * *
2832600 TAAGCAGTAGGGGAATAGATCGAAGGT-AACGAGCTTTAACCCCC
1 TAAGCAGTAGGGAAACAGACCGAAGATGAA-GATC-TTAACTCCC
* * * * *
2832644 TAAGCAGTAGGGTAACAGGCTGAAGATTTACAGATCTTAACCCCC
1 TAAGCAGTAGGGAAACAGACCGAAGA-TGA-AGATCTTAACTCCC
* * * *
2832689 TAAGCAGTAGGGAAACAGATCGAAGACGAAGGGTTTTAAAC-CCC
1 TAAGCAGTAGGGAAACAGACCGAAGATGAA-GATCTT-AACTCCC
* * * * *
2832733 TAATCGGTAGGGTAACAGACCGAA-TTGCAA-ATCTTATCTCCC
1 TAAGCAGTAGGGAAACAGACCGAAGATG-AAGATCTTAACTCCC
*
2832775 TAAGCAGTAGGGAAACAGATCGAAGATGAAGATCTTAACTCCC
1 TAAGCAGTAGGGAAACAGACCGAAGATGAAGATCTTAACTCCC
* * * * ** *
2832818 TAAGCAGTAGGAAAACAGATCAAAGATGATGGGCTTTAACCCCC
1 TAAGCAGTAGGGAAACAGACCGAAGATGAAGATC-TTAACTCCC
*
2832862 TAAGCAGTAGGGTAACA
1 TAAGCAGTAGGGAAACA
2832879 AGCCAGATTT
Statistics
Matches: 187, Mismatches: 38, Indels: 20
0.76 0.16 0.08
Matches are distributed among these distances:
41 2 0.01
42 28 0.15
43 44 0.24
44 73 0.39
45 35 0.19
46 4 0.02
47 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.20
Consensus pattern (43 bp):
TAAGCAGTAGGGAAACAGACCGAAGATGAAGATCTTAACTCCC
Found at i:2832873 original size:129 final size:131
Alignment explanation
Indices: 2832641--2832878 Score: 338
Period size: 129 Copynumber: 1.8 Consensus size: 131
2832631 AGCTTTAACC
* * *
2832641 CCCTAAGCAGTAGGGTAACAGGCTGAAGATTTACAGATCTTAACCCCCTAAGCAGTAGGGAAACA
1 CCCTAAGCAGTAGGGAAACAGGCTGAAGATTGACAGATCTTAACCCCCTAAGCAGTAGGAAAACA
* * * *
2832706 GATCGAAGACGAAGGGTTTTAAACCCCTAATCGGTAGGGTAACAGACCGAATTGCAAATCTTATC
66 GATCAAAGACGAAGGGCTTTAAACCCCTAAGCAGTAGGGTAACAGACCGAATTGCAAATCTTATC
2832771 T
131 T
* *
2832772 CCCTAAGCAGTAGGGAAACA-GATCGAAGA-TGA-AGATCTTAACTCCCTAAGCAGTAGGAAAAC
1 CCCTAAGCAGTAGGGAAACAGGCT-GAAGATTGACAGATCTTAACCCCCTAAGCAGTAGGAAAAC
* * *
2832834 AGATCAAAGATGATGGGCTTTAACCCCCTAAGCAGTAGGGTAACA
65 AGATCAAAGACGAAGGGCTTTAAACCCCTAAGCAGTAGGGTAACA
2832879 AGCCAGATTT
Statistics
Matches: 94, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
129 66 0.70
130 4 0.04
131 24 0.26
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.20
Consensus pattern (131 bp):
CCCTAAGCAGTAGGGAAACAGGCTGAAGATTGACAGATCTTAACCCCCTAAGCAGTAGGAAAACA
GATCAAAGACGAAGGGCTTTAAACCCCTAAGCAGTAGGGTAACAGACCGAATTGCAAATCTTATC
T
Found at i:2833081 original size:42 final size:41
Alignment explanation
Indices: 2833034--2833183 Score: 115
Period size: 42 Copynumber: 3.5 Consensus size: 41
2833024 GGTCTTAAAC
2833034 CCCTAAGCAGTAGGGAAACAGACCAAATTGCAGATCTTATCT
1 CCCTAAGCAGTAGGG-AACAGACCAAATTGCAGATCTTATCT
** * * * * *
2833076 CCCTAAGCAGTAGTGGAGTAGATCGAAGA-CGAAGAACCTTAAACT
1 CCCTAAGCAGTAG-GGAACAGA-CCAA-ATTGCAG-ATCTT-ATCT
***
2833121 -CCTAAGCAGTAGGGTAACAGGTTAAATTGCAGATCTTATCT
1 CCCTAAGCAGTAGGG-AACAGACCAAATTGCAGATCTTATCT
*
2833162 CCCTAAGCAGTAGTGGAGCAGA
1 CCCTAAGCAGTAG-GGAACAGA
2833184 TCGAAGACGA
Statistics
Matches: 81, Mismatches: 18, Indels: 18
0.69 0.15 0.15
Matches are distributed among these distances:
41 3 0.04
42 38 0.47
43 17 0.21
44 20 0.25
45 3 0.04
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (41 bp):
CCCTAAGCAGTAGGGAACAGACCAAATTGCAGATCTTATCT
Found at i:2833227 original size:86 final size:86
Alignment explanation
Indices: 2833027--2833318 Score: 356
Period size: 86 Copynumber: 3.4 Consensus size: 86
2833017 TTCATAGGGT
* * *
2833027 CTTAAACCCCTAAGCAGTAGGGAAACAGACCAAATTGCAGATCTTATCTCCCTAAGCAGTAGTGG
1 CTTAAACCCCTAAGCAGTAGGGTAACAGGCTAAATTGCAGATCTTATCTCCCTAAGCAGTAGTGG
*
2833092 AGTAGATCGAAGACGAAGAAC
66 AGCAGATCGAAGACGAAGAAC
* *
2833113 CTTAAACTCCTAAGCAGTAGGGTAACAGGTTAAATTGCAGATCTTATCTCCCTAAGCAGTAGTGG
1 CTTAAACCCCTAAGCAGTAGGGTAACAGGCTAAATTGCAGATCTTATCTCCCTAAGCAGTAGTGG
2833178 AGCAGATCGAAGACGAAGAAC
66 AGCAGATCGAAGACGAAGAAC
* * * * * ***
2833199 CTTAAACCCCCAAGCAGTAGGGTAACAGGTTGAGTATACAGATC-TAAAACCCTAAGCAGTAG-G
1 CTTAAACCCCTAAGCAGTAGGGTAACAGGCTAAAT-TGCAGATCTTATCTCCCTAAGCAGTAGTG
* * * *
2833262 GAAACAGATCAAAGATGACA-AGC
65 G-AGCAGATCGAAGACGA-AGAAC
* *
2833285 CTTAATCCCTTAAGCAGTAGGGTAACAGGCTAAA
1 CTTAAACCCCTAAGCAGTAGGGTAACAGGCTAAA
2833319 AATTAAATAT
Statistics
Matches: 179, Mismatches: 24, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
85 2 0.01
86 169 0.94
87 8 0.04
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.20
Consensus pattern (86 bp):
CTTAAACCCCTAAGCAGTAGGGTAACAGGCTAAATTGCAGATCTTATCTCCCTAAGCAGTAGTGG
AGCAGATCGAAGACGAAGAAC
Found at i:2834816 original size:19 final size:18
Alignment explanation
Indices: 2834792--2834837 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 18
2834782 TCTTATGTTG
2834792 TTTATTATTCTATTTATTA
1 TTTATTATTCTA-TTATTA
2834811 TTTATTATATTCTATTATTA
1 TTTA-T-TATTCTATTATTA
2834831 -TTATTAT
1 TTTATTAT
2834838 CATTCTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 3 0.12
18 1 0.04
19 7 0.28
20 7 0.28
21 7 0.28
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTATTATTCTATTATTA
Found at i:2834821 original size:16 final size:16
Alignment explanation
Indices: 2834793--2834834 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
2834783 CTTATGTTGT
*
2834793 TTATTATTCTATT-TA
1 TTATTATTATATTCTA
2834808 TTATTTATTATATTCTA
1 TTA-TTATTATATTCTA
2834825 TTATTATTAT
1 TTATTATTAT
2834835 TATCATTCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 3 0.12
16 16 0.67
17 5 0.21
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (16 bp):
TTATTATTATATTCTA
Found at i:2835018 original size:21 final size:23
Alignment explanation
Indices: 2834994--2835035 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
2834984 GTATGCATGC
2834994 ATATGTT-T-ATATATATATATT
1 ATATGTTCTAATATATATATATT
*
2835015 ATATTTTCTAATATATATATA
1 ATATGTTCTAATATATATATA
2835036 GATATATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 1 0.06
23 11 0.61
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (23 bp):
ATATGTTCTAATATATATATATT
Found at i:2837687 original size:23 final size:23
Alignment explanation
Indices: 2837543--2837687 Score: 99
Period size: 23 Copynumber: 6.6 Consensus size: 23
2837533 CAGCTCGTAT
**
2837543 GAGCTTACTGTTT-AGCTCGATA
1 GAGCTTACTGTTTCAGCTTAATA
** * *
2837565 GAGCTTACCATTTCAGCTCAATG
1 GAGCTTACTGTTTCAGCTTAATA
* *
2837588 GAGCTTACTGTTTTCAGCTCACT-
1 GAGCTTACTG-TTTCAGCTTAATA
**
2837611 GAAGCTTACCATTTC-G--T-AT-
1 G-AGCTTACTGTTTCAGCTTAATA
2837630 GAGCTTACTG-TTCAGCTTAATA
1 GAGCTTACTGTTTCAGCTTAATA
* *
2837652 GAGCTTACCGTTTCAGCTTAATG
1 GAGCTTACTGTTTCAGCTTAATA
*
2837675 GAGCTTATTGTTT
1 GAGCTTACTGTTT
2837688 ATCAGCTCAG
Statistics
Matches: 97, Mismatches: 17, Indels: 17
0.74 0.13 0.13
Matches are distributed among these distances:
17 3 0.03
18 8 0.08
19 2 0.02
20 1 0.01
21 2 0.02
22 21 0.22
23 42 0.43
24 18 0.19
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.37
Consensus pattern (23 bp):
GAGCTTACTGTTTCAGCTTAATA
Found at i:2837687 original size:87 final size:88
Alignment explanation
Indices: 2837537--2837696 Score: 259
Period size: 87 Copynumber: 1.8 Consensus size: 88
2837527 TCACCACAGC
* *
2837537 TCGTATGAGCTTACTGTTTAGCTCGATAGAGCTTACCATTTCAGCTCAATGGAGCTTACTGTTT-
1 TCGTATGAGCTTACTGTTCAGCTCAATAGAGCTTACCATTTCAGCTCAATGGAGCTTACTGTTTA
2837601 TCAGCTCACTGAAGCTTACCATT
66 TCAGCTCACTGAAGCTTACCATT
* * * *
2837624 TCGTATGAGCTTACTGTTCAGCTTAATAGAGCTTACCGTTTCAGCTTAATGGAGCTTATTGTTTA
1 TCGTATGAGCTTACTGTTCAGCTCAATAGAGCTTACCATTTCAGCTCAATGGAGCTTACTGTTTA
2837689 TCAGCTCA
66 TCAGCTCA
2837697 GGAAGAGCTT
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
87 58 0.88
88 8 0.12
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.37
Consensus pattern (88 bp):
TCGTATGAGCTTACTGTTCAGCTCAATAGAGCTTACCATTTCAGCTCAATGGAGCTTACTGTTTA
TCAGCTCACTGAAGCTTACCATT
Found at i:2842365 original size:30 final size:30
Alignment explanation
Indices: 2842331--2842393 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
2842321 ACTTAACAAG
*
2842331 CAAATGCTTTTAAAATAATAAAAAAATTAA
1 CAAATGCCTTTAAAATAATAAAAAAATTAA
*
2842361 CAAATGCCTTTAAAATAATAAGAAAATTAA
1 CAAATGCCTTTAAAATAATAAAAAAATTAA
2842391 CAA
1 CAA
2842394 TAAAATAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.59, C:0.10, G:0.05, T:0.27
Consensus pattern (30 bp):
CAAATGCCTTTAAAATAATAAAAAAATTAA
Found at i:2850022 original size:2 final size:2
Alignment explanation
Indices: 2850015--2850045 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2850005 ATAATGTAGT
2850015 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2850046 TCATAAGATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2850660 original size:21 final size:20
Alignment explanation
Indices: 2850607--2850672 Score: 80
Period size: 21 Copynumber: 3.2 Consensus size: 20
2850597 AATAAGGATG
*
2850607 ATATAAAAATATATACATGT
1 ATATAAAAATATATACATAT
2850627 ATA-AAAATATATATACATAAT
1 ATATAAAA-ATATATACAT-AT
*
2850648 ATATAAAAGTATATGACATAT
1 ATATAAAAATATAT-ACATAT
2850669 ATAT
1 ATAT
2850673 TAGAAACGAT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
19 4 0.10
20 13 0.32
21 15 0.38
22 8 0.20
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.35
Consensus pattern (20 bp):
ATATAAAAATATATACATAT
Found at i:2852608 original size:11 final size:11
Alignment explanation
Indices: 2852592--2852620 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
2852582 ACATTCTATA
2852592 ATTAATTTAAT
1 ATTAATTTAAT
2852603 ATTAATTTAAT
1 ATTAATTTAAT
2852614 ATTAATT
1 ATTAATT
2852621 ATTTAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
