Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 107 of 230
Found at i:30790378 original size:23 final size:21
Alignment explanation
Indices: 30790329--30790380 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
30790319 TGTATATGTA
*
30790329 TATTATTTTGTGTTTTTTTTC
1 TATTATTTTATGTTTTTTTTC
30790350 TA-TATTTTAATGATTTTTTCTT-
1 TATTATTTT-ATG-TTTTTT-TTC
30790372 TATTATTTT
1 TATTATTTT
30790381 TCATTGTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 6 0.23
21 4 0.15
22 8 0.31
23 8 0.31
ACGTcount: A:0.17, C:0.04, G:0.06, T:0.73
Consensus pattern (21 bp):
TATTATTTTATGTTTTTTTTC
Found at i:30808774 original size:20 final size:20
Alignment explanation
Indices: 30808749--30808813 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
30808739 TCATTTTGCA
**
30808749 ATAAAAATACATAAGATTTT
1 ATAAAAATACATAAGAAATT
* **
30808769 ATAAAAATATATATTAAATT
1 ATAAAAATACATAAGAAATT
30808789 ATAAAAATACATACA-AAATT
1 ATAAAAATACATA-AGAAATT
30808809 ATAAA
1 ATAAA
30808814 TAAATGAATA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.32
Consensus pattern (20 bp):
ATAAAAATACATAAGAAATT
Found at i:30814853 original size:24 final size:26
Alignment explanation
Indices: 30814801--30814855 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 26
30814791 AAAATAAAAA
*
30814801 TATATTTATATTATTTTTAATAATTT
1 TATATTTATATTATTTTTAATAATGT
30814827 TATATTT-T-TTATTTATTAA-AATGT
1 TATATTTATATTATTT-TTAATAATGT
30814851 TATAT
1 TATAT
30814856 ATAATCATCT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 15 0.56
25 5 0.19
26 7 0.26
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (26 bp):
TATATTTATATTATTTTTAATAATGT
Found at i:30814856 original size:26 final size:27
Alignment explanation
Indices: 30814800--30814857 Score: 70
Period size: 26 Copynumber: 2.2 Consensus size: 27
30814790 TAAAATAAAA
30814800 ATATATTTATATTATTTTTAATAATTT
1 ATATATTTATATTATTTTTAATAATTT
30814827 -TATATTT-T-TTATTTATTAA-AATGTT
1 ATATATTTATATTATTT-TTAATAAT-TT
30814852 ATATAT
1 ATATAT
30814858 AATCATCTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
24 9 0.32
25 7 0.25
26 12 0.43
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (27 bp):
ATATATTTATATTATTTTTAATAATTT
Found at i:30815427 original size:9 final size:9
Alignment explanation
Indices: 30815415--30815458 Score: 61
Period size: 9 Copynumber: 4.7 Consensus size: 9
30815405 TTAAAATGAT
30815415 TAAAAATCA
1 TAAAAATCA
30815424 TAAAAAGTCA
1 TAAAAA-TCA
*
30815434 TTAAAAATTA
1 -TAAAAATCA
30815444 TAAAAATCA
1 TAAAAATCA
30815453 TAAAAA
1 TAAAAA
30815459 AATATTAAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
9 20 0.65
10 5 0.16
11 6 0.19
ACGTcount: A:0.66, C:0.07, G:0.02, T:0.25
Consensus pattern (9 bp):
TAAAAATCA
Found at i:30815438 original size:20 final size:19
Alignment explanation
Indices: 30815407--30815458 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
30815397 ATATTCTATT
*
30815407 AAAATGATTAAAAATCATA
1 AAAATCATTAAAAATCATA
*
30815426 AAAAGTCATTAAAAATTATA
1 AAAA-TCATTAAAAATCATA
30815446 AAAATCA-TAAAAA
1 AAAATCATTAAAAA
30815459 AATATTAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
18 6 0.20
19 7 0.23
20 17 0.57
ACGTcount: A:0.65, C:0.06, G:0.04, T:0.25
Consensus pattern (19 bp):
AAAATCATTAAAAATCATA
Found at i:30815465 original size:29 final size:29
Alignment explanation
Indices: 30815415--30815478 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
30815405 TTAAAATGAT
*
30815415 TAAAAATCATAAAAAGTCATTAAAAATTA
1 TAAAAATCATAAAAAATCATTAAAAATTA
*
30815444 TAAAAATCATAAAAAAAT-ATTAAAGATTA
1 TAAAAATCAT-AAAAAATCATTAAAAATTA
30815473 TAAAAA
1 TAAAAA
30815479 ATAAGGAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 26 0.81
30 6 0.19
ACGTcount: A:0.66, C:0.05, G:0.03, T:0.27
Consensus pattern (29 bp):
TAAAAATCATAAAAAATCATTAAAAATTA
Found at i:30815488 original size:29 final size:27
Alignment explanation
Indices: 30815415--30815499 Score: 73
Period size: 29 Copynumber: 2.9 Consensus size: 27
30815405 TTAAAATGAT
**
30815415 TAAAAATCATAAAAAGTCATTAAAAATTA
1 TAAAAA-CATAAAAA-AAATTAAAAATTA
*
30815444 TAAAAATCATAAAAAAATATTAAAGATTA
1 TAAAAA-CATAAAAAAA-ATTAAAAATTA
30815473 TAAAAA-ATAAGGAAAAAATTATAAAAT
1 TAAAAACATAA--AAAAAATTA-AAAAT
30815500 ATTTAAAATA
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
27 4 0.08
28 4 0.08
29 40 0.83
ACGTcount: A:0.66, C:0.04, G:0.05, T:0.26
Consensus pattern (27 bp):
TAAAAACATAAAAAAAATTAAAAATTA
Found at i:30815498 original size:9 final size:9
Alignment explanation
Indices: 30815415--30815843 Score: 119
Period size: 10 Copynumber: 44.7 Consensus size: 9
30815405 TTAAAATGAT
*
30815415 TAAAAATCA
1 TAAAAATTA
*
30815424 TAAAAAGTCA
1 TAAAAA-TTA
30815434 TTAAAAATTA
1 -TAAAAATTA
*
30815444 TAAAAATCA
1 TAAAAATTA
*
30815453 TAAAAAAATA
1 T-AAAAATTA
*
30815463 TTAAAGATTA
1 -TAAAAATTA
*
30815473 TAAAAAATAA
1 T-AAAAATTA
*
30815483 GGAAAAAATTA
1 --TAAAAATTA
30815494 TAAAATATT-
1 TAAAA-ATTA
30815503 TAAAATATT-
1 TAAAA-ATTA
30815512 TAAAAA-TA
1 TAAAAATTA
*
30815520 TTAAAATTAA
1 TAAAAATT-A
*
30815530 TATAAACTTA
1 TA-AAAATTA
* *
30815540 TAATACTTA
1 TAAAAATTA
*
30815549 TAAAAGCTTA
1 TAAAA-ATTA
*
30815559 TAAATATTA
1 TAAAAATTA
*
30815568 TAAAAACATA
1 TAAAAA-TTA
30815578 TAATAAATCTA
1 TAA-AAAT-TA
**
30815589 -ATTAATTA
1 TAAAAATTA
30815597 TAAAAATATA
1 TAAAAAT-TA
30815607 TAAAAAATTAA
1 T-AAAAATT-A
30815618 TAAACATATTA
1 TAAA-A-ATTA
*
30815629 -AAATATT-
1 TAAAAATTA
*
30815636 TAAAATTTTA
1 TAAAA-ATTA
*
30815646 TAAAAACCTA
1 TAAAAA-TTA
*
30815656 T-AAAATTCT
1 TAAAAATT-A
30815665 TAAAAATTA
1 TAAAAATTA
*
30815674 T-TAAA-TA
1 TAAAAATTA
* *
30815681 TTAAAACTA
1 TAAAAATTA
*
30815690 TTAAAATTGA
1 TAAAAATT-A
*
30815700 TATAAATTA
1 TAAAAATTA
*
30815709 TAATAA-TA
1 TAAAAATTA
30815717 TAATAAATTA
1 TAA-AAATTA
30815727 TAAATAGATT-
1 TAAA-A-ATTA
30815737 TATAAAATTAA
1 TA-AAAATT-A
*
30815748 TAAAATATATT
1 TAAAA-AT-TA
30815759 TAAAATATT-
1 TAAAA-ATTA
*
30815768 TAATAATTTA
1 TAA-AAATTA
* *
30815778 TAACAAGTAA
1 TAA-AAATTA
30815788 TAAAAATTCA
1 TAAAAATT-A
30815798 TAAAAAACTTA
1 T-AAAAA-TTA
30815809 TAAATAA-TA
1 TAAA-AATTA
*
30815818 TAATAAATTC
1 TAA-AAATTA
*
30815828 TAATAAATTG
1 TAA-AAATTA
30815838 TAAAAA
1 TAAAAA
30815844 AATTATAAAT
Statistics
Matches: 322, Mismatches: 50, Indels: 96
0.69 0.11 0.21
Matches are distributed among these distances:
7 4 0.01
8 26 0.08
9 106 0.33
10 120 0.37
11 60 0.19
12 6 0.02
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (9 bp):
TAAAAATTA
Found at i:30815596 original size:29 final size:28
Alignment explanation
Indices: 30815564--30815618 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
30815554 GCTTATAAAT
*
30815564 ATTATAAAAACATATAATAAATCTAATTA
1 ATTATAAAAACATATAAAAAAT-TAATTA
*
30815593 ATTATAAAAATATATAAAAAATTAAT
1 ATTATAAAAACATATAAAAAATTAAT
30815619 AAACATATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 4 0.17
29 20 0.83
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (28 bp):
ATTATAAAAACATATAAAAAATTAATTA
Found at i:30815630 original size:20 final size:20
Alignment explanation
Indices: 30815436--30815852 Score: 91
Period size: 19 Copynumber: 21.6 Consensus size: 20
30815426 AAAAGTCATT
30815436 AAAAATTATAAAAATCATA-A
1 AAAAATTATAAAAAT-ATATA
*
30815456 AAAAA-TATTAAAGAT-TATA
1 AAAAATTA-TAAAAATATATA
* *
30815475 AAAAATAAGGAAAAA-ATTATA
1 AAAAATTA-TAAAAATA-TATA
* *
30815496 AAATATT-T-AAAATAT-TT
1 AAAAATTATAAAAATATATA
*
30815513 AAAAA-TATTAAAAT-TAATA
1 AAAAATTATAAAAATAT-ATA
* * * *
30815532 TAAACTTATAATACT-TATA
1 AAAAATTATAAAAATATATA
** *
30815551 AAAGCTTATAAATAT-TATA
1 AAAAATTATAAAAATATATA
* *
30815570 AAAACA-TATAATAA-ATCTA
1 AAAA-ATTATAAAAATATATA
**
30815589 ATTAATTATAAAAATATATA
1 AAAAATTATAAAAATATATA
*
30815609 AAAAATTAATAAACATAT-TA
1 AAAAATT-ATAAAAATATATA
* * *
30815629 AAATATT-TAAAATTTTATA
1 AAAAATTATAAAAATATATA
** * *
30815648 AAAACCTAT-AAAAT-TCTT
1 AAAAATTATAAAAATATATA
*
30815666 AAAAATTAT-TAAATAT-T-
1 AAAAATTATAAAAATATATA
* *
30815683 -AAAACTATTAAAAT-TGAT-
1 AAAAATTATAAAAATAT-ATA
* *
30815701 ATAAATTAT-AATA-ATATA
1 AAAAATTATAAAAATATATA
* * * *
30815719 ATAAATTATAAATAGATTTA
1 AAAAATTATAAAAATATATA
* *
30815739 TAAAATTAATAAAATATATTTA
1 AAAAATT-ATAAAA-ATATATA
* * *
30815761 AAATATT-TAATAATTTATA
1 AAAAATTATAAAAATATATA
* * *
30815780 ACAAGTAATAAAAAT-TCATA
1 AAAAATTATAAAAATAT-ATA
*
30815800 AAAAACTTATAAATA-ATATA
1 AAAAA-TTATAAAAATATATA
* * *
30815820 ATAAATTCTAATAAAT-TGTAA
1 AAAAATTATAA-AAATATAT-A
30815841 AAAAATTATAAA
1 AAAAATTATAAA
30815853 TTATACCCCT
Statistics
Matches: 285, Mismatches: 76, Indels: 72
0.66 0.18 0.17
Matches are distributed among these distances:
16 9 0.03
17 13 0.05
18 47 0.16
19 86 0.30
20 78 0.27
21 41 0.14
22 11 0.04
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (20 bp):
AAAAATTATAAAAATATATA
Found at i:30815753 original size:22 final size:21
Alignment explanation
Indices: 30815721--30815773 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
30815711 ATAATATAAT
30815721 AAATT-AT-AAATAGATTTATA
1 AAATTAATAAAATAGATTTA-A
*
30815741 AAATTAATAAAATATATTTAA
1 AAATTAATAAAATAGATTTAA
30815762 AATATTTAATAA
1 AA-A-TTAATAA
30815774 TTTATAACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 5 0.18
21 5 0.18
22 11 0.39
23 7 0.25
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
AAATTAATAAAATAGATTTAA
Found at i:30816634 original size:35 final size:34
Alignment explanation
Indices: 30816544--30816635 Score: 80
Period size: 35 Copynumber: 2.6 Consensus size: 34
30816534 TTTCATATTT
* * *
30816544 TTTTATAATTTATTA-GATTTTTTATTTTTATAAG
1 TTTTAT-ATTTTTTATGATTTTTAATTTTTATAAA
* **
30816578 TTTGTATTAATTTAAAT-ATTTTTAATTTTTAATAAA
1 TTT-TA-TATTTTTTATGATTTTTAATTTTT-ATAAA
30816614 TTTTATATTTTTTATGATTTTT
1 TTTTATATTTTTTATGATTTTT
30816636 TTTATATTTT
Statistics
Matches: 44, Mismatches: 9, Indels: 9
0.71 0.15 0.15
Matches are distributed among these distances:
