Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001129.1 Hibiscus syriacus cultivar Beakdansim tig00002237_pilon, whole genome shotgun sequence
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: 21326069
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 83 of 89
Found at i:20023512 original size:22 final size:22
Alignment explanation
Indices: 20023465--20023535 Score: 64
Period size: 22 Copynumber: 3.5 Consensus size: 22
20023455 AATTATATTA
* *
20023465 TATATCTATATATTTT-TAATAC
1 TATAT-TATATGTTTTCTAAAAC
*
20023487 TATATT-TA--TTTTC--AAAT
1 TATATTATATGTTTTCTAAAAC
20023504 TATATTATATGTTTTCTAAAAC
1 TATATTATATGTTTTCTAAAAC
20023526 TATATTATAT
1 TATATTATAT
20023536 ATATATATAT
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
17 8 0.20
18 6 0.15
20 7 0.17
21 1 0.03
22 18 0.45
ACGTcount: A:0.37, C:0.07, G:0.01, T:0.55
Consensus pattern (22 bp):
TATATTATATGTTTTCTAAAAC
Found at i:20023538 original size:2 final size:2
Alignment explanation
Indices: 20023526--20023591 Score: 125
Period size: 2 Copynumber: 33.5 Consensus size: 2
20023516 TTTCTAAAAC
20023526 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20023567 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
20023592 CTTTCAAACT
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 62 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20023605 original size:42 final size:42
Alignment explanation
Indices: 20023526--20023703 Score: 136
Period size: 42 Copynumber: 4.2 Consensus size: 42
20023516 TTTCTAAAAC
* * *
20023526 TATATTATATATATATATATATATATATATAT-ATA-TATATA
1 TATA-TATATATATATATATATATATATCTTTCAAACTATATA
*
20023567 TATATATAT--ATATATATATATATATCTTTCAAACTATATG
1 TATATATATATATATATATATATATATCTTTCAAACTATATA
* * * *
20023607 T-TTTCTA-AAACTATATTATATATATATCTTTCAAACTATATG
1 TATATATATATA-TATA-TATATATATATCTTTCAAACTATATA
* * *
20023649 T-TTTATAAAACTATATTATATATATATATTTTTCAAAACTATACTA
1 TATATAT-ATA-TATA-TATATATATATATCTTTC-AAACTATA-TA
20023695 TATATATAT
1 TATATATAT
20023704 TTTCAAAATT
Statistics
Matches: 112, Mismatches: 12, Indels: 21
0.77 0.08 0.14
Matches are distributed among these distances:
38 18 0.16
39 6 0.05
40 12 0.11
41 8 0.07
42 31 0.28
43 1 0.01
44 18 0.16
45 11 0.10
46 3 0.03
47 4 0.04
ACGTcount: A:0.43, C:0.07, G:0.01, T:0.49
Consensus pattern (42 bp):
TATATATATATATATATATATATATATCTTTCAAACTATATA
Found at i:20023673 original size:26 final size:25
Alignment explanation
Indices: 20023643--20023824 Score: 147
Period size: 26 Copynumber: 7.6 Consensus size: 25
20023633 TCTTTCAAAC
* *
20023643 TATATGTTTTATAAAACTATATTATATA
1 TATATATTTT-TAAAACTATA--CTATA
20023671 TATATATTTTTCAAAACTATACTATA
1 TATATATTTTT-AAAACTATACTATA
*
20023697 TATATATTTTCAAAA-T-TA-TATA
1 TATATATTTTTAAAACTATACTATA
*
20023719 T-T-TATTTTCAAAACTATACTATA
1 TATATATTTTTAAAACTATACTATA
* *
20023742 TTTATGTTTTTCAAAACTATACTATA
1 TATATATTTTT-AAAACTATACTATA
*