ATTAATTTAAT
Found at i:2853028 original size:39 final size:40
Alignment explanation
Indices: 2852959--2853047 Score: 135
Period size: 39 Copynumber: 2.2 Consensus size: 40
2852949 TAAAAAGTAT
* *
2852959 TTATATTAAAAACACTATCATAAATATAATAAATGTTTTA
1 TTATATTAAAAACACTATAATAAATATAATAAATATTTTA
*
2852999 TTATATTAAAAAGACTA-AATAAATATAATAAATATTTTA
1 TTATATTAAAAACACTATAATAAATATAATAAATATTTTA
*
2853038 TTGTATTAAA
1 TTATATTAAA
2853048 TATAAATTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
39 29 0.64
40 16 0.36
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.40
Consensus pattern (40 bp):
TTATATTAAAAACACTATAATAAATATAATAAATATTTTA
Found at i:2856516 original size:2 final size:2
Alignment explanation
Indices: 2856511--2856541 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2856501 TTGGTGTGTG
2856511 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2856542 TAATATGGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2858506 original size:22 final size:21
Alignment explanation
Indices: 2858476--2858528 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 21
2858466 CAATTGAACT
2858476 AAATCTCAATCAATTATTTTTTA
1 AAAT-TCAATCAATTA-TTTTTA
2858499 AAATTCAA-C-A-TATTTTTA
1 AAATTCAATCAATTATTTTTA
2858517 AAA--CAATCAATT
1 AAATTCAATCAATT
2858529 TATAAACCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
16 3 0.11
17 1 0.04
18 10 0.37
19 3 0.11
20 1 0.04
21 1 0.04
22 4 0.15
23 4 0.15
ACGTcount: A:0.45, C:0.13, G:0.00, T:0.42
Consensus pattern (21 bp):
AAATTCAATCAATTATTTTTA
Found at i:2860514 original size:252 final size:254
Alignment explanation
Indices: 2860067--2860527 Score: 737
Period size: 252 Copynumber: 1.8 Consensus size: 254
2860057 CGAAGTGGAT
* *
2860067 ATTAAGATTCTCTTGTTCCGAAGAAATAAAATATCACATCCAGCATGTAGGACACGACATTTCAA
1 ATTAAGATTATCTAGTTCCGAAGAAATAAAATATCACATCCAGCATGTAGGACACGACATTTCAA
*
2860132 ACCTTCGATACCAAAATAACCTCATGATTTCCAAAACTTACACATTGAAACTTTAAAAAGGATAT
66 ACCTTCGATACCAAAATAACCTCATGATTCCCAAAACTTACACATTGAAACTTTAAAAAGGATAT
* * * *
2860197 TCGGTTGTTTGGTCTAACGACAAATCGAAACCCAACACGTAGGGCACAATTTCTCGAAATTTCCA
131 TCGGTCGTTCGGCCAAACGACAAATCGAAACCCAACACGTAGGGCACAATTTCTCGAAATTTCCA
2860262 AACACGAAATATTGTCTTGTTTAAAAAAAACTCGAATAAAAATGCAATTGTATGAAACA
196 AACACGAAATATTGTCTTGTTTAAAAAAAACTCGAATAAAAATGCAATTGTATGAAACA
** *
2860321 ATTAAGATTATCTAGTTTTGAAGAAATAAAATATCACATCCAGCA-GTAGGACACGATATTTCAA
1 ATTAAGATTATCTAGTTCCGAAGAAATAAAATATCACATCCAGCATGTAGGACACGACATTTCAA
* * * * * *
2860385 ACCTTCGATTCCAAAATCATCTCATGATTCCCAAAACTT-TACATTGAAATTTTGAAAAGGATAT
66 ACCTTCGATACCAAAATAACCTCATGATTCCCAAAACTTACACATTGAAACTTTAAAAAGGATAT
* *
2860449 TCGGTCGTTCGGCCAAACGATAAATCGAAACCTAACACGTAGGGCACAATTTCTCGAAATTTCCA
131 TCGGTCGTTCGGCCAAACGACAAATCGAAACCCAACACGTAGGGCACAATTTCTCGAAATTTCCA
*
2860514 AACGCGAAATATTG
196 AACACGAAATATTG
2860528 CCTTCAACTT
Statistics
Matches: 188, Mismatches: 19, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
252 94 0.50
253 53 0.28
254 41 0.22
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.28
Consensus pattern (254 bp):
ATTAAGATTATCTAGTTCCGAAGAAATAAAATATCACATCCAGCATGTAGGACACGACATTTCAA
ACCTTCGATACCAAAATAACCTCATGATTCCCAAAACTTACACATTGAAACTTTAAAAAGGATAT
TCGGTCGTTCGGCCAAACGACAAATCGAAACCCAACACGTAGGGCACAATTTCTCGAAATTTCCA
AACACGAAATATTGTCTTGTTTAAAAAAAACTCGAATAAAAATGCAATTGTATGAAACA
Found at i:2863529 original size:39 final size:39
Alignment explanation
Indices: 2863486--2863765 Score: 418
Period size: 39 Copynumber: 7.2 Consensus size: 39
2863476 CGAAGTTTAG
* *
2863486 CTGAAGCACATAAGTGCTAAACGGAAGCCC-AGAGGCTAA
1 CTGAAGCACAAAAGTGCTAAACGGAAGCCCGA-AGGCTGA
* * *
2863525 CTGAAGCACACAAGTGCTAAACGGAAGCCCAAAGGCTAA
1 CTGAAGCACAAAAGTGCTAAACGGAAGCCCGAAGGCTGA
* *
2863564 CTGAAGCACACAAGTGCTAAACGGAAGCCCGAAGGTTGA
1 CTGAAGCACAAAAGTGCTAAACGGAAGCCCGAAGGCTGA
2863603 CTGAAGCACAAAAGTGCTAAACGGAAGCCCGAAGGCTGA
1 CTGAAGCACAAAAGTGCTAAACGGAAGCCCGAAGGCTGA
*
2863642 CTGAAGCACAGAAGTGCTAAACGGAAGCCCGAAGGCTGA
1 CTGAAGCACAAAAGTGCTAAACGGAAGCCCGAAGGCTGA
* *
2863681 CTGAAGCACAAAAGTGCTAAATGGAAGCTCGAAGGCTGA
1 CTGAAGCACAAAAGTGCTAAACGGAAGCCCGAAGGCTGA
* * * *
2863720 CTAAAGCACAGAAGTGCTAAACAGAAGCCCGAAGGCTAA
1 CTGAAGCACAAAAGTGCTAAACGGAAGCCCGAAGGCTGA
2863759 CTGAAGC
1 CTGAAGC
2863766 TCACCAGAGC
Statistics
Matches: 223, Mismatches: 17, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
39 222 1.00
40 1 0.00
ACGTcount: A:0.39, C:0.23, G:0.27, T:0.12
Consensus pattern (39 bp):
CTGAAGCACAAAAGTGCTAAACGGAAGCCCGAAGGCTGA
Found at i:2866753 original size:3 final size:3
Alignment explanation
Indices: 2866745--2866791 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
2866735 AACATGAAGA
2866745 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2866792 GGAGATTAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2867079 original size:2 final size:2
Alignment explanation
Indices: 2867072--2867122 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
2867062 AAAAGAAAAC
2867072 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2867114 AT AT AT AT A
1 AT AT AT AT A
2867123 CGCGAATAGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2875082 original size:12 final size:12
Alignment explanation
Indices: 2875065--2875093 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
2875055 AATATCAATC
2875065 ATAAAAAAAATT
1 ATAAAAAAAATT
2875077 AT-AAAAAAATT
1 ATAAAAAAAATT
2875088 ATAAAA
1 ATAAAA
2875094 TCTTGTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
ATAAAAAAAATT
Found at i:2875084 original size:11 final size:11
Alignment explanation
Indices: 2875068--2875093 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2875058 ATCAATCATA
2875068 AAAAAAATTAT
1 AAAAAAATTAT
2875079 AAAAAAATTAT
1 AAAAAAATTAT
2875090 AAAA
1 AAAA
2875094 TCTTGTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (11 bp):
AAAAAAATTAT
Found at i:2875720 original size:22 final size:21
Alignment explanation
Indices: 2875676--2875720 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2875666 TAATTTTTTA
*
2875676 AAAATATGTAAATATTAATAT
1 AAAATATGTAAATATTAACAT
2875697 AAAATAT-TATAATATTCAACAT
1 AAAATATGTA-AATATT-AACAT
2875719 AA
1 AA
2875721 TTAAACATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 2 0.10
21 13 0.62
22 6 0.29
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (21 bp):
AAAATATGTAAATATTAACAT
Found at i:2878935 original size:20 final size:21
Alignment explanation
Indices: 2878891--2878936 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
2878881 TTTAATAAAA
2878891 TAAATTTTAGCAATAATAATTT
1 TAAATTTTA-CAATAATAATTT
2878913 TAAATTTTA-AATAAT-ATTAT
1 TAAATTTTACAATAATAATT-T
2878933 TAAA
1 TAAA
2878937 ATATTATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 3 0.13
20 11 0.48
22 9 0.39
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (21 bp):
TAAATTTTACAATAATAATTT
Found at i:2878941 original size:11 final size:11
Alignment explanation
Indices: 2878925--2878954 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
2878915 AATTTTAAAT
2878925 AATATTATTAA
1 AATATTATTAA
2878936 AATATTATTAA
1 AATATTATTAA
2878947 AATTATTA
1 AA-TATTA
2878955 ATAATAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
AATATTATTAA
Found at i:2881456 original size:28 final size:27
Alignment explanation
Indices: 2881424--2881479 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
2881414 GTATACTCTG
*
2881424 ATATTG-TAAGGGGCTATGGCCCAGATTA
1 ATATTGAT-AGGGGCTAAGGCCCAG-TTA
*
2881452 ATATTGATATGGGCTAAGGCCCAGTTA
1 ATATTGATAGGGGCTAAGGCCCAGTTA
2881479 A
1 A
2881480 CTTTGATTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 4 0.16
28 20 0.80
29 1 0.04
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (27 bp):
ATATTGATAGGGGCTAAGGCCCAGTTA
Found at i:2882577 original size:33 final size:36
Alignment explanation
Indices: 2882530--2882595 Score: 93
Period size: 34 Copynumber: 1.9 Consensus size: 36
2882520 ATTCTGTAGT
*
2882530 TAGGGTAATACTG-AAACTGTAGAA-ACTGAGATAG
1 TAGGGTAAAACTGAAAACTGTAGAAGACTGAGATAG
*
2882564 TAGGG-AAAACTGAAAACTTTAGAAGACTGAGA
1 TAGGGTAAAACTGAAAACTGTAGAAGACTGAGA
2882596 CTGTAGGTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 6 0.21
34 15 0.54
35 7 0.25
ACGTcount: A:0.44, C:0.09, G:0.26, T:0.21
Consensus pattern (36 bp):
TAGGGTAAAACTGAAAACTGTAGAAGACTGAGATAG
Found at i:2883877 original size:21 final size:23
Alignment explanation
Indices: 2883840--2883882 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
2883830 TTATTCCTTC
2883840 TCTTCTTCTCTCTTCTTCTATTT
1 TCTTCTTCTCTCTTCTTCTATTT
*
2883863 TCTT-TTCTC-CTTCTTTTATT
1 TCTTCTTCTCTCTTCTTCTATT
2883883 CTCTAGCCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 10 0.53
22 5 0.26
23 4 0.21
ACGTcount: A:0.05, C:0.28, G:0.00, T:0.67
Consensus pattern (23 bp):
TCTTCTTCTCTCTTCTTCTATTT
Found at i:2888588 original size:3 final size:3
Alignment explanation
Indices: 2888580--2888609 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2888570 AAAACAAAAT
2888580 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2888610 TCAAATTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2891346 original size:22 final size:23
Alignment explanation
Indices: 2891294--2891338 Score: 83
Period size: 22 Copynumber: 2.0 Consensus size: 23
2891284 AAATAAAACG
2891294 TAAGTTATGTTTTTTTAGTTTTT
1 TAAGTTATGTTTTTTTAGTTTTT
2891317 TAAGTTATG-TTTTTTAGTTTTT