34 10 0.23
35 26 0.59
36 8 0.18
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.65
Consensus pattern (34 bp):
TTTTATATTTTTTATGATTTTTAATTTTTATAAA
Found at i:30823756 original size:33 final size:33
Alignment explanation
Indices: 30823684--30823792 Score: 150
Period size: 33 Copynumber: 3.3 Consensus size: 33
30823674 AATTTTTTTA
*
30823684 AAAATTAATTAAATTAGGTTTTAGGGGTTTTAAG
1 AAAATTAATTAAATTAGGGTTTA-GGGTTTTAAG
* *
30823718 TAAATTAATTAAATTAGGGTTTAGTGTTTTAAG
1 AAAATTAATTAAATTAGGGTTTAGGGTTTTAAG
*
30823751 AAAATTAACTAAATTAGGGTTTAGGGTTTTTAA-
1 AAAATTAATTAAATTAGGGTTTAGGG-TTTTAAG
30823784 AAAA-TAATT
1 AAAATTAATT
30823793 TTGTGTTTAG
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
32 4 0.06
33 36 0.54
34 27 0.40
ACGTcount: A:0.40, C:0.01, G:0.17, T:0.41
Consensus pattern (33 bp):
AAAATTAATTAAATTAGGGTTTAGGGTTTTAAG
Found at i:30824138 original size:124 final size:125
Alignment explanation
Indices: 30823876--30824140 Score: 358
Period size: 124 Copynumber: 2.1 Consensus size: 125
30823866 ATTTTGTGTT
*
30823876 TTTTTCTACT-GTAGTTTCTGAAAAAATAAATTTGAGAAGACGATTTTGAAAAAATAGTGACAAA
1 TTTTTCTA-TAGTAGTTTCTGAAAAAATAAATTTGAGAAGACGATTCTGAAAAAATAGTGACAAA
* * * *
30823940 AATGCTTCAAGCAGGATGCACTGTCAGCTAAAGTACTAAAAAAGCTCCCACATTGACGCTC
65 AACGCTTCAAACAGGATGCACTGTCAGCAAAAGTACTAAAAAAGCTCCCACATGGACGCTC
* * *
30824001 TTTTTCTACAGTAGTTTCTG-AAAAATAATTTTGAGAAGACTG-TTCT-AAAAAATAGTGTCAAA
1 TTTTTCTATAGTAGTTTCTGAAAAAATAAATTTGAGAAGAC-GATTCTGAAAAAATAGTGACAAA
* * * * *
30824063 AACGCTTCAAACAGGATGCATTGTCAGCAAAATTATTGAAAAAAGCTCGCACGTGGACGCTC
65 AACGCTTCAAACAGGATGCACTGTCAGCAAAAGTACT-AAAAAAGCTCCCACATGGACGCTC
30824125 TTTTTCTATAGTAGTT
1 TTTTTCTATAGTAGTT
30824141 CTTGCTTGGC
Statistics
Matches: 123, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
123 46 0.37
124 58 0.47
125 19 0.15
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.31
Consensus pattern (125 bp):
TTTTTCTATAGTAGTTTCTGAAAAAATAAATTTGAGAAGACGATTCTGAAAAAATAGTGACAAAA
ACGCTTCAAACAGGATGCACTGTCAGCAAAAGTACTAAAAAAGCTCCCACATGGACGCTC
Found at i:30827637 original size:18 final size:18
Alignment explanation
Indices: 30827611--30827653 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
30827601 GACTGGGAAA
* *
30827611 AGGAAACATATAAGGGTT
1 AGGATACATATAAGGGCT
*
30827629 AGGATACATATGAGGGCT
1 AGGATACATATAAGGGCT
30827647 AGGATAC
1 AGGATAC
30827654 TCACCTAGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.40, C:0.09, G:0.30, T:0.21
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:30829071 original size:9 final size:9
Alignment explanation
Indices: 30829065--30829089 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
30829055 ATAAAAAAAG
30829065 GCCAAAATA
1 GCCAAAATA
30829074 GCCAAAATA
1 GCCAAAATA
30829083 GCCAAAA
1 GCCAAAA
30829090 ATTTGTCCAT
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:0.56, C:0.24, G:0.12, T:0.08
Consensus pattern (9 bp):
GCCAAAATA
Found at i:30830112 original size:51 final size:51
Alignment explanation
Indices: 30830039--30830254 Score: 222
Period size: 51 Copynumber: 4.3 Consensus size: 51
30830029 TATGAACATG
* * * *
30830039 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATC-GATAGATAATGGTCACA
1 TGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGAT-GACAATGGTCACA
* * ** *
30830090 TGTGTAGTACTATGTGTAGGCTACCATGTGTACCGGATGACCTTGGTCACG
1 TGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGATGACAATGGTCACA
* * * * * *
30830141 TGTGTAGTACTATGTGTAGGCTACTACGTGAACCAGA-AAGC-TTGATCACG
1 TGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGATGA-CAATGGTCACA
**
30830191 TGTGTAGTACTATGTGTAGGCTACTACGTGTTTCGGATGACAATGGTCACA
1 TGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGATGACAATGGTCACA
* *
30830242 TGGGTGGTACTAT
1 TGTGTAGTACTAT
30830255 ATGCAAACCA
Statistics
Matches: 136, Mismatches: 25, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
50 43 0.32
51 90 0.66
52 3 0.02
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.31
Consensus pattern (51 bp):
TGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGATGACAATGGTCACA
Found at i:30830228 original size:101 final size:101
Alignment explanation
Indices: 30830038--30830259 Score: 257
Period size: 101 Copynumber: 2.2 Consensus size: 101
30830028 CTATGAACAT
* * * * *
30830038 GTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCGATAGATAATGGTCACATGTGTAGTACTAT
1 GTGTGTAGTACTATGTGCAGGCTACTACGTGAACCGAAAGAT-ATGATCACATGTGTAGTACTAT
* **
30830103 GTGTAGGCTACCATGTGTACCGGATGACCTTGGTCAC
65 GTGTAGGCTACCACGTGTACCGGATGACAATGGTCAC
* * *
30830140 GTGTGTAGTACTATGTGTAGGCTACTACGTGAACCAGAAAGCT-TGATCACGTGTGTAGTACTAT
1 GTGTGTAGTACTATGTGCAGGCTACTACGTGAACC-GAAAGATATGATCACATGTGTAGTACTAT
* **
30830204 GTGTAGGCTACTACGTGTTTCGGATGACAATGGTCAC
65 GTGTAGGCTACCACGTGTACCGGATGACAATGGTCAC
* * * *
30830241 ATGGGTGGTACTATATGCA
1 GTGTGTAGTACTATGTGCA
30830260 AACCACCGAA
Statistics
Matches: 100, Mismatches: 19, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
101 64 0.64
102 31 0.31
103 5 0.05
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.31
Consensus pattern (101 bp):
GTGTGTAGTACTATGTGCAGGCTACTACGTGAACCGAAAGATATGATCACATGTGTAGTACTATG
TGTAGGCTACCACGTGTACCGGATGACAATGGTCAC
Found at i:30836081 original size:10 final size:10
Alignment explanation
Indices: 30836039--30836093 Score: 53
Period size: 10 Copynumber: 5.6 Consensus size: 10
30836029 AAAAAATTCG
*
30836039 TTATTTGTAA
1 TTATTTATAA
30836049 TT-TTTAATAA
1 TTATTT-ATAA
30836059 TT-TTCTATAA
1 TTATT-TATAA
30836069 TTATTTATAA
1 TTATTTATAA
*
30836079 TTATTGATAA
1 TTATTTATAA
30836089 -TATTT
1 TTATTT
30836094 CTTGTCAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
9 7 0.18
10 29 0.74
11 3 0.08
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.60
Consensus pattern (10 bp):
TTATTTATAA
Found at i:30838227 original size:21 final size:21
Alignment explanation
Indices: 30838189--30838280 Score: 73
Period size: 21 Copynumber: 4.5 Consensus size: 21
30838179 ACATCGTTTC
*
30838189 CAGAAGC-C-TGAAAGCTAAA
1 CAGAAGCTCATGAGAGCTAAA
30838208 CAGAAGCTCATGAGAGCTAAA
1 CAGAAGCTCATGAGAGCTAAA
* * * * *
30838229 CAGAAACCCAT-ATGGGTTGAA
1 CAGAAGCTCATGA-GAGCTAAA
* * *
30838250 CAGAAGCTCGTAAGAGCTGAA
1 CAGAAGCTCATGAGAGCTAAA
30838271 CAGAAGCTCA
1 CAGAAGCTCA
30838281 AAAGAACTGG
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
19 7 0.12
20 2 0.04
21 47 0.82
22 1 0.02
ACGTcount: A:0.41, C:0.21, G:0.24, T:0.14
Consensus pattern (21 bp):
CAGAAGCTCATGAGAGCTAAA
Found at i:30838285 original size:21 final size:21
Alignment explanation
Indices: 30838201--30838285 Score: 80
Period size: 21 Copynumber: 4.0 Consensus size: 21
30838191 GAAGCCTGAA
*
30838201 AGCTAAACAGAAGCTCATGAG
1 AGCTAAACAGAAGCTCATAAG
* * *
30838222 AGCTAAACAGAAACCCATATG
1 AGCTAAACAGAAGCTCATAAG
* * * *
30838243 GGTTGAACAGAAGCTCGTAAG
1 AGCTAAACAGAAGCTCATAAG
* *
30838264 AGCTGAACAGAAGCTCAAAAG
1 AGCTAAACAGAAGCTCATAAG
30838285 A
1 A
30838286 ACTGGGCAGA
Statistics
Matches: 49, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.14
Consensus pattern (21 bp):
AGCTAAACAGAAGCTCATAAG
Found at i:30845981 original size:42 final size:42
Alignment explanation
Indices: 30845935--30846021 Score: 129
Period size: 42 Copynumber: 2.1 Consensus size: 42
30845925 AGCTAAAAAG
*
30845935 AAGCTCATAAGAGCTAAACAGAAACCCATAAGGGTTGAACAA
1 AAGCTCATAAGAGCTAAACAGAAACCCATAAGAGTTGAACAA
* * * *
30845977 AAGCTCGTACGAGCTGAACAGAAACTCATAAGAGTTGAACAA
1 AAGCTCATAAGAGCTAAACAGAAACCCATAAGAGTTGAACAA
30846019 AAG
1 AAG
30846022 ATCGAAAGAC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (42 bp):
AAGCTCATAAGAGCTAAACAGAAACCCATAAGAGTTGAACAA
Found at i:30846015 original size:21 final size:21
Alignment explanation
Indices: 30845904--30846017 Score: 95
Period size: 21 Copynumber: 5.4 Consensus size: 21
30845894 GAAGCCCGAA
* * *
30845904 AGCTGAACAGAAGCTCGTGAG
1 AGCTGAACAGAAACTCATAAG
* * *
30845925 AGCTAAAAAGAAGCTCATAAG
1 AGCTGAACAGAAACTCATAAG
* *
30845946 AGCTAAACAGAAACCCATAAG
1 AGCTGAACAGAAACTCATAAG
* * * *
30845967 GGTTGAACA-AAAGCTCGTACG
1 AGCTGAACAGAAA-CTCATAAG
30845988 AGCTGAACAGAAACTCATAAG
1 AGCTGAACAGAAACTCATAAG
*
30846009 AGTTGAACA
1 AGCTGAACA
30846018 AAAGATCGAA
Statistics
Matches: 73, Mismatches: 18, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
20 3 0.04
21 67 0.92
22 3 0.04
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.15
Consensus pattern (21 bp):
AGCTGAACAGAAACTCATAAG
Found at i:30848826 original size:57 final size:59
Alignment explanation
Indices: 30848748--30848869 Score: 176
Period size: 57 Copynumber: 2.1 Consensus size: 59
30848738 CATTTTCATT
**
30848748 TTTTCATTTTTCATTTTGGAGAAAACCACCTTCATTTCCAAATGAGTC-CATTTCTCCA
1 TTTTCATTTTTCATTTTGGAGAAAACCACAATCATTTCCAAATGAGTCTCATTTCTCCA
* * **
30848806 TTTTCA-TTTTCATTTTGGAGAAAATCATAATCATTTCCAAATGTTTCTCATTTCTCCA
1 TTTTCATTTTTCATTTTGGAGAAAACCACAATCATTTCCAAATGAGTCTCATTTCTCCA
30848864 TTTTCA
1 TTTTCA
30848870 CTATTTTTTA
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
57 35 0.61
58 22 0.39
ACGTcount: A:0.26, C:0.21, G:0.07, T:0.45
Consensus pattern (59 bp):
TTTTCATTTTTCATTTTGGAGAAAACCACAATCATTTCCAAATGAGTCTCATTTCTCCA
Found at i:30851989 original size:33 final size:34
Alignment explanation
Indices: 30851946--30852021 Score: 109
Period size: 33 Copynumber: 2.3 Consensus size: 34
30851936 TATTGGGCCA
*
30851946 GGCTGTGTGATCCACACGGCTAAGGCCA-TTTAG
1 GGCTGTGTGATCCACACGGCCAAGGCCATTTTAG
* * *
30851979 TGCTGTGTGATCTACATGGCCAAGGCCATTTTAG
1 GGCTGTGTGATCCACACGGCCAAGGCCATTTTAG
30852013 GGCTGTGTG
1 GGCTGTGTG
30852022 GGCCACACTG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
33 24 0.65
34 13 0.35
ACGTcount: A:0.18, C:0.21, G:0.32, T:0.29
Consensus pattern (34 bp):
GGCTGTGTGATCCACACGGCCAAGGCCATTTTAG
Found at i:30853335 original size:25 final size:25
Alignment explanation
Indices: 30853307--30853394 Score: 81