20023768 -A-ATATTTTTCAAA--AT--TATA
1 TATATATTTTTAAAACTATACTATA
*
20023787 TAT-TATTTTCAAAACTATACTATA
1 TATATATTTTTAAAACTATACTATA
*
20023811 TATAT-TTTTCAAAA
1 TATATATTTTTAAAA
20023825 TAAAACAAAA
Statistics
Matches: 130, Mismatches: 10, Indels: 32
0.76 0.06 0.19
Matches are distributed among these distances:
19 4 0.03
20 21 0.16
21 4 0.03
22 9 0.07
23 10 0.08
24 25 0.19
25 10 0.08
26 28 0.22
27 1 0.01
28 18 0.14
ACGTcount: A:0.42, C:0.09, G:0.01, T:0.48
Consensus pattern (25 bp):
TATATATTTTTAAAACTATACTATA
Found at i:20023675 original size:70 final size:72
Alignment explanation
Indices: 20023601--20023815 Score: 291
Period size: 70 Copynumber: 3.0 Consensus size: 72
20023591 TCTTTCAAAC
* * * *
20023601 TATATG-TTTTCTAAAACTATATTATATATATATCTTTC-AAACTATATGTT-TTAT-AAAACTA
1 TATATGTTTTTC-AAAACTATACTATATATATAT-TTTCAAAATTATATATTATTTTCAAAACTA
*
20023662 TATTATATA
64 TACTATATA
*
20023671 TATATATTTTTCAAAACTATACTATATATATATTTTCAAAATTATATATTTATTTTCAAAACTAT
1 TATATGTTTTTCAAAACTATACTATATATATATTTTCAAAATTATATA-TTATTTTCAAAACTAT
20023736 ACTATAT-
65 ACTATATA
*
20023743 T-TATGTTTTTCAAAACTATACTATAAATAT-TTTTCAAAATTATATATTATTTTCAAAACTATA
1 TATATGTTTTTCAAAACTATACTATATATATATTTTCAAAATTATATATTATTTTCAAAACTATA
20023806 CTATATA
66 CTATATA
20023813 TAT
1 TAT
20023816 TTTTCAAAAT
Statistics
Matches: 130, Mismatches: 8, Indels: 13
0.86 0.05 0.09
Matches are distributed among these distances:
69 27 0.21
70 50 0.38
71 35 0.27
72 4 0.03
73 14 0.11
ACGTcount: A:0.41, C:0.09, G:0.01, T:0.48
Consensus pattern (72 bp):
TATATGTTTTTCAAAACTATACTATATATATATTTTCAAAATTATATATTATTTTCAAAACTATA
CTATATA
Found at i:20023718 original size:18 final size:18
Alignment explanation
Indices: 20023695--20023744 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 18
20023685 AACTATACTA
*
20023695 TATATATATTTTCAAAAT
1 TATATATATTTTCAAAAC
20023713 TATATATTTATTTTCAAAAC
1 TATATA--TATTTTCAAAAC
20023733 TATACTATATTT
1 TATA-TATATTT
20023745 ATGTTTTTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 6 0.21
19 5 0.18
20 15 0.54
21 2 0.07
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (18 bp):
TATATATATTTTCAAAAC
Found at i:20023727 original size:45 final size:47
Alignment explanation
Indices: 20023667--20023824 Score: 163
Period size: 45 Copynumber: 3.4 Consensus size: 47
20023657 AACTATATTA
*
20023667 TATATATATATTTTTCAAAACTATACTATATATAT-ATTTTCAAAAT
1 TATATATATATTTTTCAAAACTATACTATATATATGATTTTCAAAAC
* * *
20023713 TATATATTTA-TTTTCAAAACTATACTATATTTATGTTTTTCAAAAC
1 TATATATATATTTTTCAAAACTATACTATATATATGATTTTCAAAAC
20023759 TATACTATAAATATTTTTC-AAA--AT--TATATAT-T-ATTTTCAAAAC
1 TATA-TAT--ATATTTTTCAAAACTATACTATATATATGATTTTCAAAAC
20023802 TATACTATATATATTTTTCAAAA
1 --TA-TATATATATTTTTCAAAA
20023825 TAAAACAAAA
Statistics
Matches: 96, Mismatches: 7, Indels: 20
0.78 0.06 0.16
Matches are distributed among these distances:
43 19 0.20
44 4 0.04
45 34 0.35