1 TAAGTTATGTTTTTTTAGTTTTT
2891339 CTTTTTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.18, C:0.00, G:0.13, T:0.69
Consensus pattern (23 bp):
TAAGTTATGTTTTTTTAGTTTTT
Found at i:2892013 original size:3 final size:3
Alignment explanation
Indices: 2892005--2892064 Score: 77
Period size: 3 Copynumber: 20.0 Consensus size: 3
2891995 ACATTTTTTA
* *
2892005 TAT TAT TAT TAT TGT TAT TAT TAT TAT TAT TAT TAT TACT T-C TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT
*
2892050 TAT TAT TAT CAT TAT
1 TAT TAT TAT TAT TAT
2892065 ACTATTAAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
2 1 0.02
3 46 0.94
4 2 0.04
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:2892414 original size:26 final size:26
Alignment explanation
Indices: 2892358--2892425 Score: 68
Period size: 26 Copynumber: 2.7 Consensus size: 26
2892348 TTATTACAAA
* * **
2892358 TTATTTCATATATTATTTGTTTTGAGT
1 TTATTT-ATATATTATTTATTTTAAAC
*
2892385 TTATTTATATATTGTTTATTTTAAAC
1 TTATTTATATATTATTTATTTTAAAC
2892411 TTA--TATATATTATTT
1 TTATTTATATATTATTT
2892426 TAAATTCTGT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
24 11 0.31
26 18 0.51
27 6 0.17
ACGTcount: A:0.28, C:0.03, G:0.06, T:0.63
Consensus pattern (26 bp):
TTATTTATATATTATTTATTTTAAAC
Found at i:2892521 original size:22 final size:21
Alignment explanation
Indices: 2892496--2892545 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
2892486 ATTTTCTCAC
2892496 ATTAT-ATGTTATAAATTCATTT
1 ATTATCAT-TTATAAATT-ATTT
*
2892518 ATTATCATTTTTAAATTATTT
1 ATTATCATTTATAAATTATTT
2892539 -TTA-CATT
1 ATTATCATT
2892546 CTATTTCGAC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 4 0.15
20 3 0.12
21 4 0.15
22 13 0.50
23 2 0.08
ACGTcount: A:0.34, C:0.06, G:0.02, T:0.58
Consensus pattern (21 bp):
ATTATCATTTATAAATTATTT
Found at i:2899258 original size:18 final size:17
Alignment explanation
Indices: 2899216--2899269 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 17
2899206 GTTTATAAAT
2899216 AATTCAAAAAAATATAA
1 AATTCAAAAAAATATAA
*
2899233 AAAT-AAAAATAA-ATCAA
1 AATTCAAAAA-AATAT-AA
2899250 AATTCAAAAAATATATAA
1 AATTCAAAAAA-ATATAA
2899268 AA
1 AA
2899270 AGTAAAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
16 7 0.23
17 11 0.37
18 10 0.33
19 2 0.07
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.22
Consensus pattern (17 bp):
AATTCAAAAAAATATAA
Found at i:2899270 original size:19 final size:19
Alignment explanation
Indices: 2899209--2899270 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 19
2899199 ATGTCATGTT
2899209 TATAAATAATTCAAAAAA-A
1 TATAAA-AATTCAAAAAATA
2899228 TATAAAAA-T--AAAAATA
1 TATAAAAATTCAAAAAATA
* *
2899244 AATCAAAATTCAAAAAATA
1 TATAAAAATTCAAAAAATA
2899263 TATAAAAA
1 TATAAAAA
2899271 GTAAAAAGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
15 5 0.14
16 7 0.20
17 2 0.06
18 2 0.06
19 19 0.54
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (19 bp):
TATAAAAATTCAAAAAATA
Found at i:2899276 original size:18 final size:17
Alignment explanation
Indices: 2899221--2899277 Score: 55
Period size: 19 Copynumber: 3.3 Consensus size: 17
2899211 TAAATAATTC
2899221 AAAAAA-ATATAAAAAT
1 AAAAAATATATAAAAAT
* *
2899237 -AAAAATAAATCAAAATT
1 AAAAAATATAT-AAAAAT
2899254 CAAAAAATATATAAAAAGT
1 -AAAAAATATATAAAAA-T
2899273 AAAAA
1 AAAAA
2899278 GAAAACATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
15 5 0.16
16 3 0.09
17 5 0.16
18 9 0.28
19 10 0.31
ACGTcount: A:0.75, C:0.04, G:0.02, T:0.19
Consensus pattern (17 bp):
AAAAAATATATAAAAAT
Found at i:2902022 original size:2 final size:2
Alignment explanation
Indices: 2902015--2902051 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2902005 TGCTTCCATT
2902015 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2902052 TGTATTACTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2902611 original size:20 final size:19
Alignment explanation
Indices: 2902567--2902611 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
2902557 TGGTTTAATC
2902567 TATTATGAATTTTTAATTT
1 TATTATGAATTTTTAATTT
*
2902586 TTTTATGGAA-TTTTAATTT
1 TATTAT-GAATTTTTAATTT
2902605 TAATTAT
1 T-ATTAT
2902612 AGTTATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (19 bp):
TATTATGAATTTTTAATTT
Found at i:2905261 original size:28 final size:27
Alignment explanation
Indices: 2905195--2905261 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 27
2905185 ATACACAAAG
* * *
2905195 TAAAAATATAATAAAAAGTGATTATAT
1 TAAAAATAAAATAAAAAGTAAATATAT
* *
2905222 TAAAATTGAAAATAAAATGTAAATATGAT
1 TAAAAAT-AAAATAAAAAGTAAATAT-AT
2905251 TAAAAATAAAA
1 TAAAAATAAAA
2905262 ATATATATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
27 6 0.19
28 18 0.56
29 8 0.25
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (27 bp):
TAAAAATAAAATAAAAAGTAAATATAT
Found at i:2907269 original size:22 final size:22
Alignment explanation
Indices: 2907250--2907291 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2907240 AAAACAGAGG
2907250 ATGTCAGATACA-ATTGCAGAAC
1 ATGTCAGATACAGA-TGCAGAAC
*
2907272 ATTTCAGATACAGATGCAGA
1 ATGTCAGATACAGATGCAGA
2907292 TTTCTACCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.24
Consensus pattern (22 bp):
ATGTCAGATACAGATGCAGAAC
Found at i:2912490 original size:31 final size:31
Alignment explanation
Indices: 2912455--2912516 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
2912445 GCACCATCAA
*
2912455 ACTTTTATAATTTTCAAATTCAGAGACAAAT
1 ACTTTTATAATTTTCAAATTCAAAGACAAAT
*
2912486 ACTTTTATAATTTTCAAATTTAAAGACAAAT
1 ACTTTTATAATTTTCAAATTCAAAGACAAAT
2912517 GATCTATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.44, C:0.11, G:0.05, T:0.40
Consensus pattern (31 bp):
ACTTTTATAATTTTCAAATTCAAAGACAAAT
Found at i:2925623 original size:122 final size:122
Alignment explanation
Indices: 2925462--2925848 Score: 436
Period size: 122 Copynumber: 3.1 Consensus size: 122
2925452 ACACAAATAC
* * * * * * *
2925462 ATATTTTCAGCTTAGACGAGCAATTGATATACCGGAGATACTTGTGACACAGGTTTAGCCTTGAT
1 ATATTTTCAGCTTGGATGAGCAATTGATATATCGAAGATACTTATGACACAGGTTTAGCCTAGAC
2925527 TGGTAACATGATGTCAATTTAAAGGTTTAGCCTAGACGAGTAACTTGAAATGTATAT
66 TGGTAACATGATGTCAATTTAAAGGTTTAGCCTAGACGAGTAACTTGAAATGTATAT
* *
2925584 ATATTTTCATCTTGGATGAGCAATTGATATATCGAAGATACTTATGACACAAGTTTAGCCTAGAC
1 ATATTTTCAGCTTGGATGAGCAATTGATATATCGAAGATACTTATGACACAGGTTTAGCCTAGAC
* * * *
2925649 TGGTAACTTGATGTCAATTTAAAGGTTTAGCCTAGGCTAGTAACTTGACATTTGTATATAT
66 TGGTAACATGATGTCAATTTAAAGGTTTAGCCTAGACGAGTAACTTGA-A-ATG--TATAT
* * * * * * * **
2925710 ATATTTTCAGCTCGGA-CAACTAATTAATGTATCGAAGATACTTCTGACATAGGTTTAGCCGGGA
1 ATATTTTCAGCTTGGATGAGC-AATTGATATATCGAAGATACTTATGACACAGGTTTAGCCTAGA
* * * * * *
2925774 CTGGTAACCTAATGTCAACTTAAAGGTTTAG-CTAGGACGAGTAACCTGACATGTGTAT
65 CTGGTAACATGATGTCAATTTAAAGGTTTAGCCTA-GACGAGTAACTTGAAATGTATAT
* *
2925832 ATATATTCAACTTGGAT
1 ATATTTTCAGCTTGGAT
2925849 AATTGGTGTA
Statistics
Matches: 222, Mismatches: 36, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
122 118 0.53
123 1 0.00
124 4 0.02
125 5 0.02
126 94 0.42
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.34
Consensus pattern (122 bp):
ATATTTTCAGCTTGGATGAGCAATTGATATATCGAAGATACTTATGACACAGGTTTAGCCTAGAC
TGGTAACATGATGTCAATTTAAAGGTTTAGCCTAGACGAGTAACTTGAAATGTATAT
Found at i:2925777 original size:126 final size:126
Alignment explanation
Indices: 2925482--2925837 Score: 418
Period size: 126 Copynumber: 2.9 Consensus size: 126
2925472 CTTAGACGAG
* * * * * *
2925482 CAATTGATATACCGGAGATACTTGTGACACAGGTTTAGCCTTGATTGGTAACATGATGTCAATTT
1 CAATTAATATATCGAAGATACTTATGACACAGGTTTAGCCTAGACTGGTAACATGATGTCAATTT
* * * * *
2925547 AAAGGTTTAGCCTAGACGAGTAACTTGA-A-ATG--TATATATATTTTCATCTTGGATGAG
66 AAAGGTTTAGCCTAGGCGAGTAACTTGACATATGTATATATATATTTTCAGCTCGGATCAA
* * *
2925604 CAATTGATATATCGAAGATACTTATGACACAAGTTTAGCCTAGACTGGTAACTTGATGTCAATTT
1 CAATTAATATATCGAAGATACTTATGACACAGGTTTAGCCTAGACTGGTAACATGATGTCAATTT
* *
2925669 AAAGGTTTAGCCTAGGCTAGTAACTTGACATTTGTATATATATATTTTCAGCTCGGA-CAA
66 AAAGGTTTAGCCTAGGCGAGTAACTTGACATATGTATATATATATTTTCAGCTCGGATCAA
* * * ** * * *
2925729 CTAATTAATGTATCGAAGATACTTCTGACATAGGTTTAGCCGGGACTGGTAACCTAATGTCAACT
1 C-AATTAATATATCGAAGATACTTATGACACAGGTTTAGCCTAGACTGGTAACATGATGTCAATT
* *
2925794 TAAAGGTTTAG-CTAGGACGAGTAACCTGACATGTGTATATATAT
65 TAAAGGTTTAGCCTAGG-CGAGTAACTTGACATATGTATATATAT
2925838 TCAACTTGGA
Statistics
Matches: 201, Mismatches: 27, Indels: 8
0.85 0.11 0.03
Matches are distributed among these distances:
122 84 0.42
123 1 0.00
124 2 0.01
125 7 0.03
126 107 0.53
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Consensus pattern (126 bp):
CAATTAATATATCGAAGATACTTATGACACAGGTTTAGCCTAGACTGGTAACATGATGTCAATTT
AAAGGTTTAGCCTAGGCGAGTAACTTGACATATGTATATATATATTTTCAGCTCGGATCAA
Found at i:2933413 original size:30 final size:30
Alignment explanation
Indices: 2933379--2933438 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
2933369 TATTTTATTA
*
2933379 TTAATTTTGTTATTATTTTAAAGACATTTG
1 TTAATTCTGTTATTATTTTAAAGACATTTG
*
2933409 TTAATTCTGTTATTATTTTAGAGACATTTG
1 TTAATTCTGTTATTATTTTAAAGACATTTG
2933439 CTTGTTAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.28, C:0.05, G:0.12, T:0.55
Consensus pattern (30 bp):
TTAATTCTGTTATTATTTTAAAGACATTTG
Found at i:2934152 original size:19 final size:18
Alignment explanation
Indices: 2934122--2934171 Score: 57