Period size: 25 Copynumber: 3.5 Consensus size: 25
30853297 TTGTTTTTGA
* *
30853307 TAGTATATCCTGAAACTGCTATAGG
1 TAGTATATACTGAAACTACTATAGG
* *
30853332 TAGTATATACTGAGACTACTATAGA
1 TAGTATATACTGAAACTACTATAGG
* *
30853357 TAG-ACTATACTGAAAATACTCA-AGT
1 TAGTA-TATACTGAAACTACT-ATAGG
*
30853382 TAGTGTATACTGA
1 TAGTATATACTGA
30853395 TACTGTAGTA
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
24 1 0.02
25 50 0.96
26 1 0.02
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.32
Consensus pattern (25 bp):
TAGTATATACTGAAACTACTATAGG
Found at i:30860505 original size:73 final size:73
Alignment explanation
Indices: 30860381--30860528 Score: 251
Period size: 73 Copynumber: 2.0 Consensus size: 73
30860371 TAGAGAATAT
* *
30860381 TTACTATTCATGCGTCTTTTCGTGCAGGGAATATTTACTGTTTACGCCAGAGAATTTTTCCTGTT
1 TTACTATTCATGCGTCTTTTCGTGCAGGGAATATTTACTGTTTACGCCAGAGAATATTTCATGTT
*
30860446 CACTTTTC
66 CACTTGTC
* *
30860454 TTACTATTCATGCGTCTTTTCTTGCAGGGAATATTTACTGTTTACGTCAGAGAATATTTCATGTT
1 TTACTATTCATGCGTCTTTTCGTGCAGGGAATATTTACTGTTTACGCCAGAGAATATTTCATGTT
30860519 CACTTGTC
66 CACTTGTC
30860527 TT
1 TT
30860529 TTTTTGCATC
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
73 70 1.00
ACGTcount: A:0.20, C:0.19, G:0.16, T:0.45
Consensus pattern (73 bp):
TTACTATTCATGCGTCTTTTCGTGCAGGGAATATTTACTGTTTACGCCAGAGAATATTTCATGTT
CACTTGTC
Found at i:30869542 original size:62 final size:59
Alignment explanation
Indices: 30869469--30869584 Score: 178
Period size: 62 Copynumber: 1.9 Consensus size: 59
30869459 AGTGATTATC
* *
30869469 TTAATATTAAATTTAATTTAATATTTATCTTGTAGATAAACATTATATTATTTTAATCAGAT
1 TTAATATTAAATTTAATCTAATATTTATC-T-T-GATAAACATTATATTAATTTAATCAGAT
*
30869531 TTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTATATTAATTTAAT
1 TTAATATTAAATTTAATCTAATATTTATCTTGATAAACATTATATTAATTTAAT
30869585 ATTAAAGTGA
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
59 21 0.41
60 1 0.02
61 1 0.02
62 28 0.55
ACGTcount: A:0.41, C:0.04, G:0.03, T:0.51
Consensus pattern (59 bp):
TTAATATTAAATTTAATCTAATATTTATCTTGATAAACATTATATTAATTTAATCAGAT
Found at i:30870451 original size:41 final size:41
Alignment explanation
Indices: 30870394--30870543 Score: 230
Period size: 41 Copynumber: 3.7 Consensus size: 41
30870384 TTTAACATAT
*
30870394 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
* *
30870435 TCACCGGCACGTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
* *
30870476 TCACCGGCACTTAGCCTGCTAAG-TTCATAACCTGGTTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTT-ATAACCTGATTCAGA
*
30870517 TCACCGGCACTTAGCCTGCTAGACTTA
1 TCACCGGCACTTAGCCTGCTAGGCTTA
30870544 AAGTCTGAAT
Statistics
Matches: 99, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
40 2 0.02
41 95 0.96
42 2 0.02
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
Found at i:30870562 original size:82 final size:83
Alignment explanation
Indices: 30870392--30870568 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 83
30870382 AATTTAACAT
* *
30870392 ATTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCACGTAGCCTGCTAG
1 ATTCACCGGCACTTAGCCTGCTAAGCTTATAACCTGATTCAGATCACCGGCACGTAGCCTGCTAG
**
30870457 GTTTATAACCTGATTCAG
66 ACTTATAACCTGATTCAG
* *
30870475 A-TCACCGGCACTTAGCCTGCTAAG-TTCATAACCTGGTTCAGATCACCGGCACTTAGCCTGCTA
1 ATTCACCGGCACTTAGCCTGCTAAGCTT-ATAACCTGATTCAGATCACCGGCACGTAGCCTGCTA
*
30870538 GACTTA-AAGTCTGAATT-A-
65 GACTTATAA-CCTG-ATTCAG
30870556 ATTCACCGGCACT
1 ATTCACCGGCACT
30870569 ACATCTGCTA
Statistics
Matches: 83, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
81 5 0.06
82 74 0.89
83 4 0.05
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (83 bp):
ATTCACCGGCACTTAGCCTGCTAAGCTTATAACCTGATTCAGATCACCGGCACGTAGCCTGCTAG
ACTTATAACCTGATTCAG
Found at i:30873443 original size:5 final size:5
Alignment explanation
Indices: 30873429--30873491 Score: 83
Period size: 5 Copynumber: 12.8 Consensus size: 5
30873419 TAGATCTTCA
* * *
30873429 TTTT- TTTTC TTTTC TTTTC TCTTC TTTTC TTTTC TTTCC TTTTC TTTCC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
*
30873478 TTTTC TTTTG TTTT
1 TTTTC TTTTC TTTT
30873492 TGTTTTTTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
4 4 0.08
5 47 0.92
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.78
Consensus pattern (5 bp):
TTTTC
Found at i:30875277 original size:26 final size:26
Alignment explanation
Indices: 30875248--30875324 Score: 109
Period size: 26 Copynumber: 2.9 Consensus size: 26
30875238 TTTTTGATGT
*
30875248 AATATGAAAGAAAGCCTTTGTGGTGG
1 AATATGAAAGAAAGCCTTTGTGGCGG
*
30875274 AATATGAAAGAAAACCTTTGTGGCGG
1 AATATGAAAGAAAGCCTTTGTGGCGG
* *
30875300 AATATGAAAGGAATGTCTTTGTGGC
1 AATATGAAA-GAAAGCCTTTGTGGC
30875325 AAACTCCGTA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
26 33 0.73
27 12 0.27
ACGTcount: A:0.35, C:0.09, G:0.29, T:0.27
Consensus pattern (26 bp):
AATATGAAAGAAAGCCTTTGTGGCGG
Found at i:30889545 original size:13 final size:13
Alignment explanation
Indices: 30889524--30889585 Score: 88
Period size: 13 Copynumber: 4.8 Consensus size: 13
30889514 ACACTCAAAT
30889524 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
*
30889537 TTCTCAAAAGCAC
1 TTTTCAAAAGCAC
* * *
30889550 ATTTCCACAGCAC
1 TTTTCAAAAGCAC
30889563 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
30889576 TTTTCAAAAG
1 TTTTCAAAAG
30889586 TAATGAAGAA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 41 1.00
ACGTcount: A:0.37, C:0.26, G:0.08, T:0.29
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:30894640 original size:38 final size:40
Alignment explanation
Indices: 30894571--30894659 Score: 112
Period size: 38 Copynumber: 2.2 Consensus size: 40
30894561 TTAAAAATAT
* *
30894571 TTATATTAAAAAACACTACCATAAATATAATAAATG-TTTTG
1 TTATATT-AAAAACACTACAATAAATATAATAAA-GATTTTA
30894612 TTATATTAAAAACAC-A-AATAAATATAATAAAGATTTTA
1 TTATATTAAAAACACTACAATAAATATAATAAAGATTTTA
*
30894650 TTGTATTAAA
1 TTATATTAAA
30894660 TATAAATTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
37 1 0.02
38 27 0.61
39 1 0.02
40 8 0.18
41 7 0.16
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.37
Consensus pattern (40 bp):
TTATATTAAAAACACTACAATAAATATAATAAAGATTTTA
Found at i:30894769 original size:6 final size:6
Alignment explanation
Indices: 30894758--30894799 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
30894748 TTAGTGATTT
30894758 AATATA AATATA AATATA AATATA AATATA AATATA AATATA
1 AATATA AATATA AATATA AATATA AATATA AATATA AATATA
30894800 CATAATTATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
AATATA
Found at i:30898233 original size:11 final size:11
Alignment explanation
Indices: 30898217--30898241 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
30898207 TCGTCCTTGC
30898217 AAAAAAAAGAA
1 AAAAAAAAGAA
30898228 AAAAAAAAGAA
1 AAAAAAAAGAA
30898239 AAA
1 AAA
30898242 TAATGACCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:30908542 original size:37 final size:37
Alignment explanation
Indices: 30908492--30908567 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
30908482 AATAGAAAGG
30908492 ATGGTGATGAATTCCTGCCAGTGGCCAACTGAATGAT
1 ATGGTGATGAATTCCTGCCAGTGGCCAACTGAATGAT
30908529 ATGGTGATGAATTCCTGCCAGTGGCCAACTGAATGAT
1 ATGGTGATGAATTCCTGCCAGTGGCCAACTGAATGAT
30908566 AT
1 AT
30908568 TCATATGGCC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (37 bp):
ATGGTGATGAATTCCTGCCAGTGGCCAACTGAATGAT
Found at i:30911410 original size:51 final size:50
Alignment explanation
Indices: 30911355--30911543 Score: 204
Period size: 51 Copynumber: 3.7 Consensus size: 50
30911345 ATACCTGATT
* * * *
30911355 CACATAGTAGCCTGGACATAGTACTACACATGTGACCATTTTCATCTGATA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCA-TATCATCCGATA
* * * *
30911406 CACATAGTAGCCTGCACATAATACTACACACGTGATCGA-AGCTATCCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGA-CCATATC-ATCCGATA
* * *
30911457 CGCATAGTAGCCTGCACATAGTACTACACA-TTCGACC-TATCATTCCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGT-GACCATATCA-TCCGATA
*
30911507 CACGTAGTAGCCTGCACATAGTACTACACACGTGACC
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACC
30911544 TAGCAACTTC
Statistics
Matches: 116, Mismatches: 16, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
49 1 0.01
50 44 0.38
51 69 0.59
52 2 0.02
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (50 bp):
CACATAGTAGCCTGCACATAGTACTACACACGTGACCATATCATCCGATA
Found at i:30911534 original size:101 final size:101
Alignment explanation
Indices: 30911357--30911541 Score: 275
Period size: 101 Copynumber: 1.8 Consensus size: 101
30911347 ACCTGATTCA
* * *
30911357 CATAGTAGCCTGGACATAGTACTACACATGTGACCATTTTCATCTGATACACATAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGTGACCA-TATCATCCGATACACATAGTAGCCTGCA
30911422 CATAATACTACACACGTGATCGAAGCTATCCGGTACG
65 CATAATACTACACACGTGATCGAAGCTATCCGGTACG
* *
30911459 CATAGTAGCCTGCACATAGTACTACACAT-TCGACC-TATCATTCCGGTACACGTAGTAGCCTGC
1 CATAGTAGCCTGCACATAGTACTACACATGT-GACCATATCA-TCCGATACACATAGTAGCCTGC
*
30911522 ACATAGTACTACACACGTGA
64 ACATAATACTACACACGTGA
30911542 CCTAGCAACT
Statistics
Matches: 75, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
100 4 0.05
101 39 0.52
102 32 0.43
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (101 bp):
CATAGTAGCCTGCACATAGTACTACACATGTGACCATATCATCCGATACACATAGTAGCCTGCAC
ATAATACTACACACGTGATCGAAGCTATCCGGTACG
Found at i:30915396 original size:21 final size:21
Alignment explanation
Indices: 30915362--30915402 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
30915352 GCGTAAAAGC
* *
30915362 AAAGAGGAAGGAGAGGATGAT
1 AAAGAAGAAAGAGAGGATGAT
*
30915383 AAAGAAGAAAGAGATGATGA
1 AAAGAAGAAAGAGAGGATGA
30915403 AATGGATTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.37, T:0.10
Consensus pattern (21 bp):
AAAGAAGAAAGAGAGGATGAT
Found at i:30918921 original size:5 final size:5
Alignment explanation
Indices: 30918911--30918963 Score: 106