46 24 0.25
47 5 0.05
49 5 0.05
50 5 0.05
ACGTcount: A:0.42, C:0.09, G:0.01, T:0.48
Consensus pattern (47 bp):
TATATATATATTTTTCAAAACTATACTATATATATGATTTTCAAAAC
Found at i:20023845 original size:15 final size:16
Alignment explanation
Indices: 20023821--20023854 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
20023811 TATATTTTTC
20023821 AAAATAAAACAAAACA
1 AAAATAAAACAAAACA
20023837 AAAAT-AAACAAAACA
1 AAAATAAAACAAAACA
20023852 AAA
1 AAA
20023855 GGAAACTCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.82, C:0.12, G:0.00, T:0.06
Consensus pattern (16 bp):
AAAATAAAACAAAACA
Found at i:20023860 original size:15 final size:15
Alignment explanation
Indices: 20023827--20023860 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
20023817 TTTCAAAATA
*
20023827 AAACAAAACAAAAAT
1 AAACAAAACAAAAAG
*
20023842 AAACAAAACAAAAGG
1 AAACAAAACAAAAAG
20023857 AAAC
1 AAAC
20023861 TCTAGGATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.76, C:0.15, G:0.06, T:0.03
Consensus pattern (15 bp):
AAACAAAACAAAAAG
Found at i:20026831 original size:18 final size:18
Alignment explanation
Indices: 20026808--20026867 Score: 84
Period size: 18 Copynumber: 3.3 Consensus size: 18
20026798 TCTTGAGAAG
20026808 ACCTAAAGAAAATAAAAT
1 ACCTAAAGAAAATAAAAT
** * *
20026826 ACCTAAAGGGATTAAAAC
1 ACCTAAAGAAAATAAAAT
20026844 ACCTAAAGAAAATAAAAT
1 ACCTAAAGAAAATAAAAT
20026862 ACCTAA
1 ACCTAA
20026868 GATAATCCTA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.60, C:0.15, G:0.08, T:0.17
Consensus pattern (18 bp):
ACCTAAAGAAAATAAAAT
Found at i:20026933 original size:24 final size:24
Alignment explanation
Indices: 20026905--20026956 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
20026895 AAGTACTTAT
*
20026905 TAATAGCAATCTTAAAATCCTAAG
1 TAATAGCAATCTAAAAATCCTAAG
*
20026929 TAATAGCAATCTAAAAATCCTAAT
1 TAATAGCAATCTAAAAATCCTAAG
20026953 TAAT
1 TAAT
20026957 TAAATAAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.48, C:0.15, G:0.06, T:0.31
Consensus pattern (24 bp):
TAATAGCAATCTAAAAATCCTAAG
Found at i:20027394 original size:18 final size:18
Alignment explanation
Indices: 20027371--20027406 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
20027361 TCTCACAATT
20027371 TGTCAAGGAATGCCAAAC
1 TGTCAAGGAATGCCAAAC
20027389 TGTCAAGGAATGCCAAAC
1 TGTCAAGGAATGCCAAAC
20027407 GAGTCAATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.17
Consensus pattern (18 bp):
TGTCAAGGAATGCCAAAC
Found at i:20028477 original size:93 final size:92
Alignment explanation
Indices: 20028315--20028526 Score: 308
Period size: 93 Copynumber: 2.3 Consensus size: 92
20028305 TATATTTCAA
* * *
20028315 TCTTTCCTCTATTCGAACAAG-AGCAATTCACCACATATGTATTAATGTAATCTATATGGAAATC
1 TCTTT-CTCTATTCGAACAAGAAGTAATTCACAACATATGTATTAATGCAATCTATATGGAAATC
*
20028379 TGATTAAACAATTCAATATGTATAACAT
65 GGATTAAACAATTCAATATGTATAACAT
*
20028407 TCTTTCTGCTATTCGAACAAGAAGTAATTCACAACATATGTATTCATGCAATCTATATGGAAATC