Period size: 19 Copynumber: 2.8 Consensus size: 18
2934112 TTTTTAGTGT
*
2934122 TTTTTAAT-TTTTATATA
1 TTTTTAATATTTTATAAA
2934139 TTTTTAATACTTTTATAAA
1 TTTTTAATA-TTTTATAAA
* *
2934158 TTTTAAATAATTTA
1 TTTTTAATATTTTA
2934172 ATGACATGTC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 8 0.29
18 4 0.14
19 16 0.57
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTTTAATATTTTATAAA
Found at i:2937261 original size:19 final size:18
Alignment explanation
Indices: 2937239--2937289 Score: 50
Period size: 19 Copynumber: 2.8 Consensus size: 18
2937229 TCAAAATATT
2937239 TATAAAATTTTAAAATTTA
1 TATAAAATTTTAAAA-TTA
***
2937258 TATACTTTTTTAAAATTA
1 TATAAAATTTTAAAATTA
*
2937276 TA-AAAATTCTAAAA
1 TATAAAATTTTAAAA
2937290 ATTTTTAAAA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
17 8 0.32
18 5 0.20
19 12 0.48
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (18 bp):
TATAAAATTTTAAAATTA
Found at i:2937294 original size:27 final size:27
Alignment explanation
Indices: 2937223--2937304 Score: 76
Period size: 27 Copynumber: 3.0 Consensus size: 27
2937213 AATAATTTTC
* *
2937223 AAAAATTC-AAAATATTTATAAAATTTT
1 AAAAATTCTAAAA-ATTTTTAAAATTAT
* * * **
2937250 AAAATTTATATACTTTTTTAAAATTAT
1 AAAAATTCTAAAAATTTTTAAAATTAT
*
2937277 AAAAATTCTAAAAATTTTTAAAAATAT
1 AAAAATTCTAAAAATTTTTAAAATTAT
2937304 A
1 A
2937305 TAAAGAAAGT
Statistics
Matches: 41, Mismatches: 13, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
27 39 0.95
28 2 0.05
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43
Consensus pattern (27 bp):
AAAAATTCTAAAAATTTTTAAAATTAT
Found at i:2937744 original size:22 final size:22
Alignment explanation
Indices: 2937719--2937762 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2937709 AAATCTTAGA
2937719 AACCTTTTTGATTAATCATATT
1 AACCTTTTTGATTAATCATATT
*
2937741 AACCTTTTTGATTAATCTTATT
1 AACCTTTTTGATTAATCATATT
2937763 CCTCCAAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.30, C:0.14, G:0.05, T:0.52
Consensus pattern (22 bp):
AACCTTTTTGATTAATCATATT
Found at i:2941458 original size:5 final size:5
Alignment explanation
Indices: 2941450--2941476 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
2941440 AACCCAACCT
2941450 AACTC AACTC AACTC AACTC AACTC AA
1 AACTC AACTC AACTC AACTC AACTC AA
2941477 AAATTAAACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.44, C:0.37, G:0.00, T:0.19
Consensus pattern (5 bp):
AACTC
Found at i:2944693 original size:129 final size:130
Alignment explanation
Indices: 2944400--2944811 Score: 458
Period size: 129 Copynumber: 3.1 Consensus size: 130
2944390 CTTAGAAAAT
* * * *
2944400 ACGATAGGGCACTATTCCCCGAATTGCCAAACACCGAACATCT-CTTTTGTTTTAAAGAGTTTTT
1 ACGATAGGGCACGATT-CCCGAATTGCCAAACACCGAAGAT-TGCCTTCGTTTTAAAG-GTTTTT
* * * * *
2944464 AGAAAACATGAGTGAAATTCCGAAAGGAATCTTCGATCGTTTTGGAACAAATGA-AAATGCGCAA
63 AGAAAACATGAATGAAA-TCCTAAAGGAATATTCGATTGTTTT-GAACAAACGAGAAAT-CGCAA
2944528 CCCAGC
125 CCCAGC
* * * * *
2944534 ACGATAAGGCACGATTCTCAAATCGCCAAACATCGAAGATTGCCTTCGTTTTGAAAGGTTTTTA-
1 ACGATAGGGCACGATTCCCGAATTGCCAAACACCGAAGATTGCCTTCGTTTT-AAAGGTTTTTAG
*
2944598 ATAAACATGAATG-AA-CCTAAAGGAATATTCGATTGTTTTGAACAAACGAGAAATCACAACCCA
65 A-AAACATGAATGAAATCCTAAAGGAATATTCGATTGTTTTGAACAAACGAGAAATCGCAACCCA
2944661 GC
129 GC
* *
2944663 ACGATAGGGCATGATTCCCGAATTGTCAAACACCG-AGTATTGCCTTCGTTTTAAAGGATTTTTA
1 ACGATAGGGCACGATTCCCGAATTGCCAAACACCGAAG-ATTGCCTTCGTTTTAAAGG-TTTTTA
* * * * * * *
2944727 GAAGACATGAATGAAATTCTAAAGGGACATTCGATTATTTTGAGCAAACGAGAAATTGCAACCCA
64 GAAAACATGAATGAAATCCTAAAGGAATATTCGATTGTTTTGAACAAACGAGAAATCGCAACCCA
*
2944792 AC
129 GC
*
2944794 ACGTTAGGGCACGATTCC
1 ACGATAGGGCACGATTCC
2944812 ACAAATTACC
Statistics
Matches: 236, Mismatches: 33, Indels: 21
0.81 0.11 0.07
Matches are distributed among these distances:
128 7 0.03
129 77 0.33
130 28 0.12
131 58 0.25
132 4 0.02
133 44 0.19
134 18 0.08
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (130 bp):
ACGATAGGGCACGATTCCCGAATTGCCAAACACCGAAGATTGCCTTCGTTTTAAAGGTTTTTAGA
AAACATGAATGAAATCCTAAAGGAATATTCGATTGTTTTGAACAAACGAGAAATCGCAACCCAGC
Found at i:2944853 original size:131 final size:129
Alignment explanation
Indices: 2944400--2944859 Score: 414
Period size: 129 Copynumber: 3.5 Consensus size: 129
2944390 CTTAGAAAAT
* * * * * *
2944400 ACGATAGGGCACTATTCCCCGAATTGCCAAACACCGAACATCT-CTTTTGTTTTAAA-GAGTTTT
1 ACGATAGGGCACGATT-CCCAAATTGCCAAACATCGAATAT-TGCCTTCGTTTTAAAGGA-TTTT
* * ** *
2944463 TAGA-AAACATGAGTGAAATTCCGAAAGGAATC-TTCGATCGTTTTGGAACAAATGA-AAATGCG
63 TA-ATAAACATGAATG-AA--CCTAAAGGAA-CATTCGATTATTTT-GAACAAACGAGAAAT-CG
2944525 CAACCCAGC
121 CAACCCAGC
* * * *
2944534 ACGATAAGGCACGATTCTCAAATCGCCAAACATCGAAGATTGCCTTCGTTTTGAAAGG-TTTTTA
1 ACGATAGGGCACGATTCCCAAATTGCCAAACATCGAATATTGCCTTCGTTTT-AAAGGATTTTTA
* * *
2944598 ATAAACATGAATGAACCTAAAGGAATATTCGATTGTTTTGAACAAACGAGAAATCACAACCCAGC
65 ATAAACATGAATGAACCTAAAGGAACATTCGATTATTTTGAACAAACGAGAAATCGCAACCCAGC
* * * * *
2944663 ACGATAGGGCATGATTCCCGAATTGTCAAACACCGAGTATTGCCTTCGTTTTAAAGGATTTTTAG
1 ACGATAGGGCACGATTCCCAAATTGCCAAACATCGAATATTGCCTTCGTTTTAAAGGATTTTTA-
* * * * *
2944728 A-AGACATGAATGAAATTCTAAAGGGACATTCGATTATTTTGAGCAAACGAGAAATTGCAACCCA
65 ATAAACATGAATG-AA-CCTAAAGGAACATTCGATTATTTTGAACAAACGAGAAATCGCAACCCA
*
2944792 AC
128 GC
* * ** * *
2944794 ACGTTAGGGCACGATTCCACAAATTACCAAGTATCGAATATCGCCTTCG-TTTAAGGGATTTTTA
1 ACGATAGGGCACGATTCC-CAAATTGCCAAACATCGAATATTGCCTTCGTTTTAAAGGATTTTTA
2944858 AT
65 AT
2944860 TATTGTGAGA
Statistics
Matches: 270, Mismatches: 44, Indels: 27
0.79 0.13 0.08
Matches are distributed among these distances:
128 5 0.02
129 78 0.29
130 28 0.10
131 72 0.27
132 26 0.10
133 43 0.16
134 17 0.06
135 1 0.00
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.27
Consensus pattern (129 bp):
ACGATAGGGCACGATTCCCAAATTGCCAAACATCGAATATTGCCTTCGTTTTAAAGGATTTTTAA
TAAACATGAATGAACCTAAAGGAACATTCGATTATTTTGAACAAACGAGAAATCGCAACCCAGC
Found at i:2948054 original size:15 final size:15
Alignment explanation
Indices: 2948027--2948072 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
2948017 TTTTGCCCGG
2948027 GCTAAAAAGCCCAACA
1 GCTAAAAA-CCCAACA
*
2948043 TCTAAAAACCCAACA
1 GCTAAAAACCCAACA
**
2948058 GCCCAAAACCCAACA
1 GCTAAAAACCCAACA
2948073 ACCTCCAAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
15 19 0.73
16 7 0.27
ACGTcount: A:0.50, C:0.37, G:0.07, T:0.07
Consensus pattern (15 bp):
GCTAAAAACCCAACA
Found at i:2948175 original size:13 final size:13
Alignment explanation
Indices: 2948157--2948209 Score: 60
Period size: 13 Copynumber: 4.4 Consensus size: 13
2948147 TCTTCACTCC
2948157 AACCACCCCACTA
1 AACCACCCCACTA
*
2948170 AACCA-CTC-C--
1 AACCACCCCACTA
*
2948179 AACCACCCTACTA
1 AACCACCCCACTA
2948192 AACCACCCCACTA
1 AACCACCCCACTA
2948205 AACCA
1 AACCA
2948210 TTCCAACCAC
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
9 5 0.16
10 1 0.03
11 2 0.06
12 2 0.06
13 22 0.69
ACGTcount: A:0.40, C:0.51, G:0.00, T:0.09
Consensus pattern (13 bp):
AACCACCCCACTA
Found at i:2948179 original size:22 final size:22
Alignment explanation
Indices: 2948151--2948197 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
2948141 CAAATATCTT
2948151 CACTCCAACCACCCCACTAAAC
1 CACTCCAACCACCCCACTAAAC
*
2948173 CACTCCAACCACCCTACTAAAC
1 CACTCCAACCACCCCACTAAAC
2948195 CAC
1 CAC
2948198 CCCACTAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.36, C:0.53, G:0.00, T:0.11
Consensus pattern (22 bp):
CACTCCAACCACCCCACTAAAC
Found at i:2948629 original size:19 final size:18
Alignment explanation
Indices: 2948592--2948633 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
2948582 GGAGAGAGTG
*
2948592 TTATTTTTAATATTGTTA
1 TTATTTTTAATATTATTA
*
2948610 TTATTTTCTATTATTATTA
1 TTATTTT-TAATATTATTA
2948629 TTATT
1 TTATT
2948634 ACTAATACCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (18 bp):
TTATTTTTAATATTATTA
Found at i:2948692 original size:33 final size:39
Alignment explanation
Indices: 2948618--2948699 Score: 104
Period size: 33 Copynumber: 2.3 Consensus size: 39
2948608 TATTATTTTC
*
2948618 TATTATTATTATTATTACTAATACCACTATTATCATCAT
1 TATTACTATTATTATTACTAATACCACTATTATCATCAT
*
2948657 TATTACTATTA-TATTA-TAATA-C-CT-TT-TCATTAT
1 TATTACTATTATTATTACTAATACCACTATTATCATCAT
2948690 TATTACTATT
1 TATTACTATT
2948700 GTCTTTTTAC
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
33 16 0.39
34 2 0.05
35 2 0.05
36 1 0.02
37 5 0.12
38 5 0.12
39 10 0.24
ACGTcount: A:0.34, C:0.13, G:0.00, T:0.52
Consensus pattern (39 bp):
TATTACTATTATTATTACTAATACCACTATTATCATCAT
Found at i:2948729 original size:23 final size:23
Alignment explanation
Indices: 2948645--2948729 Score: 64
Period size: 23 Copynumber: 3.6 Consensus size: 23
2948635 CTAATACCAC
* *
2948645 TATTATCATCATTATTACTATTA-
1 TATTATTAT-ATTTTTACTATTAT
* * *
2948668 TATTATAATACCTTTTCATTATTAT
1 TATTATTATA--TTTTTACTATTAT
* * *
2948693 TACTATTGTCTTTTTACTATTAT
1 TATTATTATATTTTTACTATTAT
2948716 TATTATTATATTTT
1 TATTATTATATTTT
2948730 CTTTTTTTGT
Statistics
Matches: 46, Mismatches: 13, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
22 1 0.02
23 30 0.65
24 9 0.20
25 6 0.13
ACGTcount: A:0.29, C:0.11, G:0.01, T:0.59
Consensus pattern (23 bp):
TATTATTATATTTTTACTATTAT
Found at i:2959331 original size:206 final size:206
Alignment explanation
Indices: 2958963--2960042 Score: 1894