Period size: 5 Copynumber: 10.6 Consensus size: 5
30918901 CCCGAGTTAC
30918911 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
30918961 AAA
1 AAA
30918964 TCATAACAGT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 48 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:30919547 original size:18 final size:19
Alignment explanation
Indices: 30919526--30919566 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
30919516 ATTAAATGTT
*
30919526 ATAAGTTATAAT-TAATAA
1 ATAAGTTATAATATAAAAA
*
30919544 ATAATTTATAATATAAAAA
1 ATAAGTTATAATATAAAAA
30919563 ATAA
1 ATAA
30919567 AAAAATAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (19 bp):
ATAAGTTATAATATAAAAA
Found at i:30920809 original size:20 final size:19
Alignment explanation
Indices: 30920786--30920830 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
30920776 AATATGAATT
*
30920786 ATGAAATTTATATATGTGAA
1 ATGAAATGTA-ATATGTGAA
30920806 ATGAAAATGTAATATGTGAA
1 ATG-AAATGTAATATGTGAA
30920826 ATGAA
1 ATGAA
30920831 TTAGAATGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 2 0.09
20 15 0.65
21 6 0.26
ACGTcount: A:0.49, C:0.00, G:0.18, T:0.33
Consensus pattern (19 bp):
ATGAAATGTAATATGTGAA
Found at i:30921845 original size:54 final size:54
Alignment explanation
Indices: 30921786--30921913 Score: 150
Period size: 54 Copynumber: 2.4 Consensus size: 54
30921776 CACGGCATGC
* * * * *
30921786 GACACGGCTGTGTGACCCAAGTCAGTAAGTTACAC-AGGTAGAGACATGGGCTGG
1 GACACGGCCGTGTGTCCCAAGTCAGTAAGTTACACTA-GTAGAGACACGGCCTAG
* * ** *
30921840 GACACGACCGTGTGTCTCAAGTTTGTGAGTTACACTAGTAGAGACACGGCCTAG
1 GACACGGCCGTGTGTCCCAAGTCAGTAAGTTACACTAGTAGAGACACGGCCTAG
30921894 GACACGGCCGTGTGTCCCAA
1 GACACGGCCGTGTGTCCCAA
30921914 ATTCGAAAGC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
54 60 0.98
55 1 0.02
ACGTcount: A:0.26, C:0.23, G:0.30, T:0.20
Consensus pattern (54 bp):
GACACGGCCGTGTGTCCCAAGTCAGTAAGTTACACTAGTAGAGACACGGCCTAG
Found at i:30924687 original size:50 final size:50
Alignment explanation
Indices: 30924576--30924821 Score: 230
Period size: 50 Copynumber: 4.8 Consensus size: 50
30924566 ATTTGGGTAA
* *
30924576 AGAGATCCCATGTAAGACCATGTTTGGGACATGGCATTGGCATCATTGAGGTTATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGA-G--ATG
* *
30924632 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* *** * * *
30924682 AGAGGTCCCCCATAAGACCATGTCTGGGATATGGCATGGGCACCGATATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * *
30924732 AGA-ACTCCCATGTAAGACCATATCTGGGATATGGCATTGGCA--GTACA-G
1 AGAGA-TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
* * * *
30924780 AAACATCTCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
30924822 TGTTATTATC
Statistics
Matches: 164, Mismatches: 23, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
48 37 0.23
49 3 0.02
50 81 0.49
52 1 0.01
53 2 0.01
55 1 0.01
56 39 0.24
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (50 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:30933098 original size:24 final size:24
Alignment explanation
Indices: 30933062--30933199 Score: 161
Period size: 24 Copynumber: 5.8 Consensus size: 24
30933052 TAACACACCA
*
30933062 CGTTGTGGACAAGCCACTGTATAT
1 CGTTGTGGTCAAGCCACTGTATAT
* *
30933086 CGTTGTAGTCAAGCCACTAG-ATAA
1 CGTTGTGGTCAAGCCACT-GTATAT
* *
30933110 CGTTGTGGTTAAGCCATTGTATAT
1 CGTTGTGGTCAAGCCACTGTATAT
* *
30933134 CATTGTGGTCAAGCCACTATATAT
1 CGTTGTGGTCAAGCCACTGTATAT
* * * *
30933158 CCTTGTGGTCAAGTCACTGAATAA
1 CGTTGTGGTCAAGCCACTGTATAT
30933182 CGTTGTGGTCAAGCCACT
1 CGTTGTGGTCAAGCCACT
30933200 TTCTATTGCA
Statistics
Matches: 94, Mismatches: 18, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
23 1 0.01
24 92 0.98
25 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.31
Consensus pattern (24 bp):
CGTTGTGGTCAAGCCACTGTATAT
Found at i:30933132 original size:48 final size:48
Alignment explanation
Indices: 30933061--30933199 Score: 179
Period size: 48 Copynumber: 2.9 Consensus size: 48
30933051 ATAACACACC
* *
30933061 ACGTTGTGGACAAGCCACTGTATATCGTTGTAGTCAAGCCACTAGATA
1 ACGTTGTGGTCAAGCCACTGTATATCGTTGTGGTCAAGCCACTAGATA
* * * *
30933109 ACGTTGTGGTTAAGCCATTGTATATCATTGTGGTCAAGCCACTATATA
1 ACGTTGTGGTCAAGCCACTGTATATCGTTGTGGTCAAGCCACTAGATA
* * * * *
30933157 TCCTTGTGGTCAAGTCACTGAATAACGTTGTGGTCAAGCCACT
1 ACGTTGTGGTCAAGCCACTGTATATCGTTGTGGTCAAGCCACT
30933200 TTCTATTGCA
Statistics
Matches: 77, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 77 1.00
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (48 bp):
ACGTTGTGGTCAAGCCACTGTATATCGTTGTGGTCAAGCCACTAGATA
Found at i:30933182 original size:72 final size:72
Alignment explanation
Indices: 30933064--30933197 Score: 198
Period size: 72 Copynumber: 1.9 Consensus size: 72
30933054 ACACACCACG
* * *
30933064 TTGTGGACAAGCCACTGTATATCGTTGTAGTCAAGCCACTAGATAACGTTGTGGTTAAGCCATTG
1 TTGTGGACAAGCCACTATATATCCTTGTAGTCAAGCCACTAGATAACGTTGTGGTCAAGCCATTG
30933129 TATATCA
66 TATATCA
* * *
30933136 TTGTGGTCAAGCCACTATATATCCTTGTGGTCAAGTCACT-GAATAACGTTGTGGTCAAGCCA
1 TTGTGGACAAGCCACTATATATCCTTGTAGTCAAGCCACTAG-ATAACGTTGTGGTCAAGCCA
30933198 CTTTCTATTG
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
71 1 0.02
72 54 0.98
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.31
Consensus pattern (72 bp):
TTGTGGACAAGCCACTATATATCCTTGTAGTCAAGCCACTAGATAACGTTGTGGTCAAGCCATTG
TATATCA
Found at i:30941458 original size:16 final size:15
Alignment explanation
Indices: 30941439--30941481 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
30941429 TTTATTCTTT
30941439 TTATTTTATATTTTGA
1 TTATTTTAT-TTTTGA
*
30941455 TTATTTTATTTTTGG
1 TTATTTTATTTTTGA
30941470 TT-TGTTTATTTT
1 TTAT-TTTATTTT
30941482 GTTTTTCTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 1 0.04
15 15 0.60
16 9 0.36
ACGTcount: A:0.16, C:0.00, G:0.09, T:0.74
Consensus pattern (15 bp):
TTATTTTATTTTTGA
Found at i:30941478 original size:20 final size:20
Alignment explanation
Indices: 30941450--30941487 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
30941440 TATTTTATAT
30941450 TTTGATTATTTTATTTTTGG
1 TTTGATTATTTTATTTTTGG
* *
30941470 TTTGTTTATTTTGTTTTT
1 TTTGATTATTTTATTTTT
30941488 CTATGCAAGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.00, G:0.13, T:0.76
Consensus pattern (20 bp):
TTTGATTATTTTATTTTTGG
Found at i:30952337 original size:61 final size:58
Alignment explanation
Indices: 30952230--30952429 Score: 204
Period size: 61 Copynumber: 3.2 Consensus size: 58
30952220 ATTACTTTAA
* *
30952230 TATTAAATTAATATAATACTTATCAAGATAAATATTAGATTAAATTTAATATTAAATC
1 TATTAAATTAATAGAATACTTATCAAGATAAATATTAAATTAAATTTAATATTAAATC
30952288 TATTAAATTAATAGAATACTTATGTACAAGATAAATATTAAATTAAATTTAATATTAGGATAATC
1 TATTAAATTAATAGAATACTTA--T-CAAGATAAATATTAAATTAAATTTAATATT---A-AAT-
30952353 AC
58 -C
* * * *
30952355 TTTAATATTAAATTAATAAAATA-TTATCAAGATAAGTATTAAACTAAATTTAATATTAAAAC
1 -----TATTAAATTAATAGAATACTTATCAAGATAAATATTAAATTAAATTTAATATTAAATC
*
30952417 TATTAAAATAATA
1 TATTAAATTAATA
30952430 TTATTTTTGA
Statistics
Matches: 121, Mismatches: 7, Indels: 29
0.77 0.04 0.18
Matches are distributed among these distances:
57 12 0.10
58 21 0.17
60 1 0.01
61 29 0.24
62 1 0.01
64 3 0.02
65 4 0.03
67 1 0.01
68 28 0.23
69 1 0.01
71 3 0.02
72 17 0.14
ACGTcount: A:0.52, C:0.05, G:0.04, T:0.39
Consensus pattern (58 bp):
TATTAAATTAATAGAATACTTATCAAGATAAATATTAAATTAAATTTAATATTAAATC
Found at i:30952371 original size:20 final size:18
Alignment explanation
Indices: 30952321--30952372 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 18
30952311 GTACAAGATA
30952321 AATATTAAATTAA-ATTT
1 AATATTAAATTAATATTT
*
30952338 AATATTAGGA-TAATCACTTT
1 AATATTA-AATTAAT-A-TTT
30952358 AATATTAAATTAATA
1 AATATTAAATTAATA
30952373 AAATATTATC
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
17 10 0.36
18 1 0.04
19 3 0.11
20 14 0.50
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (18 bp):
AATATTAAATTAATATTT
Found at i:30952429 original size:68 final size:71
Alignment explanation
Indices: 30952288--30952432 Score: 163
Period size: 68 Copynumber: 2.1 Consensus size: 71
30952278 ATATTAAATC
* * **
30952288 TATTAAATTAATAGAATACTTATGTACAAGATAAATATTAAATTAAATTTAATATTAGGATAATC
1 TATTAAATTAATAAAATACTTA-GTACAAGATAAATATTAAACTAAATTTAATATTAAAATAATC
***
30952353 ACTTTAA
65 AAAATAA
* *
30952360 TATTAAATTAATAAAATA-TTA-T-CAAGATAAGTATTAAACTAAATTTAATATTAAAACT-ATT
1 TATTAAATTAATAAAATACTTAGTACAAGATAAATATTAAACTAAATTTAATATTAAAA-TAATC
30952421 AAAATAA
65 AAAATAA
30952428 TATTA
1 TATTA
30952433 TTTTTGAAAT
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
68 41 0.65
69 2 0.03
71 3 0.05
72 17 0.27
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.39
Consensus pattern (71 bp):
TATTAAATTAATAAAATACTTAGTACAAGATAAATATTAAACTAAATTTAATATTAAAATAATCA
AAATAA
Found at i:30955138 original size:3 final size:3
Alignment explanation
Indices: 30955130--30955171 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
30955120 ATTTTGGAGG
30955130 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
30955172 ATAACATGTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:30955482 original size:29 final size:30
Alignment explanation
Indices: 30955435--30955496 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
30955425 TAATTAATTA
* *
30955435 ATTTTTTAAGATTTAAAAAATT-TAAAAAAT
1 ATTTTTAAAAATTT-AAAAATTATAAAAAAT
*
30955465 ATTTTTAAAAATTT-AAAATTATCAAAAAT
1 ATTTTTAAAAATTTAAAAATTATAAAAAAT
30955494 ATT
1 ATT
30955497 AAAAAAATGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 6 0.21
29 10 0.36
30 12 0.43
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (30 bp):
ATTTTTAAAAATTTAAAAATTATAAAAAAT
Found at i:30959543 original size:19 final size:19
Alignment explanation
Indices: 30959500--30959558 Score: 68
Period size: 19 Copynumber: 3.1 Consensus size: 19
30959490 AAATTACAAA
30959500 AAAAATTCCAAAATAATTT-T
1 AAAAATT-CAAAAT-ATTTAT