1 TCTTTCT-CTATTCGAACAAGAAGTAATTCACAACATATGTATTAATGCAATCTATATGGAAATC
*
20028472 GGATTAAAGAATTCAATATGTATAACAT
65 GGATTAAACAATTCAATATGTATAACAT
*
20028500 TC--T-T-TATTCGAACAAGAAATAATTCAC
1 TCTTTCTCTATTCGAACAAGAAGTAATTCAC
20028527 TCAATTATAT
Statistics
Matches: 111, Mismatches: 7, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
88 22 0.20
90 1 0.01
91 3 0.03
92 18 0.16
93 67 0.60
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.34
Consensus pattern (92 bp):
TCTTTCTCTATTCGAACAAGAAGTAATTCACAACATATGTATTAATGCAATCTATATGGAAATCG
GATTAAACAATTCAATATGTATAACAT
Found at i:20029059 original size:41 final size:41
Alignment explanation
Indices: 20029014--20029373 Score: 268
Period size: 41 Copynumber: 8.8 Consensus size: 41
20029004 TCGATATTGG
* * * *
20029014 CAGCATGTATTAATTCACAATTCGATTCAATTCAATCGTGA
1 CAGCATGCAATAATTCACAATTCAATTCAATTCAATCATGA
* * *
20029055 CAGCATGCAATAGTTCAACATTTC-ATTCAATTAAATCATGGA
1 CAGCATGCAATAATTC-ACAATTCAATTCAATTCAATCAT-GA
*
20029097 -AGCATGCAATAATTCACAATTCAATTCAATTCAATCGTGGA
1 CAGCATGCAATAATTCACAATTCAATTCAATTCAATCAT-GA
* *
20029138 -AGCATGCAATAATTCACCAA-TCAACTT-GATTCAATCATGG
1 CAGCATGCAATAATTCA-CAATTCAA-TTCAATTCAATCATGA
* * * *
20029178 TAGCATGCAATAATTGACAATTCTATTCAATTCAATCATGG
1 CAGCATGCAATAATTCACAATTCAATTCAATTCAATCATGA
* * * * *
20029219 CATCATGCAGTAATTCACCATTCAACTT-GATTCGATCATGGA
1 CAGCATGCAATAATTCACAATTCAA-TTCAATTCAATCAT-GA
* * * * * *
20029261 -AACATGCAATGATTCATAATTCAACTCAATTCGATCATGG
1 CAGCATGCAATAATTCACAATTCAATTCAATTCAATCATGA
* * * * **
20029301 TAACATGCAATTATTCATAACCCAATTCAATT-AGATCATGA
1 CAGCATGCAATAATTCACAATTCAATTCAATTCA-ATCATGA
* * * * *
20029342 TAACATGTATTAATTCACAATCCAATTCAATT
1 CAGCATGCAATAATTCACAATTCAATTCAATT
20029374 TAAATAAAGG
Statistics
Matches: 262, Mismatches: 44, Indels: 26
0.79 0.13 0.08
Matches are distributed among these distances:
40 14 0.05
41 232 0.89
42 16 0.06
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.32
Consensus pattern (41 bp):
CAGCATGCAATAATTCACAATTCAATTCAATTCAATCATGA
Found at i:20029110 original size:82 final size:82
Alignment explanation
Indices: 20029015--20029373 Score: 300
Period size: 82 Copynumber: 4.4 Consensus size: 82
20029005 CGATATTGGC
* * * * *
20029015 AGCATGTATTAATTCACAATTCGATTCAATTCAATCGT-GACAGCATGCAATAGTTCAACATTTC
1 AGCATGCAATAATTCACAATTCAATTCAATTCAATCGTGGA-AGCATGCAATAATTCAACA-ATC
20029079 -A-TTCAATTAAATCATGGA
64 AACTT-AATTAAATCATGGA
*
20029097 AGCATGCAATAATTCACAATTCAATTCAATTCAATCGTGGAAGCATGCAATAATTCACCAATCAA
1 AGCATGCAATAATTCACAATTCAATTCAATTCAATCGTGGAAGCATGCAATAATTCAACAATCAA
* * *
20029162 CTTGATTCAATCATGGT
66 CTTAATTAAATCATGGA
* * * * * * * *
20029179 AGCATGCAATAATTGACAATTCTATTCAATTCAATCATGGCATCATGCAGTAATTCACCATTCAA
1 AGCATGCAATAATTCACAATTCAATTCAATTCAATCGTGGAAGCATGCAATAATTCAACAATCAA
* **
20029244 CTTGATTCGATCATGGA
66 CTTAATTAAATCATGGA
* * * * * * * **