Period size: 206 Copynumber: 5.2 Consensus size: 206
2958953 CTGGCTAAAG
* * *
2958963 AAGATCTAAGATGGTTTGGCATCCTTGTGCTTACAATGAGCAAATCGAAGACATAGCTGATTTGG
1 AAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCTGATTTGG
* *
2959028 CTTTCGCGTGCTTACGCTAAAGCAAGTCTAAGATGATTTGGCATCTCTGTATTGTCAAAGAATAA
66 CTTTCGCGTGCTTACGCTAAAGCAAGTCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAA
* * *
2959093 GTCGAAGTCTGGCATCTCTATTTCGACGGAGAGCAGATACATAACAGATCTGGCCTTCAAATGTT
131 GTCGAAGTCTGGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTGGCCTTCAGATGTT
2959158 TATACTGAAGC
196 TATACTGAAGC
* *
2959169 AAGATCCAAGATGATTTGGCATCTTTGTGCTTACAAAGAGCAAATCGAAGACATAGCTGATTTGG
1 AAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCTGATTTGG
2959234 CTTTCGCGTGCTTACGCTAAAGCAAGTCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAA
66 CTTTCGCGTGCTTACGCTAAAGCAAGTCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAA
*
2959299 GTCGAATTCTGGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTGGCCTTCAGATGTT
131 GTCGAAGTCTGGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTGGCCTTCAGATGTT
2959364 TATACTGAAGC
196 TATACTGAAGC
*
2959375 AAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCTGGTTTGG
1 AAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCTGATTTGG
* *
2959440 CTTTCACGTGCTTATGCTAAAGCAAGTCTAAGATGATTTGGCATCTCTGTATTGTCAGA-AACAA
66 CTTTCGCGTGCTTACGCTAAAGCAAGTCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAA
*
2959504 GTCGAAGTCTGGCATCTCCATTTCGACGGAGAGCAGATACATAGTAGATCTGGCCTTCAGATGTT
131 GTCGAAGTCTGGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTGGCCTTCAGATGTT
2959569 TATACTGAAGC
196 TATACTGAAGC
* * *
2959580 AAGATCCAAGATGATTTGGCATCCTTGTGCTTATAATGAGCAAATCGAAGACATAGCTAATTTGG
1 AAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCTGATTTGG
*
2959645 CTTTCGCGTGCTTACGCTAAAGCAAGTCTAAGATGATTTGGCATCTCTGTATTTTCAGAGAACAA
66 CTTTCGCGTGCTTACGCTAAAGCAAGTCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAA
**
2959710 GTTAAAGTCTGGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTGGCCTTCAGATGTT
131 GTCGAAGTCTGGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTGGCCTTCAGATGTT
2959775 TATACTGAAGC
196 TATACTGAAGC
* *
2959786 AAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGATATAGCTGATTTGG
1 AAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCTGATTTGG
*
2959851 CTTTCGCGTGCTTACGCTAAAGCAAGTCTAAGATGATTTGGCATCTCTGTATTATCAGAGAACAA
66 CTTTCGCGTGCTTACGCTAAAGCAAGTCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAA
*
2959916 GTCGAAGTCTGGCATCTCCATTTCGACAGAGAGCAGATACATAGCAGATCTGGCCTTCAGATGTT
131 GTCGAAGTCTGGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTGGCCTTCAGATGTT
2959981 TATA-TCGAAGC
196 TATACT-GAAGC
* *
2959992 AATATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGA
1 AAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGA
2960043 AGCAGATTTG
Statistics
Matches: 835, Mismatches: 37, Indels: 4
0.95 0.04 0.00
Matches are distributed among these distances:
205 197 0.24
206 638 0.76
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (206 bp):
AAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCTGATTTGG
CTTTCGCGTGCTTACGCTAAAGCAAGTCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAA
GTCGAAGTCTGGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTGGCCTTCAGATGTT
TATACTGAAGC
Found at i:2959740 original size:411 final size:412
Alignment explanation
Indices: 2958963--2960042 Score: 1894
Period size: 411 Copynumber: 2.6 Consensus size: 412
2958953 CTGGCTAAAG
* * *
2958963 AAGATCTAAGATGGTTTGGCATCCTTGTGCTTACAATGAGCAAATCGAAGACATAGCTGATTTGG
1 AAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCTGATTTGG
* *
2959028 CTTTCGCGTGCTTACGCTAAAGCAAGTCTAAGATGATTTGGCATCTCTGTATTGTCAAAGAATAA
66 CTTTCGCGTGCTTACGCTAAAGCAAGTCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAA
* * *
2959093 GTCGAAGTCTGGCATCTCTATTTCGACGGAGAGCAGATACATAACAGATCTGGCCTTCAAATGTT
131 GTCGAAGTCTGGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTGGCCTTCAGATGTT
*
2959158 TATACTGAAGCAAGATCCAAGATGATTTGGCATCTTTGTGCTTACAAAGAGCAAATCGAAGACAT
196 TATACTGAAGCAAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAAGAGCAAATCGAAGACAT
*
2959223 AGCTGATTTGGCTTTCGCGTGCTTACGCTAAAGCAAGTCTAAGATGATTTGGCATCTCTGTATTG
261 AGCTAATTTGGCTTTCGCGTGCTTACGCTAAAGCAAGTCTAAGATGATTTGGCATCTCTGTATTG
* *
2959288 TCAGAGAACAAGTCGAATTCTGGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTGGC
326 TCAGAGAACAAGTCAAAGTCTGGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTGGC
2959353 CTTCAGATGTTTATACTGAAGC
391 CTTCAGATGTTTATACTGAAGC
*
2959375 AAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCTGGTTTGG
1 AAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCTGATTTGG
* *
2959440 CTTTCACGTGCTTATGCTAAAGCAAGTCTAAGATGATTTGGCATCTCTGTATTGTCAGA-AACAA
66 CTTTCGCGTGCTTACGCTAAAGCAAGTCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAA
*
2959504 GTCGAAGTCTGGCATCTCCATTTCGACGGAGAGCAGATACATAGTAGATCTGGCCTTCAGATGTT
131 GTCGAAGTCTGGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTGGCCTTCAGATGTT
* *
2959569 TATACTGAAGCAAGATCCAAGATGATTTGGCATCCTTGTGCTTATAATGAGCAAATCGAAGACAT
196 TATACTGAAGCAAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAAGAGCAAATCGAAGACAT
*
2959634 AGCTAATTTGGCTTTCGCGTGCTTACGCTAAAGCAAGTCTAAGATGATTTGGCATCTCTGTATTT
261 AGCTAATTTGGCTTTCGCGTGCTTACGCTAAAGCAAGTCTAAGATGATTTGGCATCTCTGTATTG
*
2959699 TCAGAGAACAAGTTAAAGTCTGGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTGGC
326 TCAGAGAACAAGTCAAAGTCTGGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTGGC
2959764 CTTCAGATGTTTATACTGAAGC
391 CTTCAGATGTTTATACTGAAGC
* *
2959786 AAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGATATAGCTGATTTGG
1 AAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCTGATTTGG
*
2959851 CTTTCGCGTGCTTACGCTAAAGCAAGTCTAAGATGATTTGGCATCTCTGTATTATCAGAGAACAA
66 CTTTCGCGTGCTTACGCTAAAGCAAGTCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAA
*
2959916 GTCGAAGTCTGGCATCTCCATTTCGACAGAGAGCAGATACATAGCAGATCTGGCCTTCAGATGTT
131 GTCGAAGTCTGGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTGGCCTTCAGATGTT
* * *
2959981 TATA-TCGAAGCAATATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGA
196 TATACT-GAAGCAAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAAGAGCAAATCGAAGA
2960043 AGCAGATTTG
Statistics
Matches: 634, Mismatches: 32, Indels: 4
0.95 0.05 0.01
Matches are distributed among these distances:
411 393 0.62
412 241 0.38
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (412 bp):
AAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCTGATTTGG
CTTTCGCGTGCTTACGCTAAAGCAAGTCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAA
GTCGAAGTCTGGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTGGCCTTCAGATGTT
TATACTGAAGCAAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAAGAGCAAATCGAAGACAT
AGCTAATTTGGCTTTCGCGTGCTTACGCTAAAGCAAGTCTAAGATGATTTGGCATCTCTGTATTG
TCAGAGAACAAGTCAAAGTCTGGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTGGC
CTTCAGATGTTTATACTGAAGC
Found at i:2960226 original size:45 final size:45
Alignment explanation
Indices: 2960130--2960226 Score: 142
Period size: 45 Copynumber: 2.2 Consensus size: 45
2960120 AGATTGACGA
* * *
2960130 AGCAAATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGAT
1 AGCAGATTTGGCGTCTCTGTATTAGACGGGGAACAGATCAAAGAT
*
2960175 -GACAGATTTGGCTTCTCTGTATTAGACGGGGAACAGATCAAAGAT
1 AG-CAGATTTGGCGTCTCTGTATTAGACGGGGAACAGATCAAAGAT
2960220 AGCAGAT
1 AGCAGAT
2960227 ATCGCTTTCG
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
44 1 0.02
45 44 0.96
46 1 0.02
ACGTcount: A:0.31, C:0.15, G:0.29, T:0.25
Consensus pattern (45 bp):
AGCAGATTTGGCGTCTCTGTATTAGACGGGGAACAGATCAAAGAT
Found at i:2960463 original size:17 final size:16
Alignment explanation
Indices: 2960417--2960463 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
2960407 CCTGGGCTAA
*
2960417 AAAGCCCAACAGC-CC
1 AAAGCCCAACACCTCC
*
2960432 AAAACCCAACAACCTCC
1 AAAGCCCAAC-ACCTCC
2960449 AAAGCCCAATCACCT
1 AAAGCCCAA-CACCT
2960464 AAACCCTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 9 0.35
16 2 0.08
17 14 0.54
18 1 0.04
ACGTcount: A:0.43, C:0.45, G:0.06, T:0.06
Consensus pattern (16 bp):
AAAGCCCAACACCTCC
Found at i:2960546 original size:13 final size:13
Alignment explanation
Indices: 2960528--2960558 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
2960518 TCTTCACTCC
2960528 AACCACCCCACTA
1 AACCACCCCACTA
2960541 AACCACCCCACTA
1 AACCACCCCACTA
2960554 AACCA
1 AACCA
2960559 TCTCAACCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.42, C:0.52, G:0.00, T:0.06
Consensus pattern (13 bp):
AACCACCCCACTA
Found at i:2960969 original size:3 final size:3
Alignment explanation
Indices: 2960937--2960985 Score: 53
Period size: 3 Copynumber: 16.0 Consensus size: 3
2960927 GGAGAGAGTG
* * * *
2960937 TTA TTT TTA ATA TTG TTA TTA TTT TCTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA
2960983 TTA
1 TTA
2960986 CTACTAATAC
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
3 35 0.95
4 2 0.05
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2960974 original size:19 final size:18
Alignment explanation
Indices: 2960937--2960978 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
2960927 GGAGAGAGTG
*
2960937 TTATTTTTAATATTGTTA
1 TTATTTTTAATATTATTA
*