30959520 CAAAAATTCAAAATATTTAT
1 -AAAAATTCAAAATATTTAT
*
30959540 AAAAATTCCAAA-ATTTAT
1 AAAAATTCAAAATATTTAT
30959558 A
1 A
30959559 TATTTTAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
18 7 0.19
19 15 0.42
20 7 0.19
21 7 0.19
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAAATTCAAAATATTTAT
Found at i:30959560 original size:20 final size:20
Alignment explanation
Indices: 30959500--30959553 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 20
30959490 AAATTACAAA
30959500 AAAAATTCCAAAATAATTT-T
1 AAAAATTCCAAAAT-ATTTAT
30959520 CAAAAATT-CAAAATATTTAT
1 -AAAAATTCCAAAATATTTAT
30959540 AAAAATTCCAAAAT
1 AAAAATTCCAAAAT
30959554 TTATATATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 11 0.35
20 13 0.42
21 7 0.23
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAAATTCCAAAATATTTAT
Found at i:30959577 original size:25 final size:26
Alignment explanation
Indices: 30959532--30959580 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
30959522 AAAATTCAAA
30959532 ATATTTATAAAAATTCCAAAATTTAT
1 ATATTTATAAAAATTCCAAAATTTAT
**
30959558 ATATTT-TAAAAATTTTAAAATTT
1 ATATTTATAAAAATTCCAAAATTT
30959581 TTTTAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (26 bp):
ATATTTATAAAAATTCCAAAATTTAT
Found at i:30959598 original size:20 final size:20
Alignment explanation
Indices: 30959500--30959597 Score: 63
Period size: 21 Copynumber: 4.6 Consensus size: 20
30959490 AAATTACAAA
* * *
30959500 AAAAATTCCAAAATAATTTTC
1 AAAAATTCTAAAAT-TTTTTT
* *
30959521 AAAAATTC-AAAATATTTAT
1 AAAAATTCTAAAATTTTTTT
*
30959540 AAAAATTCCAAAATTTATATATTTT
1 AAAAATTCTAAAA--T-T-T-TTTT
*
30959565 AAAAATTTTAAAATTTTTTT
1 AAAAATTCTAAAATTTTTTT
30959585 AAAAAATTCTAAA
1 -AAAAATTCTAAA
30959598 TAATATATAA
Statistics
Matches: 63, Mismatches: 7, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
19 12 0.19
20 13 0.21
21 20 0.32
22 2 0.03
23 1 0.02
24 1 0.02
25 14 0.22
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (20 bp):
AAAAATTCTAAAATTTTTTT
Found at i:30960567 original size:19 final size:19
Alignment explanation
Indices: 30960539--30960580 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
30960529 GAAAATTAAT
*
30960539 ATTTTATCTATTATATTAC
1 ATTTTATCTATTAGATTAC
* *
30960558 ATTTTTTCTATTAGATTCC
1 ATTTTATCTATTAGATTAC
30960577 ATTT
1 ATTT
30960581 GAAATATAGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.12, G:0.02, T:0.60
Consensus pattern (19 bp):
ATTTTATCTATTAGATTAC
Found at i:30961218 original size:38 final size:38
Alignment explanation
Indices: 30961171--30961244 Score: 87
Period size: 38 Copynumber: 1.9 Consensus size: 38
30961161 ATTATATTTA
* * * *
30961171 TAATGTTTAT-CAGTTTATATTATAATAGTATATATATC
1 TAATCTTTATACAGTATAAATTAT-ATAATATATATATC
*
30961209 TAATCTTTATATAGTATAAATTATATAATATATATA
1 TAATCTTTATACAGTATAAATTATATAATATATATA
30961245 AATAAAATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
38 20 0.67
39 10 0.33
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.49
Consensus pattern (38 bp):
TAATCTTTATACAGTATAAATTATATAATATATATATC
Found at i:30961237 original size:25 final size:25
Alignment explanation
Indices: 30961190--30961237 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
30961180 TCAGTTTATA
* *
30961190 TTATAATAGTATATATATCTAATCT
1 TTATAATAGTATAAATATATAATCT
30961215 TTAT-ATAGTATAAATTATATAAT
1 TTATAATAGTATAAA-TATATAAT
30961238 ATATATAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (25 bp):
TTATAATAGTATAAATATATAATCT
Found at i:30961844 original size:21 final size:23
Alignment explanation
Indices: 30961818--30961878 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
30961808 CTTAAATAGA
30961818 CATAACTATTCA-A-TTTAGTGG
1 CATAACTATTCATATTTTAGTGG
* *
30961839 CATAACTTTTGATATTTTAGTGG
1 CATAACTATTCATATTTTAGTGG
* *
30961862 CATAACTTTTGATATTT
1 CATAACTATTCATATTT
30961879 AAGATCATCA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.28
22 1 0.03
23 25 0.69
ACGTcount: A:0.30, C:0.11, G:0.13, T:0.46
Consensus pattern (23 bp):
CATAACTATTCATATTTTAGTGG
Found at i:30961860 original size:23 final size:23
Alignment explanation
Indices: 30961831--30961878 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
30961821 AACTATTCAA
30961831 TTTAGTGGCATAACTTTTGATAT
1 TTTAGTGGCATAACTTTTGATAT
30961854 TTTAGTGGCATAACTTTTGATAT
1 TTTAGTGGCATAACTTTTGATAT
30961877 TT
1 TT
30961879 AAGATCATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.25, C:0.08, G:0.17, T:0.50
Consensus pattern (23 bp):
TTTAGTGGCATAACTTTTGATAT
Found at i:30963279 original size:28 final size:28
Alignment explanation
Indices: 30963241--30963305 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
30963231 GTTTTGAATA
30963241 AAGTTTAAATTGG-ACTTAAGCTTGAGTTT
1 AAGTTT-AATTGGTA-TTAAGCTTGAGTTT
**
30963270 AAGTTTAATTGGTATTGGGCTTGAGTTT
1 AAGTTTAATTGGTATTAAGCTTGAGTTT
*
30963298 AGGTTTAA
1 AAGTTTAA
30963306 ATATATATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 25 0.78
29 7 0.22
ACGTcount: A:0.28, C:0.05, G:0.25, T:0.43
Consensus pattern (28 bp):
AAGTTTAATTGGTATTAAGCTTGAGTTT
Found at i:30964210 original size:18 final size:19
Alignment explanation
Indices: 30964187--30964235 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 19
30964177 AATCGTGTCG
30964187 TTCATTTTCAAAAT-ATTA
1 TTCATTTTCAAAATCATTA
*
30964205 TTCATTTAC-AAATCATTA
1 TTCATTTTCAAAATCATTA
*
30964223 TTCAATTTCAAAA
1 TTCATTTTCAAAA
30964236 CTTTTTTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 4 0.15
18 19 0.73
19 3 0.12
ACGTcount: A:0.41, C:0.14, G:0.00, T:0.45
Consensus pattern (19 bp):
TTCATTTTCAAAATCATTA
Found at i:30968274 original size:22 final size:22
Alignment explanation
Indices: 30968246--30968287 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
30968236 AATAAACTAT
*
30968246 TAATTAATTAATTAA-CTATGAC
1 TAATTAA-CAATTAACCTATGAC
30968268 TAATTAACAATTAACCTATG
1 TAATTAACAATTAACCTATG
30968288 TATAAAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (22 bp):
TAATTAACAATTAACCTATGAC
Found at i:30975974 original size:59 final size:59
Alignment explanation
Indices: 30975866--30976199 Score: 334
Period size: 59 Copynumber: 5.7 Consensus size: 59
30975856 TTAACAGAGG
* * * * *
30975866 TCGCCACTAAGGCTTTCCTTTTAGAGATTTTCCACAAAGGCATCTTTTTCATTCAGTAC
1 TCGCCACAAAGGCTTTCCTTTCAAAGATTTGCCACAAAGGCATCCTTTTCATTCAGTAC
** * * * * *
30975925 TCAG-CACAAAGGCTTTATTTTTAAAGATTTGCCATAAAGACATCATTTTCATTCGGTAC
1 TC-GCCACAAAGGCTTTCCTTTCAAAGATTTGCCACAAAGGCATCCTTTTCATTCAGTAC
* * ** * * * * * *
30975984 TCACCATAAAGATTTTCCTTTCAGATATTTTCCACAAAGACAACCTTTTCTTTCAGTAC
1 TCGCCACAAAGGCTTTCCTTTCAAAGATTTGCCACAAAGGCATCCTTTTCATTCAGTAC
* * * *
30976043 TCGCCACAAAGGCTTTCCTTTTAGAGGTTTGCCACAAAGGCATCCTTTGT--TTTAGTAC
1 TCGCCACAAAGGCTTTCCTTTCAAAGATTTGCCACAAAGGCATCCTTT-TCATTCAGTAC
* * * *
30976101 TCGCCACAAAGGCTTTCTTTTCAAATATTTGCCACAAAGGCAACC-TTTCTTTCAGTAC
1 TCGCCACAAAGGCTTTCCTTTCAAAGATTTGCCACAAAGGCATCCTTTTCATTCAGTAC
* *
30976159 TCGCCACAAGGGCTTTCCTTTCAAATATTTGCCACAAAGGC
1 TCGCCACAAAGGCTTTCCTTTCAAAGATTTGCCACAAAGGC
30976200 TTTCCTTTCA
Statistics
Matches: 226, Mismatches: 44, Indels: 11
0.80 0.16 0.04
Matches are distributed among these distances:
56 1 0.00
57 2 0.01
58 92 0.41
59 129 0.57
60 2 0.01
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.34
Consensus pattern (59 bp):
TCGCCACAAAGGCTTTCCTTTCAAAGATTTGCCACAAAGGCATCCTTTTCATTCAGTAC
Found at i:30976109 original size:30 final size:29
Alignment explanation
Indices: 30976015--30976167 Score: 87
Period size: 28 Copynumber: 5.2 Consensus size: 29
30976005 CAGATATTTT
* * *
30976015 CCACAAAGACAACCTTTTCTTTCAGTACTCG
1 CCACAAAGGCATCC-TTT-TTTAAGTACTCG
* ** * *
30976046 CCACAAAGGCTTTCCTTTTAGAGGT--TTG
1 CCACAAAGGC-ATCCTTTTTTAAGTACTCG
*
30976074 CCACAAAGGCATCCTTTGTTTTAGTACTCG
1 CCACAAAGGCATCCTTT-TTTAAGTACTCG
* * * * * *
30976104 CCACAAAGGCTTTC-TTTTCAAATATTTG
1 CCACAAAGGCATCCTTTTTTAAGTACTCG
* *
30976132 CCACAAAGGCAACCTTTCTTTCAGTACTCG
1 CCACAAAGGCATCCTTT-TTTAAGTACTCG
30976162 CCACAA
1 CCACAA
30976168 GGGCTTTCCT
Statistics
Matches: 87, Mismatches: 29, Indels: 13
0.67 0.22 0.10
Matches are distributed among these distances:
27 6 0.07
28 33 0.38
29 4 0.05
30 30 0.34
31 12 0.14
32 2 0.02
ACGTcount: A:0.27, C:0.28, G:0.14, T:0.31
Consensus pattern (29 bp):
CCACAAAGGCATCCTTTTTTAAGTACTCG
Found at i:30976141 original size:28 final size:28
Alignment explanation
Indices: 30976103--30976225 Score: 133
Period size: 28 Copynumber: 4.3 Consensus size: 28
30976093 TTTAGTACTC
*
30976103 GCCACAAAGGCTTTCTTTTCAAATATTT
1 GCCACAAAGGCTTTCCTTTCAAATATTT
* * *
30976131 GCCACAAAGGCAACCTTT-CTTTC-AGTACTC
1 GCCACAAAGG----CTTTCCTTTCAAATATTT
*
30976161 GCCACAAGGGCTTTCCTTTCAAATATTT
1 GCCACAAAGGCTTTCCTTTCAAATATTT
* *
30976189 GCCACAAAGGCTTTCCTTTCAGAGATTT
1 GCCACAAAGGCTTTCCTTTCAAATATTT
30976217 GCCACAAAG
1 GCCACAAAG
30976226 ACATCCTTTT
Statistics
Matches: 78, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
26 4 0.05
27 5 0.06
28 48 0.62
30 13 0.17
31 4 0.05
32 4 0.05
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.31
Consensus pattern (28 bp):
GCCACAAAGGCTTTCCTTTCAAATATTT
Found at i:30981384 original size:40 final size:41
Alignment explanation
Indices: 30981313--30981397 Score: 102
Period size: 40 Copynumber: 2.1 Consensus size: 41
30981303 AGCAATTCTG
* * *
30981313 ACTTATTTGAAAATCATTTTTGATGTGTTAAAATGATTTTA
1 ACTTAATTGAAAATCATTTTTGATGTCTTAAAATCATTTTA
* *
30981354 ACTTAATTG-AAATCA-TTTTGACTTTCTTAAAATCATTTTC
1 ACTTAATTGAAAATCATTTTTGA-TGTCTTAAAATCATTTTA
30981394 ACTT
1 ACTT
30981398 GATGTTAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
39 6 0.16
40 24 0.63
41 8 0.21
ACGTcount: A:0.33, C:0.11, G:0.08, T:0.48
Consensus pattern (41 bp):
ACTTAATTGAAAATCATTTTTGATGTCTTAAAATCATTTTA
Found at i:30981386 original size:20 final size:20
Alignment explanation
Indices: 30981322--30981397 Score: 64
Period size: 20 Copynumber: 3.8 Consensus size: 20