20029261 AACATGCAATGATTCATAATTCAACTCAATTCGATCATGGTAA-CATGCAATTATTCATA-ACCC
1 AGCATGCAATAATTCACAATTCAATTCAATTCAATCGTGG-AAGCATGCAATAATTCA-ACAATC
*
20029324 AA-TTCAATTAGATCAT-GA
64 AACTT-AATTAAATCATGGA
* * * *
20029342 TAACATGTATTAATTCACAATCCAATTCAATT
1 -AGCATGCAATAATTCACAATTCAATTCAATT
20029374 TAAATAAAGG
Statistics
Matches: 231, Mismatches: 39, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
81 6 0.03
82 220 0.95
83 5 0.02
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.32
Consensus pattern (82 bp):
AGCATGCAATAATTCACAATTCAATTCAATTCAATCGTGGAAGCATGCAATAATTCAACAATCAA
CTTAATTAAATCATGGA
Found at i:20029209 original size:123 final size:122
Alignment explanation
Indices: 20029024--20029373 Score: 328
Period size: 123 Copynumber: 2.8 Consensus size: 122
20029014 CAGCATGTAT
* * * ** * *
20029024 TAATTCACAATTCGATTCAATTCAATCGTGACAGCATGCAATAGTTCAACATTTCATTCAATTAA
1 TAATTCACAATTCAACTCAATTCAATCATGGTAGCATGCAATAATT-AACAATTCATTCAATTAA
* * *
20029089 ATCATGGAAGCATGCAATAATTCACAATTCAATTCAATTCAATCGTGGAAGCATGCAA
65 ATCATGGAAACATGCAATAATTCACAATTCAATTCAATTCAATCATGGAAACATGCAA
** * *
20029147 TAATTCACCAA-TCAACTTGATTCAATCATGGTAGCATGCAATAATTGACAATTCTATTCAATTC
1 TAATTCA-CAATTCAACTCAATTCAATCATGGTAGCATGCAATAATTAACAATTC-ATTCAATTA
* * * * * *
20029211 AATCATGGCATCATGCAGTAATTCACCATTCAACTT-GATTCGATCATGGAAACATGCAA
64 AATCATGGAAACATGCAATAATTCACAATTCAA-TTCAATTCAATCATGGAAACATGCAA
* * * * * * * ** *
20029270 TGATTCATAATTCAACTCAATTCGATCATGGTAACATGCAATTATTCATAACCCAATTCAATTAG
1 TAATTCACAATTCAACTCAATTCAATCATGGTAGCATGCAATAATTAACAATTC-ATTCAATTAA
* * *
20029335 ATCAT-GATAACATGTATTAATTCACAATCCAATTCAATT
65 ATCATGGA-AACATGCAATAATTCACAATTCAATTCAATT
20029374 TAAATAAAGG
Statistics
Matches: 181, Mismatches: 40, Indels: 12
0.78 0.17 0.05
Matches are distributed among these distances:
122 11 0.06
123 165 0.91
124 5 0.03
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.32
Consensus pattern (122 bp):
TAATTCACAATTCAACTCAATTCAATCATGGTAGCATGCAATAATTAACAATTCATTCAATTAAA
TCATGGAAACATGCAATAATTCACAATTCAATTCAATTCAATCATGGAAACATGCAA
Found at i:20037556 original size:20 final size:20
Alignment explanation
Indices: 20037531--20037572 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
20037521 ACTGATTTTG
* *
20037531 GATTGGATTTATATGGAATT
1 GATTGGAATTACATGGAATT
*
20037551 GATTGGAATTGCATGGAATT
1 GATTGGAATTACATGGAATT
20037571 GA
1 GA
20037573 AGTTGAGAGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.02, G:0.29, T:0.38
Consensus pattern (20 bp):
GATTGGAATTACATGGAATT
Found at i:20042694 original size:21 final size:21
Alignment explanation
Indices: 20042670--20042719 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
20042660 GAGCAGTAGA
*
20042670 CCGTTGACCGACGTTGACCGG
1 CCGTTGACCGACATTGACCGG
*
20042691 CCGTTGACCGACATTGATCGG
1 CCGTTGACCGACATTGACCGG
*
20042712 TCGTTGAC
1 CCGTTGAC
20042720 TTTTTTAGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.16, C:0.30, G:0.30, T:0.24