2960955 TTATTTTCTATTATTATTA
1 TTATTTT-TAATATTATTA
2960974 TTATT
1 TTATT
2960979 ATTATTACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (18 bp):
TTATTTTTAATATTATTA
Found at i:2961046 original size:33 final size:39
Alignment explanation
Indices: 2960967--2961053 Score: 105
Period size: 33 Copynumber: 2.4 Consensus size: 39
2960957 ATTTTCTATT
*
2960967 ATTATTATTATTATTATTACTACTAATACCACTATTATC
1 ATTATTATTACTATTATTACTACTAATACCACTATTATC
* *
2961006 ATCATTATTACTATTA-TATTA-TAATA-C-CT-TT-TC
1 ATTATTATTACTATTATTACTACTAATACCACTATTATC
2961039 ATTATTATTACTATT
1 ATTATTATTACTATT
2961054 GTGTTTTTAC
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
33 16 0.36
34 2 0.05
35 2 0.05
36 1 0.02
37 5 0.11
38 4 0.09
39 14 0.32
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.52
Consensus pattern (39 bp):
ATTATTATTACTATTATTACTACTAATACCACTATTATC
Found at i:2961083 original size:23 final size:23
Alignment explanation
Indices: 2960999--2961083 Score: 64
Period size: 23 Copynumber: 3.6 Consensus size: 23
2960989 CTAATACCAC
* *
2960999 TATTATCATCATTATTACTATTA-
1 TATTATTAT-ATTTTTACTATTAT
* * *
2961022 TATTATAATACCTTTTCATTATTAT
1 TATTATTATA--TTTTTACTATTAT
* * *
2961047 TACTATTGTGTTTTTACTATTAT
1 TATTATTATATTTTTACTATTAT
2961070 TATTATTATATTTT
1 TATTATTATATTTT
2961084 CTTTTTTTGT
Statistics
Matches: 46, Mismatches: 13, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
22 1 0.02
23 30 0.65
24 9 0.20
25 6 0.13
ACGTcount: A:0.29, C:0.09, G:0.02, T:0.59
Consensus pattern (23 bp):
TATTATTATATTTTTACTATTAT
Found at i:2963344 original size:35 final size:35
Alignment explanation
Indices: 2963253--2963347 Score: 172
Period size: 35 Copynumber: 2.7 Consensus size: 35
2963243 CATGGAAAAG
* *
2963253 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
2963288 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
1 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
2963323 TGTGAAATGTAGGTATGGTATTATC
1 TGTGAAATGTAGGTATGGTATTATC
2963348 AAATCCATAC
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 58 1.00
ACGTcount: A:0.28, C:0.09, G:0.26, T:0.36
Consensus pattern (35 bp):
TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
Found at i:2963354 original size:40 final size:36
Alignment explanation
Indices: 2963251--2963417 Score: 161
Period size: 35 Copynumber: 4.6 Consensus size: 36
2963241 TCCATGGAAA
2963251 AGTGTGAAATGTAGGTATGG--TATCATCCATACTG
1 AGTGTGAAATGTAGGTATGGTATATCATCCATACTG
2963285 AGTTGTGAAATGTAGGTATGGTAT-T-ATCCATACTG
1 AG-TGTGAAATGTAGGTATGGTATATCATCCATACTG
2963320 AGCTGTGAAATGTAGGTATGGTATTATCAAATCCATACTG
1 AG-TGTGAAATGTAGGTATGGTA-TATC--ATCCATACTG
* * * *
2963360 AGT-TAAAAATGTAGGTATGGCATTTC--CCATACCG
1 AGTGT-GAAATGTAGGTATGGTATATCATCCATACTG
*
2963394 AGT-TGAAAATTTTAGGTATGGTAT
1 AGTGTG-AAA-TGTAGGTATGGTAT
2963418 TTCAATGAGG
Statistics
Matches: 114, Mismatches: 8, Indels: 21
0.80 0.06 0.15
Matches are distributed among these distances:
34 16 0.14
35 62 0.54
36 2 0.02
37 2 0.02
38 4 0.04
39 16 0.14
40 12 0.11
ACGTcount: A:0.31, C:0.11, G:0.24, T:0.34
Consensus pattern (36 bp):
AGTGTGAAATGTAGGTATGGTATATCATCCATACTG
Found at i:2963410 original size:74 final size:74
Alignment explanation
Indices: 2963253--2963422 Score: 203
Period size: 74 Copynumber: 2.4 Consensus size: 74
2963243 CATGGAAAAG
** *
2963253 TGTGAAATGTAGGTATGGTA--TC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTATCC
1 TGTGAAATGTAGGTATGGTATTTCAAATCCATACTGAGTTGAAAAATGTAGGTATGGCATTATCC
*
2963314 ATACTGAGC
66 ATACCGAGC
2963323 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTT-AAAAATGTAGGTATGGCATT-TC
1 TGTGAAATGTAGGTATGGTATT-TCAAATCCATACTGAGTTGAAAAATGTAGGTATGGCATTAT-
2963386 CCATACCGAG-
64 CCATACCGAGC
*
2963396 T-TGAAAATTTTAGGTATGGTATTTCAA
1 TGTG-AAA-TGTAGGTATGGTATTTCAA
2963423 TGAGGAAAAC
Statistics
Matches: 87, Mismatches: 5, Indels: 13
0.83 0.05 0.12
Matches are distributed among these distances:
70 20 0.23
72 2 0.02
73 11 0.13
74 40 0.46
75 14 0.16
ACGTcount: A:0.31, C:0.11, G:0.23, T:0.35
Consensus pattern (74 bp):
TGTGAAATGTAGGTATGGTATTTCAAATCCATACTGAGTTGAAAAATGTAGGTATGGCATTATCC
ATACCGAGC
Found at i:2968285 original size:31 final size:31
Alignment explanation
Indices: 2968216--2968285 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 31
2968206 TATCAAAATA
* * *
2968216 AATATTGAAACCAAACTCAAGTACCAAATTG
1 AATATTAAAACCAAACTCAAGTACAAAATGG
* * *
2968247 AACATTAAAATCAAATTCAAGTACAAAATGG
1 AATATTAAAACCAAACTCAAGTACAAAATGG
*
2968278 TATATTAA
1 AATATTAA
2968286 CCCTATTGTA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.51, C:0.14, G:0.09, T:0.26
Consensus pattern (31 bp):
AATATTAAAACCAAACTCAAGTACAAAATGG
Found at i:2969890 original size:19 final size:18
Alignment explanation
Indices: 2969867--2969913 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 18
2969857 TAAGTTGTAC
2969867 TTTTAATTTTTTATATAA
1 TTTTAATTTTTTATATAA
**
2969885 TATTTAATAATTTATATAA
1 T-TTTAATTTTTTATATAA
2969904 TTTTAATTTT
1 TTTTAATTTT
2969914 CTAATTTTCT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTTAATTTTTTATATAA
Found at i:2970368 original size:22 final size:22
Alignment explanation
Indices: 2970343--2970385 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
2970333 GTCTAAGCAC
* *
2970343 ACAAAAGCCAAATCCAAAAAAT
1 ACAAAAACAAAATCCAAAAAAT
*
2970365 ACAAAAACAAAATCGAAAAAA
1 ACAAAAACAAAATCCAAAAAA
2970386 CAGCCCAACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.70, C:0.19, G:0.05, T:0.07
Consensus pattern (22 bp):
ACAAAAACAAAATCCAAAAAAT
Found at i:2975464 original size:9 final size:9
Alignment explanation
Indices: 2975452--2975479 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
2975442 AAAAACATTT
2975452 TAATTCTCA
1 TAATTCTCA
2975461 TAATTCTCA
1 TAATTCTCA
2975470 TAATTCTCA
1 TAATTCTCA
2975479 T
1 T
2975480 TTTAAGAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.21, G:0.00, T:0.46
Consensus pattern (9 bp):
TAATTCTCA
Found at i:2978393 original size:7 final size:7
Alignment explanation
Indices: 2978383--2978420 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
2978373 AGTCATTTCA
2978383 TATTTAG
1 TATTTAG
2978390 TATTTAG
1 TATTTAG
2978397 TATTTAG
1 TATTTAG
2978404 TATTTAG
1 TATTTAG
2978411 TATTTAG
1 TATTTAG
2978418 TAT
1 TAT
2978421 ATAACTAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (7 bp):
TATTTAG
Found at i:2979334 original size:21 final size:20
Alignment explanation
Indices: 2979310--2979370 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 20
2979300 TCGAAAAAAC
*
2979310 CACAACCCACGCCAAAGTAAT
1 CACAACCC-CGCCAAAGCAAT
*
2979331 CACAACCCCTGCCAGA-CAAT
1 CACAACCCC-GCCAAAGCAAT
2979351 CACAACCCCCGCCAAAGCAA
1 CACAA-CCCCGCCAAAGCAA
2979371 CCAAGGAGGA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 14 0.41
21 20 0.59
ACGTcount: A:0.39, C:0.44, G:0.10, T:0.07
Consensus pattern (20 bp):
CACAACCCCGCCAAAGCAAT
Found at i:2985428 original size:125 final size:125
Alignment explanation
Indices: 2985206--2985472 Score: 437
Period size: 125 Copynumber: 2.1 Consensus size: 125
2985196 TGCCAAGCAT
2985206 GAACTACTGTAGTAAAAGAGAGTCCACGTGGAAACTTTTTTCAAAAATTTTGCTGACATTGCATC
1 GAACTACTGTAG-AAAAGAGAGTCCACGTGGAAACTTTTTTCAAAAATTTTGCTGACATTGCATC
*
2985271 CTGCTTGAAGTATTTTTGACACTATTTTTTCAGAAACGTCTTCTCAAAATTA-TTTTTCAG
65 CTGCTTGAAGTATTTTTGACACTATTTGTTCAGAAACGTCTTCTCAAAATTATTTTTTCAG
* * * * *
2985331 GAACTACTGTAGAAAATGAGCGTCCACGTGGGAGCTTTTTTTAGAAATTTTGCTGACATTGCATC
1 GAACTACTGTAGAAAA-GAGAGTCCACGTGGAAACTTTTTTCAAAAATTTTGCTGACATTGCATC
* *
2985396 CTGCTTGAAGTGTTTTTGACACTATTTGTTCAGAAACGTCTTCTTAAAATTATTTTTTCAG
65 CTGCTTGAAGTATTTTTGACACTATTTGTTCAGAAACGTCTTCTCAAAATTATTTTTTCAG
2985457 GAACTACTGTAGAAAA
1 GAACTACTGTAGAAAA
2985473 ATCATAAACC
Statistics
Matches: 132, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
124 4 0.03
125 104 0.79
126 24 0.18
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (125 bp):
GAACTACTGTAGAAAAGAGAGTCCACGTGGAAACTTTTTTCAAAAATTTTGCTGACATTGCATCC
TGCTTGAAGTATTTTTGACACTATTTGTTCAGAAACGTCTTCTCAAAATTATTTTTTCAG
Found at i:2987013 original size:10 final size:10
Alignment explanation
Indices: 2986983--2987025 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
2986973 CCAAATGTAC
2986983 TTTATAAAAA
1 TTTATAAAAA
2986993 TTT-TAAAAAA
1 TTTAT-AAAAA
2987003 TTTATAAAAA
1 TTTATAAAAA
**
2987013 TCCATAAAAA
1 TTTATAAAAA
2987023 TTT
1 TTT
2987026 CCACTTTAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
9 1 0.04
10 25 0.93
11 1 0.04
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (10 bp):
TTTATAAAAA
Found at i:2990795 original size:19 final size:20
Alignment explanation
Indices: 2990771--2990810 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
2990761 GAAATATAAA
*
2990771 ATAATTTTT-AATTTTTTTT
1 ATAATTTTTGAAATTTTTTT
2990790 ATAATTTTTGAAATTTTTTT
1 ATAATTTTTGAAATTTTTTT
2990810 A
1 A
2990811 GTTTCGTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (20 bp):
ATAATTTTTGAAATTTTTTT
Found at i:2991158 original size:15 final size:15
Alignment explanation
Indices: 2991138--2991170 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
2991128 TTAAGTCAAA
2991138 GAAAAATT-ATGTACT
1 GAAAAATTAAT-TACT
2991153 GAAAAATTAATTACT
1 GAAAAATTAATTACT
2991168 GAA
1 GAA
2991171 TTTAAGTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 15 0.88
16 2 0.12