30981312 GACTTATTTG
* *
30981322 AAAATCATTTTTGA-TGTGTT
1 AAAATCA-TTTTGACTTTATT
* * *
30981342 AAAATGATTTTAACTTAATT
1 AAAATCATTTTGACTTTATT
* *
30981362 GAAATCATTTTGACTTTCTT
1 AAAATCATTTTGACTTTATT
*
30981382 AAAATCATTTTCACTT
1 AAAATCATTTTGACTT
30981398 GATGTTAAAA
Statistics
Matches: 43, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
19 5 0.12
20 38 0.88
ACGTcount: A:0.34, C:0.11, G:0.08, T:0.47
Consensus pattern (20 bp):
AAAATCATTTTGACTTTATT
Found at i:30988203 original size:22 final size:20
Alignment explanation
Indices: 30988134--30988193 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
30988124 ATTTTGATGT
* * *
30988134 GTTAAAATGATTTTAACTTA
1 GTTAAAATCATTTTCACTTG
* * *
30988154 ATTGAAATCATTTTGACTTG
1 GTTAAAATCATTTTCACTTG
30988174 GTTAAAATCATTTTCACTTG
1 GTTAAAATCATTTTCACTTG
30988194 ATTTTAAAAT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (20 bp):
GTTAAAATCATTTTCACTTG
Found at i:30992404 original size:20 final size:20
Alignment explanation
Indices: 30992379--30992422 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
30992369 AATTATGATA
30992379 GAAAGGTCTATCAATGTTAG
1 GAAAGGTCTATCAATGTTAG
30992399 GAAAGGTCTATCAATGTTAG
1 GAAAGGTCTATCAATGTTAG
30992419 GAAA
1 GAAA
30992423 ATTATTCTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.39, C:0.09, G:0.25, T:0.27
Consensus pattern (20 bp):
GAAAGGTCTATCAATGTTAG
Found at i:30997220 original size:15 final size:15
Alignment explanation
Indices: 30997202--30997234 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
30997192 AAATAATAAG
30997202 AAAGGAAATAAATGA
1 AAAGGAAATAAATGA
*
30997217 AAAGTAAATAAATGA
1 AAAGGAAATAAATGA
30997232 AAA
1 AAA
30997235 ACAAGAAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (15 bp):
AAAGGAAATAAATGA
Found at i:31002273 original size:28 final size:28
Alignment explanation
Indices: 31002191--31002366 Score: 239
Period size: 28 Copynumber: 6.3 Consensus size: 28
31002181 GAGATTGGCG
* * * *
31002191 CTAAGTGTGCGGGTTTAAATTGTGCAGCA
1 CTAAGTGTGCGAGTTT-GATTATGTAGCA
* *
31002220 CTAAGTGTGCGA-ATTGACTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATGTAGCA
*
31002247 CTAAGTGTGCGAGTTTGACTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATGTAGCA
*
31002275 CTAAGTGTGCGAGCTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATGTAGCA
31002303 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATGTAGCA
*
31002331 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATGTAGCA
*
31002358 CTGAGTGTG
1 CTAAGTGTG
31002367 TGGACTTATT
Statistics
Matches: 134, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
27 41 0.31
28 82 0.61
29 11 0.08
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATGTAGCA
Found at i:31004144 original size:52 final size:52
Alignment explanation
Indices: 31004087--31004206 Score: 143
Period size: 52 Copynumber: 2.3 Consensus size: 52
31004077 CTCAGACAGA
* * * *
31004087 GATCATACAAAACATAATAAA-CAAATCAGAGTAACGCAGAGAATTTGGTAAC
1 GATCATA-AAAACAGAACAAAGCAAATCAGAGTAACACAGAGAATTTGATAAC
* * * *
31004139 GATCATAAAACCAGAACAAAGCAAATCAGAGTATCACAGAGATTTTGATAAT
1 GATCATAAAAACAGAACAAAGCAAATCAGAGTAACACAGAGAATTTGATAAC
*
31004191 GATCATATAAACAGAA
1 GATCATAAAAACAGAA
31004207 TAGAGAATGC
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
51 10 0.18
52 47 0.82
ACGTcount: A:0.50, C:0.15, G:0.15, T:0.20
Consensus pattern (52 bp):
GATCATAAAAACAGAACAAAGCAAATCAGAGTAACACAGAGAATTTGATAAC
Found at i:31011105 original size:30 final size:31
Alignment explanation
Indices: 31011047--31011108 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
31011037 AACTTAACAG
31011047 CAGACTTGAAATAAACAAAAAAAAAATCACC
1 CAGACTTGAAATAAACAAAAAAAAAATCACC
*
31011078 CAGACTTGAAATAAAC-AAAATAAAATCACC
1 CAGACTTGAAATAAACAAAAAAAAAATCACC
31011108 C
1 C
31011109 TACACCCCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 14 0.47
31 16 0.53
ACGTcount: A:0.58, C:0.21, G:0.06, T:0.15
Consensus pattern (31 bp):
CAGACTTGAAATAAACAAAAAAAAAATCACC
Found at i:31015211 original size:21 final size:19
Alignment explanation
Indices: 31015180--31015218 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
31015170 TTTATAAAAG
31015180 TTAAGGCATTCAAAAGTGT
1 TTAAGGCATTCAAAAGTGT
*
31015199 TTAATGGCAATTCGAAAGTG
1 TTAA-GGC-ATTCAAAAGTG
31015219 AAAGTGTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 3 0.18
21 10 0.59
ACGTcount: A:0.36, C:0.10, G:0.23, T:0.31
Consensus pattern (19 bp):
TTAAGGCATTCAAAAGTGT
Found at i:31016752 original size:30 final size:30
Alignment explanation
Indices: 31016716--31016793 Score: 102
Period size: 30 Copynumber: 2.6 Consensus size: 30
31016706 ATCCGTATTT
* * **
31016716 ATGGAAAGTCAAATATATGTTTATCAAATA
1 ATGGAAAATCAAAGATATGGGTATCAAATA
*
31016746 ATGGAAATTCAAAGATATGGGTATCAAATA
1 ATGGAAAATCAAAGATATGGGTATCAAATA
*
31016776 TTGGAAAATCAAAGATAT
1 ATGGAAAATCAAAGATAT
31016794 AAGTATCGAG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.47, C:0.06, G:0.17, T:0.29
Consensus pattern (30 bp):
ATGGAAAATCAAAGATATGGGTATCAAATA
Found at i:31016800 original size:30 final size:30
Alignment explanation
Indices: 31016737--31016810 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 30
31016727 AATATATGTT
* * **
31016737 TATCAAATAATGGAAATTCAAAGATATGGG
1 TATCAAATATTGGAAAATCAAAGATATAAG
31016767 TATCAAATATTGGAAAATCAAAGATATAAG
1 TATCAAATATTGGAAAATCAAAGATATAAG
*
31016797 TATCGAGATATTGG
1 TATC-AAATATTGG
31016811 CATAAGAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
30 30 0.79
31 8 0.21
ACGTcount: A:0.46, C:0.07, G:0.19, T:0.28
Consensus pattern (30 bp):
TATCAAATATTGGAAAATCAAAGATATAAG
Found at i:31025723 original size:12 final size:11
Alignment explanation
Indices: 31025705--31025739 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
31025695 TAACTATGTG
31025705 AATAACAAATA
1 AATAACAAATA
31025716 AATGAACAAATA
1 AAT-AACAAATA
*
31025728 AATAACTAATA
1 AATAACAAATA
31025739 A
1 A
31025740 TACTATGGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.69, C:0.09, G:0.03, T:0.20
Consensus pattern (11 bp):
AATAACAAATA
Found at i:31031898 original size:27 final size:26
Alignment explanation
Indices: 31031868--31032019 Score: 126
Period size: 26 Copynumber: 5.7 Consensus size: 26
31031858 AAAATGACCA
**
31031868 AAATACCCCCAAAAGACAAAATAACTG
1 AAATA-CCCCAAAAGGTAAAATAACTG
* *
31031895 AAATATCCCAAAAGGGTAAAATGA-TCG
1 AAATACCCCAAAA-GGTAAAATAACT-G
* *
31031922 AAATACCCCAAAGGGTAAAATAACCG
1 AAATACCCCAAAAGGTAAAATAACTG
* * *
31031948 AAAGACCCCAAAGGGTGAAATAACTG
1 AAATACCCCAAAAGGTAAAATAACTG
* * * *
31031974 AAATACCCCCAAAGTATAAAATGACCG
1 AAATACCCCAAAAG-GTAAAATAACTG
*
31032001 AAATACCCCCATAAGGTAA
1 AAATA-CCCCAAAAGGTAA
31032020 CATGACTGCT
Statistics
Matches: 99, Mismatches: 21, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
26 52 0.53
27 40 0.40
28 7 0.07
ACGTcount: A:0.49, C:0.22, G:0.14, T:0.14
Consensus pattern (26 bp):
AAATACCCCAAAAGGTAAAATAACTG
Found at i:31031958 original size:53 final size:53
Alignment explanation
Indices: 31031857--31032009 Score: 166
Period size: 53 Copynumber: 2.9 Consensus size: 53
31031847 GTAGGGTCAA
* * * * * *
31031857 TAAAATGACCAAAATACCCCCAAAAGACAAAATAACTGAAATATCCCAAAAGGG
1 TAAAATGAACGAAATACCCCCAAAGGATAAAATAACCGAAATA-CCCCAAAGGG
* * *
31031911 TAAAATGATCGAAATA-CCCCAAAGGGTAAAATAACCGAAAGACCCCAAAGGG
1 TAAAATGAACGAAATACCCCCAAAGGATAAAATAACCGAAATACCCCAAAGGG
* * *
31031963 TGAAAT-AACTGAAATACCCCCAAAGTATAAAATGACCGAAATACCCC
1 TAAAATGAAC-GAAATACCCCCAAAGGATAAAATAACCGAAATACCCC
31032010 CATAAGGTAA
Statistics
Matches: 83, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
51 2 0.02
52 20 0.24
53 47 0.57
54 14 0.17
ACGTcount: A:0.50, C:0.23, G:0.14, T:0.14
Consensus pattern (53 bp):
TAAAATGAACGAAATACCCCCAAAGGATAAAATAACCGAAATACCCCAAAGGG
Found at i:31032025 original size:27 final size:26
Alignment explanation
Indices: 31031857--31032009 Score: 144
Period size: 27 Copynumber: 5.8 Consensus size: 26
31031847 GTAGGGTCAA
* * *
31031857 TAAAATGACCAAAATACCCCCAAAAGA
1 TAAAATGACCGAAATA-CCCCAAAGGG
* * * *
31031884 CAAAATAACTGAAATATCCCAAAAGGG
1 TAAAATGACCGAAATA-CCCCAAAGGG
*
31031911 TAAAATGATCGAAATACCCCAAAGGG
1 TAAAATGACCGAAATACCCCAAAGGG
* *
31031937 TAAAATAACCGAAAGACCCCAAAGGG
1 TAAAATGACCGAAATACCCCAAAGGG
* * * **
31031963 TGAAATAACTGAAATACCCCCAAAGTA
1 TAAAATGACCGAAATA-CCCCAAAGGG
31031990 TAAAATGACCGAAATACCCC
1 TAAAATGACCGAAATACCCC
31032010 CATAAGGTAA
Statistics
Matches: 101, Mismatches: 24, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
26 49 0.49
27 52 0.51
ACGTcount: A:0.50, C:0.23, G:0.14, T:0.14
Consensus pattern (26 bp):
TAAAATGACCGAAATACCCCAAAGGG
Found at i:31032367 original size:28 final size:28
Alignment explanation
Indices: 31032335--31032399 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
31032325 GGTTACATTA
*
31032335 CCACACTGTTACTGTATTGGGCTAAGAC
1 CCACACTGTTACTGTATCGGGCTAAGAC
*
31032363 CCACACTGTTACTGTATCGGGCTAAGGC
1 CCACACTGTTACTGTATCGGGCTAAGAC
31032391 CCACACTGT
1 CCACACTGT
31032400 ACTATCATTG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.23, C:0.29, G:0.22, T:0.26
Consensus pattern (28 bp):
CCACACTGTTACTGTATCGGGCTAAGAC
Found at i:31033564 original size:27 final size:27
Alignment explanation
Indices: 31033527--31033611 Score: 100
Period size: 27 Copynumber: 3.1 Consensus size: 27
31033517 ATTTATGAGT
*
31033527 AAATTACCGAAATACACTCGAAGGGTA
1 AAATTACCGAAATACACTCAAAGGGTA
* *
31033554 AAATTATCGAAATACCCTCAAAGGGTA
1 AAATTACCGAAATACACTCAAAGGGTA
* * *
31033581 AAATTACC-ATAATACCCCCTAAGGGTA
1 AAATTACCGA-AATACACTCAAAGGGTA
31033608 AAAT
1 AAAT
31033612 GATCTTTATA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
26 1 0.02
27 50 0.98
ACGTcount: A:0.45, C:0.20, G:0.14, T:0.21
Consensus pattern (27 bp):
AAATTACCGAAATACACTCAAAGGGTA
Found at i:31033622 original size:27 final size:27
Alignment explanation
Indices: 31033547--31033625 Score: 88