Consensus pattern (21 bp):
CCGTTGACCGACATTGACCGG
Found at i:20043816 original size:24 final size:24
Alignment explanation
Indices: 20043784--20043854 Score: 97
Period size: 24 Copynumber: 3.0 Consensus size: 24
20043774 ATATGATTTT
* *
20043784 TGTTCTGATTTCTACTCTGAATTC
1 TGTTATGATTTATACTCTGAATTC
*
20043808 TGTTATGATTTATGCTCTGAATTC
1 TGTTATGATTTATACTCTGAATTC
* *
20043832 TGTTATGATTTATGCTTTGAATT
1 TGTTATGATTTATACTCTGAATT
20043855 ATGTCCTGAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.20, C:0.13, G:0.15, T:0.52
Consensus pattern (24 bp):
TGTTATGATTTATACTCTGAATTC
Found at i:20043864 original size:24 final size:24
Alignment explanation
Indices: 20043789--20043872 Score: 87
Period size: 24 Copynumber: 3.5 Consensus size: 24
20043779 ATTTTTGTTC
* * * *
20043789 TGATTTCTACTCTGAATTCTGTTA
1 TGATTTATGCTCTGAATTATGTCA
* *
20043813 TGATTTATGCTCTGAATTCTGTTA
1 TGATTTATGCTCTGAATTATGTCA
* *
20043837 TGATTTATGCTTTGAATTATGTCC
1 TGATTTATGCTCTGAATTATGTCA
*
20043861 TGATTTCTGCTC
1 TGATTTATGCTC
20043873 AATATTCTAT
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.19, C:0.15, G:0.15, T:0.50
Consensus pattern (24 bp):
TGATTTATGCTCTGAATTATGTCA
Found at i:20047141 original size:27 final size:27
Alignment explanation
Indices: 20047111--20047172 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
20047101 GAAATGATTG
*
20047111 AAATATCC-TAGATTTGTAAAATGA-CCA
1 AAATATCCTTAGA-ATGT-AAATGACCCA
*
20047138 AAATACCCTTAGAATGTAAATGACCCA
1 AAATATCCTTAGAATGTAAATGACCCA
20047165 AGAATATC
1 A-AATATC
20047173 ACCAGGCCCA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
26 6 0.21
27 14 0.48
28 9 0.31
ACGTcount: A:0.45, C:0.18, G:0.11, T:0.26
Consensus pattern (27 bp):
AAATATCCTTAGAATGTAAATGACCCA
Found at i:20047691 original size:24 final size:24
Alignment explanation
Indices: 20047647--20047721 Score: 80
Period size: 24 Copynumber: 3.1 Consensus size: 24
20047637 CTGATTTCTA
*
20047647 CTCTGAATTTTGTTACGATTTATG
1 CTCTGAATTTTATTACGATTTATG
* *
20047671 CTCTGAATTTTATT-CTTATTTTTG
1 CTCTGAATTTTATTAC-GATTTATG
* * *
20047695 CTCTGAATTCTATTATGATTTCTG
1 CTCTGAATTTTATTACGATTTATG
20047719 CTC
1 CTC
20047722 AATATTCTGT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
23 1 0.02
24 41 0.98
ACGTcount: A:0.19, C:0.16, G:0.12, T:0.53
Consensus pattern (24 bp):
CTCTGAATTTTATTACGATTTATG
Found at i:20056539 original size:16 final size:16
Alignment explanation
Indices: 20056518--20056573 Score: 85
Period size: 16 Copynumber: 3.4 Consensus size: 16
20056508 TACCCAAAAG
*
20056518 AAATAATATAAAACCT
1 AAATAATCTAAAACCT
20056534 AAATAATCTAAAACCT
1 AAATAATCTAAAACCT
*
20056550 AAATAAGCTAAAACCT
1 AAATAATCTAAAACCT
20056566 AAACTAAT
1 AAA-TAAT
20056574 TTAACTTCAC
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
16 33 0.92
17 3 0.08
ACGTcount: A:0.59, C:0.16, G:0.02, T:0.23
Consensus pattern (16 bp):