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.30
Consensus pattern (15 bp):
GAAAAATTAATTACT
Found at i:2991285 original size:19 final size:18
Alignment explanation
Indices: 2991261--2991306 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
2991251 TAAAATTTTA
*
2991261 ATAATAAAATATTTAAAGG
1 ATAATAAAATA-TTAAAAG
2991280 ATAATAAAA-ATTAAAAG
1 ATAATAAAATATTAAAAG
2991297 A-AATAAAATA
1 ATAATAAAATA
2991307 AAATAATTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 7 0.28
17 8 0.32
18 1 0.04
19 9 0.36
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (18 bp):
ATAATAAAATATTAAAAG
Found at i:2991842 original size:29 final size:30
Alignment explanation
Indices: 2991794--2991875 Score: 94
Period size: 31 Copynumber: 2.7 Consensus size: 30
2991784 GATTTAGATC
2991794 AAATCAAAATTTCATGTATAAAATT-ACAAA
1 AAATCAAAATTT-ATGTATAAAATTCACAAA
* * **
2991824 AAATTAAAATTTATGTATATAATTGCACATT
1 AAATCAAAATTTATGTATAAAATT-CACAAA
*
2991855 AAATCAAAGTTTATGTATAAA
1 AAATCAAAATTTATGTATAAA
2991876 TTTAGGATTT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 11 0.26
30 11 0.26
31 21 0.49
ACGTcount: A:0.51, C:0.07, G:0.06, T:0.35
Consensus pattern (30 bp):
AAATCAAAATTTATGTATAAAATTCACAAA
Found at i:3000776 original size:1 final size:1
Alignment explanation
Indices: 3000766--3000805 Score: 53
Period size: 1 Copynumber: 40.0 Consensus size: 1
3000756 TTAAGCAGCA
* * *
3000766 TTTTTCTTTTTCTTTTTCTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3000806 GCTTTCAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (1 bp):
T
Found at i:3000777 original size:6 final size:6
Alignment explanation
Indices: 3000766--3000810 Score: 56
Period size: 6 Copynumber: 7.5 Consensus size: 6
3000756 TTAAGCAGCA
* *
3000766 TTTTTC TTTTTC TTTTTC TTTTT- TTTTTT TTTTTT TTTTTGC TTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT-C TTT
3000811 CAAATGAATC
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
5 5 0.14
6 28 0.78
7 3 0.08
ACGTcount: A:0.00, C:0.09, G:0.02, T:0.89
Consensus pattern (6 bp):
TTTTTC
Found at i:3000804 original size:12 final size:12
Alignment explanation
Indices: 3000766--3000810 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
3000756 TTAAGCAGCA
*
3000766 TTTTTCTTTTTC
1 TTTTTCTTTTTT
3000778 TTTTTCTTTTTT
1 TTTTTCTTTTTT
3000790 TTTTT-TTTTTT
1 TTTTTCTTTTTT
3000801 TTTTTGCTTT
1 TTTTT-CTTT
3000811 CAAATGAATC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 11 0.37
12 16 0.53
13 3 0.10
ACGTcount: A:0.00, C:0.09, G:0.02, T:0.89
Consensus pattern (12 bp):
TTTTTCTTTTTT
Found at i:3001383 original size:12 final size:12
Alignment explanation
Indices: 3001366--3001390 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3001356 AGCTCAAGTT
3001366 TCAAGCTTGAGC
1 TCAAGCTTGAGC
3001378 TCAAGCTTGAGC
1 TCAAGCTTGAGC
3001390 T
1 T
3001391 TACTAGGGTT
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:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (12 bp):
TCAAGCTTGAGC
Found at i:3008136 original size:9 final size:10
Alignment explanation
Indices: 3008115--3008149 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
3008105 ATAAATAAAT
3008115 AAAAATCTAA
1 AAAAATCTAA
3008125 AAAAATCTAA
1 AAAAATCTAA
*
3008135 AAAAAT-AAA
1 AAAAATCTAA
3008144 AAAAAT
1 AAAAAT
3008150 AAAGTTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 8 0.33
10 16 0.67
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.17
Consensus pattern (10 bp):
AAAAATCTAA
Found at i:3008143 original size:8 final size:8
Alignment explanation
Indices: 3008096--3008152 Score: 51
Period size: 8 Copynumber: 6.8 Consensus size: 8
3008086 CTAGACAAAT
*
3008096 AATAAATA
1 AATAAAAA
*
3008104 AATAAATA
1 AATAAAAA
3008112 AATAAAAA
1 AATAAAAA
**
3008120 TCTAAAAA
1 AATAAAAA
3008128 AATCTAAAAA
1 AA--TAAAAA
3008138 AATAAAAAA
1 AAT-AAAAA
3008147 AATAAA
1 AATAAA
3008153 GTTTATTAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
8 25 0.61
9 8 0.20
10 8 0.20
ACGTcount: A:0.77, C:0.04, G:0.00, T:0.19
Consensus pattern (8 bp):
AATAAAAA
Found at i:3010883 original size:46 final size:46
Alignment explanation
Indices: 3010822--3010999 Score: 202
Period size: 46 Copynumber: 3.8 Consensus size: 46
3010812 AATATTTAGG
3010822 TATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
1 TATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
* * * * * *
3010868 TTTTCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAA
1 TATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
3010910 CTAGGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
1 -T----ATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
***
3010961 CGCCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
3011000 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 15, Indels: 18
0.77 0.11 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 2 0.02
46 64 0.59
47 27 0.25
48 2 0.02
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.30
Consensus pattern (46 bp):
TATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
Found at i:3010982 original size:93 final size:93
Alignment explanation
Indices: 3010818--3010991 Score: 294
Period size: 93 Copynumber: 1.9 Consensus size: 93
3010808 CTAGAATATT
* ****
3010818 TAGGTATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATTTTCGAACTCGTTG
1 TAGGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTG
3010883 AGTTGAGTCCGAGTTCGTGAGATGTAAC
66 AGTTGAGTCCGAGTTCGTGAGATGTAAC
*
3010911 TAGGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTG
1 TAGGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTG
3010976 AGTTGAGTCCGAGTTC
66 AGTTGAGTCCGAGTTC
3010992 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (93 bp):
TAGGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTG
AGTTGAGTCCGAGTTCGTGAGATGTAAC
Found at i:3017784 original size:24 final size:24
Alignment explanation
Indices: 3017750--3017800 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
3017740 ATATACCACA
3017750 GCTCTTTATGAGCGTCCTGATATAG
1 GCTCTTTATGAGCGTCCTGATAT-G
*
3017775 GCTC-TTATGAGCTTCCTGATATG
1 GCTCTTTATGAGCGTCCTGATATG
3017798 GCT
1 GCT
3017801 TGCTTGAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 4 0.16
24 17 0.68
25 4 0.16
ACGTcount: A:0.18, C:0.22, G:0.24, T:0.37
Consensus pattern (24 bp):
GCTCTTTATGAGCGTCCTGATATG
Found at i:3019652 original size:30 final size:30
Alignment explanation
Indices: 3019616--3019712 Score: 79
Period size: 30 Copynumber: 3.2 Consensus size: 30
3019606 AATTGAGTTA
*
3019616 TTCGAGTCAACTTGAATAAGTAATTCAAGT
1 TTCGAGTAAACTTGAATAAGTAATTCAAGT
* * ** **
3019646 TTCGAGTTAA-TTGAATTTAGTTGTTTGAGTT
1 TTCGAGTAAACTTGAA-TAAGTAATTCAAG-T
**
3019677 ATTCGAGTAAACTCAAATAAGTAATTCAAGT
1 -TTCGAGTAAACTTGAATAAGTAATTCAAGT
3019708 TTCGA
1 TTCGA
3019713 ATTCAAGTCA
Statistics
Matches: 49, Mismatches: 14, Indels: 8
0.69 0.20 0.11
Matches are distributed among these distances:
29 5 0.10
30 22 0.45
31 2 0.04
32 17 0.35
33 3 0.06
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (30 bp):
TTCGAGTAAACTTGAATAAGTAATTCAAGT
Found at i:3019805 original size:2 final size:2
Alignment explanation
Indices: 3019800--3019851 Score: 54
Period size: 2 Copynumber: 27.0 Consensus size: 2
3019790 AACTAATGGC
* * *
3019800 AT AT AT AC AT A- AT AT AT AT AT A- AT AC AC AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
3019840 AT AT AT AC AT AT
1 AT AT AT AT AT AT
3019852 TAGAAATGAT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
1 2 0.05
2 40 0.95
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (2 bp):
AT
Found at i:3020385 original size:11 final size:12
Alignment explanation
Indices: 3020369--3020404 Score: 58
Period size: 11 Copynumber: 3.2 Consensus size: 12
3020359 AGAAAAAAAA
3020369 GAAGAGAG-AGG
1 GAAGAGAGAAGG
3020380 GAAGAGAGAAGG
1 GAAGAGAGAAGG
3020392 G-AGAGAGAAGG
1 GAAGAGAGAAGG
3020403 GA
1 GA
3020405 GGGGGAAGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 19 0.83
12 4 0.17
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (12 bp):
GAAGAGAGAAGG
Found at i:3020405 original size:11 final size:11
Alignment explanation
Indices: 3020371--3020415 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
3020361 AAAAAAAAGA
3020371 AGAGAG-AGGG
1 AGAGAGAAGGG
3020381 AAGAGAGAAGGG
1 -AGAGAGAAGGG
3020393 AGAGAGAAGGG
1 AGAGAGAAGGG
* *
3020404 AGGGGGAAGGG
1 AGAGAGAAGGG
3020415 A
1 A
3020416 AATCCGGTCG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
11 27 0.87
12 4 0.13
ACGTcount: A:0.42, C:0.00, G:0.58, T:0.00
Consensus pattern (11 bp):
AGAGAGAAGGG
Found at i:3020711 original size:14 final size:15
Alignment explanation
Indices: 3020676--3020711 Score: 65
Period size: 14 Copynumber: 2.5 Consensus size: 15
3020666 TTTTTTGGTT
3020676 TTTTTTTGCTGGAAA
1 TTTTTTTGCTGGAAA
3020691 TTTTTTT-CTGGAAA
1 TTTTTTTGCTGGAAA
3020705 TTTTTTT
1 TTTTTTT
3020712 TTGGTGATGG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.67
15 7 0.33
ACGTcount: A:0.17, C:0.06, G:0.14, T:0.64
Consensus pattern (15 bp):
TTTTTTTGCTGGAAA
Found at i:3020712 original size:15 final size:16
Alignment explanation
Indices: 3020675--3020712 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
3020665 TTTTTTTGGT
3020675 TTTTTTTTGCTGGAAA
1 TTTTTTTTGCTGGAAA
3020691 -TTTTTTT-CTGGAAA
1 TTTTTTTTGCTGGAAA
3020705 TTTTTTTT
1 TTTTTTTT