Period size: 27 Copynumber: 2.9 Consensus size: 27
31033537 AATACACTCG
*
31033547 AAGGGTAAAATTATCGA-AATACCCTCA
1 AAGGGTAAAATTATC-ATAATACCCCCA
* *
31033574 AAGGGTAAAATTACCATAATACCCCCT
1 AAGGGTAAAATTATCATAATACCCCCA
* * *
31033601 AAGGGTAAAATGATCTTTATACCCC
1 AAGGGTAAAATTATCATAATACCCC
31033626 TAGGAGATGA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
26 1 0.02
27 43 0.98
ACGTcount: A:0.41, C:0.22, G:0.14, T:0.24
Consensus pattern (27 bp):
AAGGGTAAAATTATCATAATACCCCCA
Found at i:31033989 original size:28 final size:28
Alignment explanation
Indices: 31033949--31034036 Score: 142
Period size: 28 Copynumber: 3.2 Consensus size: 28
31033939 ACTGAAATGA
* *
31033949 TACTGTATGGGGTTAAGGCCCACACTGC
1 TACTGAATTGGGTTAAGGCCCACACTGC
31033977 TACTGAATTGGGTTAAGGCCCACACTGC
1 TACTGAATTGGGTTAAGGCCCACACTGC
*
31034005 TACTGAATTGGGTTAAGGCCCTCACTG-
1 TACTGAATTGGGTTAAGGCCCACACTGC
31034032 TACTG
1 TACTG
31034037 TCACTGAATA
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 5 0.09
28 52 0.91
ACGTcount: A:0.23, C:0.24, G:0.26, T:0.27
Consensus pattern (28 bp):
TACTGAATTGGGTTAAGGCCCACACTGC
Found at i:31036194 original size:21 final size:20
Alignment explanation
Indices: 31036170--31036226 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 20
31036160 AAAATCTTAT
31036170 AATATAATTATTTAATTAATA
1 AATATAATTATTTAA-TAATA
** *
31036191 AATATCTTTTAATTAATAATA
1 AATAT-AATTATTTAATAATA
*
31036212 AATAATAAATATTTA
1 AAT-ATAATTATTTA
31036227 TTTACTTAAA
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
21 18 0.67
22 9 0.33
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (20 bp):
AATATAATTATTTAATAATA
Found at i:31036241 original size:30 final size:28
Alignment explanation
Indices: 31036186--31036247 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 28
31036176 ATTATTTAAT
31036186 TAATAAATATCTTTTAATTAATAATAAA
1 TAATAAATATCTTTTAATTAATAATAAA
* * *
31036214 TAATAAATATTTATTTACTTAAATAATAAG
1 TAATAAATATCT-TTTAATT-AATAATAAA
31036244 TAAT
1 TAAT
31036248 TTAAATCCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 11 0.38
29 6 0.21
30 12 0.41
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (28 bp):
TAATAAATATCTTTTAATTAATAATAAA
Found at i:31038820 original size:20 final size:20
Alignment explanation
Indices: 31038795--31038840 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
31038785 CTGAAATGGA
* *
31038795 AACAAAAGCAGAAAATAAAG
1 AACAAAAGAAGAAAAGAAAG
31038815 AACAAAAGAAGAAAAGAAAG
1 AACAAAAGAAGAAAAGAAAG
31038835 AA-AAAA
1 AACAAAA
31038841 AAGGATAGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 4 0.17
20 20 0.83
ACGTcount: A:0.76, C:0.07, G:0.15, T:0.02
Consensus pattern (20 bp):
AACAAAAGAAGAAAAGAAAG
Found at i:31039124 original size:24 final size:24
Alignment explanation
Indices: 31039092--31039138 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
31039082 CGGGGTTTAA
31039092 AATAGAAGACCAAAAGGTAAGCTG
1 AATAGAAGACCAAAAGGTAAGCTG
*
31039116 AATAGAAGACCAAAGGGTAAGCT
1 AATAGAAGACCAAAAGGTAAGCT
31039139 AACACCTTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.49, C:0.13, G:0.26, T:0.13
Consensus pattern (24 bp):
AATAGAAGACCAAAAGGTAAGCTG
Found at i:31042861 original size:20 final size:20
Alignment explanation
Indices: 31042825--31042862 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
31042815 AATCGATTTT
*
31042825 AAAAGCAGTCCCAAGAGTCC
1 AAAAGCAGTCCAAAGAGTCC
31042845 AAAA-CAGTCCAAGAGAGT
1 AAAAGCAGTCCAA-AGAGT
31042863 GGAAATAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.45, C:0.24, G:0.21, T:0.11
Consensus pattern (20 bp):
AAAAGCAGTCCAAAGAGTCC
Found at i:31043086 original size:23 final size:23
Alignment explanation
Indices: 31043061--31043109 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 23
31043051 TAGAACTAAT
31043061 ACAAACATCGATGCATAACAGATAC
1 ACAAACA--GATGCATAACAGATAC
*
31043086 ACAAACAGATGCATAATAGATAC
1 ACAAACAGATGCATAACAGATAC
31043109 A
1 A
31043110 GATACAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 16 0.70
25 7 0.30
ACGTcount: A:0.51, C:0.20, G:0.12, T:0.16
Consensus pattern (23 bp):
ACAAACAGATGCATAACAGATAC
Found at i:31045512 original size:24 final size:23
Alignment explanation
Indices: 31045480--31045529 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
31045470 ATATATGGGG
* *
31045480 TTGAGAATTCTTCTCTTTTTTCAA
1 TTGACAATTCTTCTCTTATTT-AA
*
31045504 TTGACAATTCTTTTCTTATTTAA
1 TTGACAATTCTTCTCTTATTTAA
31045527 TTG
1 TTG
31045530 TTATTTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 5 0.22
24 18 0.78
ACGTcount: A:0.22, C:0.14, G:0.08, T:0.56
Consensus pattern (23 bp):
TTGACAATTCTTCTCTTATTTAA
Found at i:31045542 original size:18 final size:19
Alignment explanation
Indices: 31045514--31045549 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
31045504 TTGACAATTC
31045514 TTTTCTTATTTAATTGTTA
1 TTTTCTTATTTAATTGTTA
*
31045533 TTTT-TTATTTATTTGTT
1 TTTTCTTATTTAATTGTT
31045550 TTTAACTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.17, C:0.03, G:0.06, T:0.75
Consensus pattern (19 bp):
TTTTCTTATTTAATTGTTA
Found at i:31046356 original size:29 final size:30
Alignment explanation
Indices: 31046294--31046362 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
31046284 ATTACCAAAA
**
31046294 TAGTTACTTTTGTTTGCCTCATGTTACATTT
1 TAGTTACTTTTGTTTG-CAAATGTTACATTT
*
31046325 TAGTTACTTTTGTTTG-AAATGTTACGTTT
1 TAGTTACTTTTGTTTGCAAATGTTACATTT
*
31046354 TAGTCACTT
1 TAGTTACTT
31046363 ACGTTATTGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 18 0.53
31 16 0.47
ACGTcount: A:0.19, C:0.13, G:0.14, T:0.54
Consensus pattern (30 bp):
TAGTTACTTTTGTTTGCAAATGTTACATTT
Found at i:31049584 original size:2 final size:2
Alignment explanation
Indices: 31049577--31049601 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31049567 TCCATGTATG
31049577 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 T
31049602 GAAAGATAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31062257 original size:43 final size:44
Alignment explanation
Indices: 31062196--31062280 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 44
31062186 TGGCTGTGCA
* *
31062196 GAATCTGCAAGTAGTTGCAGA-TTCCCTTGATATTAGGAAGTTT
1 GAATCTGCAAGTAGTTGCAGATTTCCATTGATATGAGGAAGTTT
31062239 GAATCTGCAAGTAGTTGCAGATTTCCATTGATATGAGGAAGT
1 GAATCTGCAAGTAGTTGCAGATTTCCATTGATATGAGGAAGT
31062281 CATGTAGACT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
43 21 0.54
44 18 0.46
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.33
Consensus pattern (44 bp):
GAATCTGCAAGTAGTTGCAGATTTCCATTGATATGAGGAAGTTT
Found at i:31066981 original size:12 final size:12
Alignment explanation
Indices: 31066964--31066988 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31066954 TAGATGTCTA
31066964 TTATGTTAAAGG
1 TTATGTTAAAGG
31066976 TTATGTTAAAGG
1 TTATGTTAAAGG
31066988 T
1 T
31066989 GATCTGCCTA
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:0.00, G:0.24, T:0.44
Consensus pattern (12 bp):
TTATGTTAAAGG
Found at i:31067099 original size:32 final size:30
Alignment explanation
Indices: 31067050--31067122 Score: 92
Period size: 32 Copynumber: 2.3 Consensus size: 30
31067040 TCTAAAACTA
*
31067050 AAAACAGAAATAGAAGGAATTTATGCAAAT
1 AAAATAGAAATAGAAGGAATTTATGCAAAT
* *
31067080 GAAAATAGAGAATAGAAGGAATTTTTGTAAAT
1 -AAAATAGA-AATAGAAGGAATTTATGCAAAT
31067112 AAGAATAGAAA
1 AA-AATAGAAA
31067123 GAAATTCATT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 11 0.30
32 26 0.70
ACGTcount: A:0.56, C:0.03, G:0.19, T:0.22
Consensus pattern (30 bp):
AAAATAGAAATAGAAGGAATTTATGCAAAT
Found at i:31077550 original size:21 final size:22
Alignment explanation
Indices: 31077520--31077577 Score: 73
Period size: 21 Copynumber: 2.5 Consensus size: 22
31077510 GTTCCGCTTT
*
31077520 TTATTATTTTATTTTAAAA-TAA
1 TTATT-TTTTATCTTAAAATTAA
31077542 TTATTTTTTATCTTAAAATTAA
1 TTATTTTTTATCTTAAAATTAA
31077564 TTAGTTTTATTATC
1 TTA-TTTT-TTATC
31077578 ATTATTATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 12 0.38
22 11 0.34
23 4 0.12
24 5 0.16
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.60
Consensus pattern (22 bp):
TTATTTTTTATCTTAAAATTAA
Found at i:31078188 original size:16 final size:17
Alignment explanation
Indices: 31078167--31078200 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
31078157 CATACATATT
*
31078167 TACATATATTTTT-ACA
1 TACATAGATTTTTCACA
31078183 TACATAGATTTTTCACA
1 TACATAGATTTTTCACA
31078200 T
1 T
31078201 TTTTATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.35, C:0.15, G:0.03, T:0.47
Consensus pattern (17 bp):
TACATAGATTTTTCACA
Found at i:31090554 original size:48 final size:47
Alignment explanation
Indices: 31090494--31090833 Score: 169
Period size: 45 Copynumber: 7.7 Consensus size: 47
31090484 GCAATTTAAA
* *
31090494 AGATCGAAGCTACAGCGGCGAATCTTACTTCGGGCGATGCAGCGGAGC
1 AGATCGAAGCTACAACAGCGAATCTTACTTC-GGCGATGCAGCGGAGC
* * *** **
31090542 AGATTGAAGCTACAACAGCGAATCTCACTTC--CGAATGCA-ATTAAA
1 AGATCGAAGCTACAACAGCGAATCTTACTTCGGCG-ATGCAGCGGAGC
*
31090587 AGATCGAAGC-ACAGC-GCGAATC-TAC-TCTGGCGATGCAGCGGAGC
1 AGATCGAAGCTACAACAGCGAATCTTACTTC-GGCGATGCAGCGGAGC
* * * ** **
31090631 AGATTGAAGCT-CAACAGCGAATC-T-CATC-CCGA--CATGCAAAAA
1 AGATCGAAGCTACAACAGCGAATCTTACTTCGGCGATGCA-GCGGAGC
31090673 AGAT-GAAGC--C-ACAGCGAATC-TACTTCGGCGATGCA--GGAGC
1 AGATCGAAGCTACAACAGCGAATCTTACTTCGGCGATGCAGCGGAGC
* * * *** **
31090713 AGAT-GAAG-TACAACAGCGAATCTCACTCCCGAC-ATTGCA-ATTAAA
1 AGATCGAAGCTACAACAGCGAATCTTACT-TCGGCGA-TGCAGCGGAGC
*
31090758 AGATCGAAGC--C-ACAGCGGGATCTTACTTCTGGCGATGCAGCGGAGC
1 AGATCGAAGCTACAACAGC-GAATCTTACTTC-GGCGATGCAGCGGAGC
*
31090804 AGAT-GAAGCTACAACAGCGAATCTCACTTC
1 AGATCGAAGCTACAACAGCGAATCTTACTTC
31090834 CCGACATTGC
Statistics
Matches: 215, Mismatches: 48, Indels: 59
0.67 0.15 0.18
Matches are distributed among these distances:
39 11 0.05
40 13 0.06
41 13 0.06
42 19 0.09
43 21 0.10