AAATAATCTAAAACCT
Found at i:20057748 original size:55 final size:54
Alignment explanation
Indices: 20057682--20057880 Score: 215
Period size: 55 Copynumber: 3.6 Consensus size: 54
20057672 AATGACGAGC
*
20057682 CTGCTCCCTATTCCTTCAG-GAAGTATAAGACTCGAACAATCTTCATAAAACGTGT
1 CTGCTCTCTATTCCTTCAGAG-AGTATAAGACTCGAACAATCTTCATAAAACG-GT
* * * *
20057737 CTTCTCTCTATTCATTCAGAGAGTATAAGACTTGAACAATCTTTAATAAAACGGGT
1 CTGCTCTCTATTCCTTCAGAGAGTATAAGACTCGAACAATC-TTCATAAAAC-GGT
* *
20057793 CCGCTCTCTATTCCTTCAGAGAGTAT-AGAACTCGAAAAATCTTCA-ATAAACAGGT
1 CTGCTCTCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCATA-AAAC-GGT
* * * *
20057848 CTGCTCCCTATTCTTTCAGGGAGTATAGGACTC
1 CTGCTCTCTATTCCTTCAGAGAGTATAAGACTC
20057881 AATCTTCAAC
Statistics
Matches: 121, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
54 1 0.01
55 73 0.60
56 46 0.38
57 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.31
Consensus pattern (54 bp):
CTGCTCTCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCATAAAACGGT
Found at i:20057811 original size:56 final size:56
Alignment explanation
Indices: 20057682--20057982 Score: 234
Period size: 51 Copynumber: 5.6 Consensus size: 56
20057672 AATGACGAGC
* *
20057682 CTGCTCCCTATTCCTTCAG-GAAGTATAAGACTCGAACAATC-TTCATAAAACGTGT
1 CTGCTCCCTATTCCTTCAGAG-AGTATAAGACTCGAACAATCTTTAATAAAACGGGT
* * * *
20057737 CTTCTCTCTATTCATTCAGAGAGTATAAGACTTGAACAATCTTTAATAAAACGGGT
1 CTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTTAATAAAACGGGT
* * * * *
20057793 CCGCTCTCTATTCCTTCAGAGAGTAT-AGAACTCGAAAAATCTTCAAT-AAACAGGT
1 CTGCTCCCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTTAATAAAACGGGT
* * * * ** **
20057848 CTGCTCCCTATTCTTTCAGGGAGTATAGGACT----CAATCTTCAA-CGAACTTGT
1 CTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTTAATAAAACGGGT
* * * * * **
20057899 CCGCTCCCTATTCATTCAGAGAGTATAGGACT----CAATCTTCAAT-GAACTTGT
1 CTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTTAATAAAACGGGT
* *
20057950 CTGCTCCCTATTCATTCAGAGAGTATAGGACTC
1 CTGCTCCCTATTCCTTCAGAGAGTATAAGACTC
20057983 AATCTTCAAC
Statistics
Matches: 213, Mismatches: 26, Indels: 17
0.83 0.10 0.07
Matches are distributed among these distances:
51 92 0.43
55 69 0.32
56 52 0.24
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.31
Consensus pattern (56 bp):
CTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTTAATAAAACGGGT
Found at i:20057906 original size:51 final size:51
Alignment explanation
Indices: 20057791--20058102 Score: 471
Period size: 51 Copynumber: 6.0 Consensus size: 51
20057781 AATAAAACGG
* * * ** **
20057791 GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAAAATCTTCAATAAACAG
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTC----AATCTTCAACGAACTT
* * *
20057846 GTCTGCTCCCTATTCTTTCAGGGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
*
20057897 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAATGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