3020713 TGGTGATGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.16, C:0.05, G:0.13, T:0.66
Consensus pattern (16 bp):
TTTTTTTTGCTGGAAA
Found at i:3021195 original size:35 final size:35
Alignment explanation
Indices: 3021151--3021256 Score: 185
Period size: 35 Copynumber: 3.0 Consensus size: 35
3021141 GGGGTGTGTG
* *
3021151 ATGGCGCTGGCGGCAGACAGCATGGGAGAGTGGGA
1 ATGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
*
3021186 GTGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
1 ATGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
3021221 ATGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
1 ATGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
3021256 A
1 A
3021257 GAGGCAAGTG
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 67 1.00
ACGTcount: A:0.23, C:0.13, G:0.49, T:0.15
Consensus pattern (35 bp):
ATGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
Found at i:3022041 original size:48 final size:50
Alignment explanation
Indices: 3021965--3022112 Score: 176
Period size: 48 Copynumber: 2.9 Consensus size: 50
3021955 ATATGACCTA
**
3021965 AGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTGAAAAACAA-AA-
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAATAAC
* *
3022013 AGG-TACAACTCACCTCTCGCAATATGAGTTGCTTTTTGAAAGACAGAAATTAAC
1 AGGCT-CAACTCACCTCTCGCAATATGAGTTGATTTTTGAAA-A-A-CAA-TAAC
* *
3022067 AGGCTCAACTCACCTCTTGCAATGTGAGTTGATTTTTGAAAAACAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAA
3022113 GAATTGGAAA
Statistics
Matches: 84, Mismatches: 8, Indels: 13
0.80 0.08 0.12
Matches are distributed among these distances:
47 1 0.01
48 36 0.43
49 1 0.01
50 1 0.01
51 4 0.05
52 1 0.01
53 3 0.04
54 36 0.43
55 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (50 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAATAAC
Found at i:3022289 original size:77 final size:70
Alignment explanation
Indices: 3022168--3022685 Score: 840
Period size: 70 Copynumber: 7.2 Consensus size: 70
3022158 TCAACTCACC
3022168 TATGAGTTGATTTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTC
1 TATGAGTTGA-TTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTC
*
3022233 TCGCCA
65 TCGCAA
*
3022239 TATGAGTTGATTTTGAAACATAAATTGAAAATTGAAATTACCTCAACGTGTTTTGAGGCTCAACT
1 TATGAGTTGATTTTGAAAC----A-T--AAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACT
3022304 CACCTCTCGCAA
59 CACCTCTCGCAA
3022316 TATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCT
1 TATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCT
*
3022381 CGCCA
66 CGCAA
*
3022386 TATGAGTTGATTTTGAAACATAAATTGAAAATTGAAATTACCTCAACGTGTTTTGAGGCTCAACT
1 TATGAGTTGATTTTGAAAC----A-T--AAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACT
3022451 CACCTCTCGCAA
59 CACCTCTCGCAA
*
3022463 TATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGA-GCTTAACTCACCTCT
1 TATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCT
3022527 CGCAA
66 CGCAA
3022532 TATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCT
1 TATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCT
3022597 CGCAA
66 CGCAA
3022602 TATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCT
1 TATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCT
3022667 CGCAA
66 CGCAA
*
3022672 TGTGAGTTGATTTT
1 TATGAGTTGATTTT
3022686 CTGTCACTTG
Statistics
Matches: 422, Mismatches: 10, Indels: 31
0.91 0.02 0.07
Matches are distributed among these distances:
69 68 0.16
70 204 0.48
71 10 0.02
72 2 0.00
73 2 0.00
74 2 0.00
75 2 0.00
77 132 0.31
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (70 bp):
TATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCT
CGCAA
Found at i:3022344 original size:147 final size:147
Alignment explanation
Indices: 3022168--3022685 Score: 926
Period size: 147 Copynumber: 3.6 Consensus size: 147
3022158 TCAACTCACC
3022168 TATGAGTTGATTTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTC
1 TATGAGTTGA-TTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTC
*
3022233 TCGCCATATGAGTTGATTTTGAAACATAAATTGAAAATTGAAATTACCTCAACGTGTTTTGAGGC
65 TCGCAATATGAGTTGATTTTGAAACATAAATTGAAAATTGAAATTACCTCAACGTGTTTTGAGGC
3022298 TCAACTCACCTCTCGCAA
130 TCAACTCACCTCTCGCAA
3022316 TATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCT
1 TATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCT
*
3022381 CGCCATATGAGTTGATTTTGAAACATAAATTGAAAATTGAAATTACCTCAACGTGTTTTGAGGCT
66 CGCAATATGAGTTGATTTTGAAACATAAATTGAAAATTGAAATTACCTCAACGTGTTTTGAGGCT
3022446 CAACTCACCTCTCGCAA
131 CAACTCACCTCTCGCAA
*
3022463 TATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGA-GCTTAACTCACCTCT
1 TATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCT
*
3022527 CGCAATATGAGTTGATTTTGAAAC----A-T--AAATTGAAATTACCTCAACGTGTCTTGAGGCT
66 CGCAATATGAGTTGATTTTGAAACATAAATTGAAAATTGAAATTACCTCAACGTGTTTTGAGGCT
3022585 CAACTCACCTCTCGCAA
131 CAACTCACCTCTCGCAA
3022602 TATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCT
1 TATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCT
*
3022667 CGCAATGTGAGTTGATTTT
66 CGCAATATGAGTTGATTTT
3022686 CTGTCACTTG
Statistics
Matches: 364, Mismatches: 5, Indels: 10
0.96 0.01 0.03
Matches are distributed among these distances:
139 97 0.27
140 32 0.09
141 1 0.00
142 1 0.00
146 37 0.10
147 186 0.51
148 10 0.03
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (147 bp):
TATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCT
CGCAATATGAGTTGATTTTGAAACATAAATTGAAAATTGAAATTACCTCAACGTGTTTTGAGGCT
CAACTCACCTCTCGCAA
Found at i:3027282 original size:53 final size:53
Alignment explanation
Indices: 3027201--3027351 Score: 205
Period size: 53 Copynumber: 2.8 Consensus size: 53
3027191 CTTACACGGT
* *
3027201 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
3027256 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** * *
3027309 TCACATTGCACCAATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
3027352 GCACACTTGT
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
52 1 0.01
53 80 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:3040486 original size:2 final size:2
Alignment explanation
Indices: 3040479--3040517 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
3040469 ATATGTGCAA
* *
3040479 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3040518 AAATATACAC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:3040686 original size:2 final size:2
Alignment explanation
Indices: 3040681--3040735 Score: 53
Period size: 2 Copynumber: 29.0 Consensus size: 2
3040671 AACTAATGGC
* * *
3040681 AT AT AT AC AT A- AT AT AT AT AT AT A- AT AC AC AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
3040720 AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT
3040736 TAGAAATGAT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
1 3 0.07
2 41 0.93
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (2 bp):
AT
Found at i:3040713 original size:22 final size:23
Alignment explanation
Indices: 3040681--3040732 Score: 88
Period size: 22 Copynumber: 2.3 Consensus size: 23
3040671 AACTAATGGC
*
3040681 ATATATACATAATATATATATAT
1 ATATACACATAATATATATATAT
3040704 A-ATACACATAATATATATATAT
1 ATATACACATAATATATATATAT
3040726 ATATACA
1 ATATACA
3040733 TATTAGAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 21 0.78
23 6 0.22
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (23 bp):
ATATACACATAATATATATATAT
Found at i:3041264 original size:11 final size:12
Alignment explanation
Indices: 3041248--3041284 Score: 60
Period size: 11 Copynumber: 3.2 Consensus size: 12
3041238 AGAAAAAAAA
3041248 GGAAGAGAG-AG
1 GGAAGAGAGAAG
3041259 GGAAGAGAGAAG
1 GGAAGAGAGAAG
3041271 GG-AGAGAGAAG
1 GGAAGAGAGAAG
3041282 GGA
1 GGA
3041285 GGGGGAAGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 20 0.83
12 4 0.17
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (12 bp):
GGAAGAGAGAAG
Found at i:3041285 original size:11 final size:11
Alignment explanation
Indices: 3041246--3041295 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
3041236 AAAGAAAAAA
*
3041246 AAGGAAGAGAG
1 AAGGGAGAGAG
3041257 -AGGGAAGAGAG
1 AAGGG-AGAGAG
3041268 AAGGGAGAGAG
1 AAGGGAGAGAG
* *
3041279 AAGGGAGGGGG
1 AAGGGAGAGAG
3041290 AAGGGA
1 AAGGGA
3041296 AATCCGGTCG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
10 3 0.09
11 27 0.79
12 4 0.12
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (11 bp):
AAGGGAGAGAG
Found at i:3041593 original size:14 final size:15
Alignment explanation
Indices: 3041558--3041593 Score: 65
Period size: 14 Copynumber: 2.5 Consensus size: 15
3041548 TTTTTTGGTT
3041558 TTTTTTTGCTGGAAA
1 TTTTTTTGCTGGAAA
3041573 TTTTTTT-CTGGAAA
1 TTTTTTTGCTGGAAA
3041587 TTTTTTT
1 TTTTTTT
3041594 TGGTGCTGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.67
15 7 0.33
ACGTcount: A:0.17, C:0.06, G:0.14, T:0.64
Consensus pattern (15 bp):
TTTTTTTGCTGGAAA
Found at i:3041594 original size:15 final size:16
Alignment explanation
Indices: 3041557--3041595 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
3041547 TTTTTTTGGT
3041557 TTTTTTTTGCTGGAAA
1 TTTTTTTTGCTGGAAA
3041573 -TTTTTTT-CTGGAAA
1 TTTTTTTTGCTGGAAA
3041587 TTTTTTTTG
1 TTTTTTTTG
3041596 GTGCTGGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.15, C:0.05, G:0.15, T:0.64
Consensus pattern (16 bp):
TTTTTTTTGCTGGAAA
Done.