44 33 0.15
45 47 0.22
46 15 0.07
47 11 0.05
48 32 0.15
ACGTcount: A:0.33, C:0.25, G:0.24, T:0.18
Consensus pattern (47 bp):
AGATCGAAGCTACAACAGCGAATCTTACTTCGGCGATGCAGCGGAGC
Found at i:31090624 original size:89 final size:93
Alignment explanation
Indices: 31090482--31090852 Score: 503
Period size: 89 Copynumber: 4.1 Consensus size: 93
31090472 AAACCATAGT
* *
31090482 TTGCAATTTAAAAGATCGAAGCTACAGCGGCGAATCTTACTTCGGGCGATGCAGCGGAGCAGATT
1 TTGCAA-TTAAAAGATCGAAGC-ACAGCAGCGAATCTTACTTCTGGCGATGCAGCGGAGCAGA-T
*
31090547 GAAGCTACAACAGCGAATCTCACTTCCGA-A
63 GAAGCTACAACAGCGAATCTCACTCCCGACA
31090577 -TGCAATTAAAAGATCGAAGCACAGC-GCGAATC-TAC-TCTGGCGATGCAGCGGAGCAGATTGA
1 TTGCAATTAAAAGATCGAAGCACAGCAGCGAATCTTACTTCTGGCGATGCAGCGGAGCAGA-TGA
31090638 AGCT-CAACAGCGAATCTCA-TCCCGACA
65 AGCTACAACAGCGAATCTCACTCCCGACA
31090665 -TGCAA--AAAAGAT-GAAGC-CA-CAGCGAATC-TACTTC-GGCGATGCA--GGAGCAGATGAA
1 TTGCAATTAAAAGATCGAAGCACAGCAGCGAATCTTACTTCTGGCGATGCAGCGGAGCAGATGAA
31090720 G-TACAACAGCGAATCTCACTCCCGACA
66 GCTACAACAGCGAATCTCACTCCCGACA
*
31090747 TTGCAATTAAAAGATCGAAGC-CA-CAGCGGGATCTTACTTCTGGCGATGCAGCGGAGCAGATGA
1 TTGCAATTAAAAGATCGAAGCACAGCAGC-GAATCTTACTTCTGGCGATGCAGCGGAGCAGATGA
31090810 AGCTACAACAGCGAATCTCACTTCCCGACA
65 AGCTACAACAGCGAATCTCAC-TCCCGACA
31090840 TTGCAATTTAAAA
1 TTGCAA-TTAAAA
31090853 TGAAGCCAAA
Statistics
Matches: 256, Mismatches: 3, Indels: 35
0.87 0.01 0.12
Matches are distributed among these distances:
80 1 0.00
81 20 0.08
82 16 0.06
83 6 0.02
84 21 0.08
85 14 0.05
86 18 0.07
87 9 0.04
88 27 0.11
89 38 0.15
90 3 0.01
91 20 0.08
92 23 0.09
93 29 0.11
94 11 0.04
ACGTcount: A:0.33, C:0.25, G:0.23, T:0.19
Consensus pattern (93 bp):
TTGCAATTAAAAGATCGAAGCACAGCAGCGAATCTTACTTCTGGCGATGCAGCGGAGCAGATGAA
GCTACAACAGCGAATCTCACTCCCGACA
Found at i:31090691 original size:39 final size:39
Alignment explanation
Indices: 31090635--31090774 Score: 104
Period size: 39 Copynumber: 3.3 Consensus size: 39
31090625 CGGAGCAGAT
31090635 TGAAGCTCAACAGCGAATCTCATCCCGACATGCAAAAAAGA
1 TGAAGC-C-ACAGCGAATCTCATCCCGACATGCAAAAAAGA
* * * **
31090676 TGAAGCCACAGCGAATCT-A-CTTCGGCGATGCAGGAGCAGA
1 TGAAGCCACAGCGAATCTCATC-CCGAC-ATGCA-AAAAAGA
*
31090716 TGAAGTACAACAGCGAATCTCACTCCCGACATTGCAATTAAAAGA
1 TGAAG--CCACAGCGAATCTCA-TCCCGACA-TGCAA--AAAAGA
31090761 TCGAAGCCACAGCG
1 T-GAAGCCACAGCG
31090775 GGATCTTACT
Statistics
Matches: 75, Mismatches: 12, Indels: 21
0.69 0.11 0.19
Matches are distributed among these distances:
37 1 0.01
38 4 0.05
39 16 0.21
40 10 0.13
41 6 0.08
42 12 0.16
43 2 0.03
44 14 0.19
45 6 0.08
46 4 0.05
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.16
Consensus pattern (39 bp):
TGAAGCCACAGCGAATCTCATCCCGACATGCAAAAAAGA
Found at i:31090821 original size:173 final size:176
Alignment explanation
Indices: 31090511--31090845 Score: 517
Period size: 173 Copynumber: 1.9 Consensus size: 176
31090501 AGCTACAGCG
*
31090511 GCGAATCTTACTTCGGGCGATGCAGCGGAGCAGATTGAAGCTACAACAGCGAATCTCACTTCCGA
1 GCGAATCTTACTTCGGGCGATGCA-CGGAGCAGATTGAAGCTACAACAGCGAATCTCACTCCCGA
31090576 ATGCAATTAAAAGATCGAAGCACAGCGCGAATCTACTCTGGCGATGCAGCGGAGCAGATTGAAGC
65 ATGCAATTAAAAGATCGAAGCACAGCGCGAATCTACTCTGGCGATGCAGCGGAGCAGATTGAAGC
31090641 TCAACAGCGAATCTCA-TCCCGACA-TGCAAAAAAGATGAAGCCACA
130 TCAACAGCGAATCTCACTCCCGACATTGCAAAAAAGATGAAGCCACA
31090686 GCGAATC-TACTTC-GGCGATGCA-GGAGCAGA-TGAAG-TACAACAGCGAATCTCACTCCCGAC
1 GCGAATCTTACTTCGGGCGATGCACGGAGCAGATTGAAGCTACAACAGCGAATCTCACTCCCGA-
*
31090746 ATTGCAATTAAAAGATCGAAGCCACAGCG-GGATCTTACTTCTGGCGATGCAGCGGAGCAGA-TG
65 A-TGCAATTAAAAGATCGAAG-CACAGCGCGAATC-TAC-TCTGGCGATGCAGCGGAGCAGATTG
31090809 AAGCTACAACAGCGAATCTCACTTCCCGACATTGCAA
126 AAGCT-CAACAGCGAATCTCAC-TCCCGACATTGCAA
31090846 TTTAAAATGA
Statistics
Matches: 149, Mismatches: 2, Indels: 17
0.89 0.01 0.10
Matches are distributed among these distances:
169 23 0.15
170 6 0.04
171 31 0.21
172 17 0.11
173 46 0.31
174 6 0.04
175 15 0.10
176 5 0.03
ACGTcount: A:0.33, C:0.26, G:0.24, T:0.18
Consensus pattern (176 bp):
GCGAATCTTACTTCGGGCGATGCACGGAGCAGATTGAAGCTACAACAGCGAATCTCACTCCCGAA
TGCAATTAAAAGATCGAAGCACAGCGCGAATCTACTCTGGCGATGCAGCGGAGCAGATTGAAGCT
CAACAGCGAATCTCACTCCCGACATTGCAAAAAAGATGAAGCCACA
Found at i:31105290 original size:18 final size:17
Alignment explanation
Indices: 31105269--31105307 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
31105259 AATAAATATT
31105269 ATTTATTAAATTAAATTA
1 ATTTATTAAATTAAA-TA
* *
31105287 ATTTTTTCAATTAAATA
1 ATTTATTAAATTAAATA
31105304 ATTT
1 ATTT
31105308 TATCAACCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTATTAAATTAAATA
Found at i:31105305 original size:17 final size:18
Alignment explanation
Indices: 31105277--31105313 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
31105267 TTATTTATTA
*
31105277 AATTAAATTAATTTTTTC
1 AATTAAATTAATTTTATC
31105295 AATTAAA-TAATTTTATC
1 AATTAAATTAATTTTATC
31105312 AA
1 AA
31105314 CCAAATTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (18 bp):
AATTAAATTAATTTTATC
Found at i:31108788 original size:33 final size:33
Alignment explanation
Indices: 31108715--31108788 Score: 112
Period size: 33 Copynumber: 2.2 Consensus size: 33
31108705 TACTATCTGT
31108715 TTGGTGTGTTGGTTGGACTAGCTCTTATGAGCA
1 TTGGTGTGTTGGTTGGACTAGCTCTTATGAGCA
* * * *
31108748 CTAGTGTGTTGGTTGGATTAGCTCTTCTGAGCA
1 TTGGTGTGTTGGTTGGACTAGCTCTTATGAGCA
31108781 TTGGTGTG
1 TTGGTGTG
31108789 CTGGAGGATT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.14, C:0.12, G:0.34, T:0.41
Consensus pattern (33 bp):
TTGGTGTGTTGGTTGGACTAGCTCTTATGAGCA
Found at i:31118072 original size:63 final size:63
Alignment explanation
Indices: 31117993--31118111 Score: 152
Period size: 63 Copynumber: 1.9 Consensus size: 63
31117983 ACACGGCTTG
* *
31117993 GACACACGCCTATGTCCCTAGCCCGTGTGACTCTAATTC-CAAAACAGTGAGTTACATGACCTA
1 GACACACGCCTATGTCCCTAGCACGTGTGACCCTAATTCAC-AAACAGTGAGTTACATGACCTA
* * * *
31118056 GACACACGCAC-ATGTCCTTGGCACGTGTGACCCTAATTGACAAATAGTGAGTTACA
1 GACACACGC-CTATGTCCCTAGCACGTGTGACCCTAATTCACAAACAGTGAGTTACA
31118112 CGGCCTGGTA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
63 46 0.96
64 2 0.04
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (63 bp):
GACACACGCCTATGTCCCTAGCACGTGTGACCCTAATTCACAAACAGTGAGTTACATGACCTA
Found at i:31127130 original size:15 final size:15
Alignment explanation
Indices: 31127110--31127143 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
31127100 TAGGACCAAT
31127110 ACTCAAATCATGTAA
1 ACTCAAATCATGTAA
31127125 ACTCAAATCATGTAA
1 ACTCAAATCATGTAA
31127140 ACTC
1 ACTC
31127144 TAATTACATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.44, C:0.24, G:0.06, T:0.26
Consensus pattern (15 bp):
ACTCAAATCATGTAA
Found at i:31129688 original size:14 final size:14
Alignment explanation
Indices: 31129669--31129700 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
31129659 CACAAAAGAA
31129669 ATATCTTAATACAT
1 ATATCTTAATACAT
31129683 ATATCTTAATACAT
1 ATATCTTAATACAT
31129697 ATAT
1 ATAT
31129701 TTTTCCTGCA
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:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (14 bp):
ATATCTTAATACAT
Found at i:31131447 original size:14 final size:14
Alignment explanation
Indices: 31131428--31131456 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
31131418 CTTCTGCAAA
31131428 AATAAAATAATTTT
1 AATAAAATAATTTT
31131442 AATAAAATAATTTT
1 AATAAAATAATTTT
31131456 A
1 A
31131457 CACGCATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AATAAAATAATTTT
Found at i:31139446 original size:23 final size:24
Alignment explanation
Indices: 31139391--31139446 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 24
31139381 TGTAAATTCA
* *
31139391 CAACAGTCAAATTTTAAATTAGAC
1 CAACAGTAAAATTATAAATTAGAC
* * *
31139415 CAACGGTAAAATTATAAA-TGGTC
1 CAACAGTAAAATTATAAATTAGAC
31139438 CAACAGTAA
1 CAACAGTAA
31139447 CTTTTTTCTA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
23 11 0.42
24 15 0.58
ACGTcount: A:0.46, C:0.16, G:0.12, T:0.25
Consensus pattern (24 bp):
CAACAGTAAAATTATAAATTAGAC
Found at i:31151374 original size:29 final size:27
Alignment explanation
Indices: 31151341--31151395 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 27
31151331 GTGATTAAAT
31151341 AAAATCGACA-CAAGCAGAATTTAAAAGAA
1 AAAATCGACAGCAAG-A-AA-TTAAAAGAA
*
31151370 AAAATTGACAGCAAGAAATTAAAAGA
1 AAAATCGACAGCAAGAAATTAAAAGA
31151396 TAAGTCCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 8 0.33
28 2 0.08
29 10 0.42
30 4 0.17
ACGTcount: A:0.60, C:0.11, G:0.15, T:0.15
Consensus pattern (27 bp):
AAAATCGACAGCAAGAAATTAAAAGAA
Found at i:31161268 original size:32 final size:32
Alignment explanation
Indices: 31161232--31161297 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
31161222 TCAATTATTC
31161232 ATGGTTTACAAACATCAAATGATATAACAATA
1 ATGGTTTACAAACATCAAATGATATAACAATA
31161264 ATGGTTTACAAACATCAAATGATATAACAATA
1 ATGGTTTACAAACATCAAATGATATAACAATA
31161296 AT
1 AT
31161298 CACACATAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.50, C:0.12, G:0.09, T:0.29
Consensus pattern (32 bp):
ATGGTTTACAAACATCAAATGATATAACAATA
Found at i:31164193 original size:23 final size:23
Alignment explanation
Indices: 31164167--31164288 Score: 93
Period size: 23 Copynumber: 5.2 Consensus size: 23
31164157 TTATGTGAAA
** *
31164167 CCTTTGTGTAATATTCTGTAACG
1 CCTTTGTGGCATATTCTGTAATG
**
31164190 CCTTTGTGGCATATTCTACAATG
1 CCTTTGTGGCATATTCTGTAATG
* *
31164213 TCTTTGTGGCATATTTTGTAATG
1 CCTTTGTGGCATATTCTGTAATG
* *
31164236 CCTTTGTGTGGCGTATTCTATAAT-
1 CC-TT-TGTGGCATATTCTGTAATG
* * * *
31164260 ACTTGTGTGGCGTATTCTTTAACG
1 CCTT-TGTGGCATATTCTGTAATG
31164284 CCTTT
1 CCTTT
31164289 AAGGCAAAAT
Statistics
Matches: 79, Mismatches: 17, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
23 58 0.73
24 6 0.08
25 15 0.19
ACGTcount: A:0.18, C:0.17, G:0.20, T:0.45
Consensus pattern (23 bp):
CCTTTGTGGCATATTCTGTAATG
Done.