*
20057948 GTCTGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
*
20057999 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAATGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
20058050 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
20058101 GT
1 GT
20058103 TTGCTTCACT
Statistics
Matches: 239, Mismatches: 18, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
51 209 0.87
55 30 0.13
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (51 bp):
GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
Found at i:20058082 original size:153 final size:154
Alignment explanation
Indices: 20057744--20058107 Score: 478
Period size: 153 Copynumber: 2.3 Consensus size: 154
20057734 TGTCTTCTCT
* * * ** * * *
20057744 CTATTCATTCAGAGAGTATAAGACTTGAACAATCTTTAATAAAACGGGTCCGCTCTCTATTCCTT
1 CTATTCATTCAGAGAGTATAGGAC-T---CAATCTTCAAT-GAACTTGTCTGCTCCCTATTCATT
* * * *
20057809 CAGAGAGTATAGAACTCGAAAAATCTTCAATAAACAGGTCTGCTCCCTATTCTTTCAGGGAGTAT
61 CAGAGAGTATAGAACTC---AAATCTTCAACAAACAGGTCCGCTCCCTATTCATTCAGAGAGTAT
20057874 AGGACTCAATCTTCAACGAACTTGTCCGCTCC
123 AGGACTCAATCTTCAACGAACTTGTCCGCTCC
20057906 CTATTCATTCAGAGAGTATAGGACTCAATCTTCAATGAACTTGTCTGCTCCCTATTCATTCAGAG
1 CTATTCATTCAGAGAGTATAGGACTCAATCTTCAATGAACTTGTCTGCTCCCTATTCATTCAGAG
* * **
20057971 AGTATAGGACTC-AATCTTCAACGAACTTGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCA
66 AGTATAGAACTCAAATCTTCAACAAACAGGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCA
*
20058035 ATCTTCAATGAACTTGTCCGCTCC
131 ATCTTCAACGAACTTGTCCGCTCC
* *
20058059 CTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTTTGCT
1 CTATTCATTCAGAGAGTATAGGACTCAATCTTCAATGAACTTGTCTGCT
20058108 TCACTACTCT
Statistics
Matches: 183, Mismatches: 19, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
153 115 0.63
157 34 0.19
158 10 0.05
161 1 0.01
162 23 0.13
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (154 bp):
CTATTCATTCAGAGAGTATAGGACTCAATCTTCAATGAACTTGTCTGCTCCCTATTCATTCAGAG
AGTATAGAACTCAAATCTTCAACAAACAGGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCA
ATCTTCAACGAACTTGTCCGCTCC
Found at i:20059259 original size:16 final size:16
Alignment explanation
Indices: 20059227--20059279 Score: 72
Period size: 16 Copynumber: 3.3 Consensus size: 16
20059217 TGAACCCCTC
*
20059227 TTTT-ATTTCTCTTTT
1 TTTTCATTTTTCTTTT
*
20059242 TTTTCATTTTTCTCTT
1 TTTTCATTTTTCTTTT
20059258 TTTTCATTTTTCATTTT
1 TTTTCATTTTTC-TTTT
20059275 TTTTC
1 TTTTC
20059280 TTCCCTTTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
15 4 0.12
16 21 0.64
17 8 0.24
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTCATTTTTCTTTT
Found at i:20059307 original size:19 final size:19
Alignment explanation
Indices: 20059273--20059358 Score: 67
Period size: 19 Copynumber: 4.7 Consensus size: 19
20059263 ATTTTTCATT
**
20059273 TTTTTTCTTCCCTTTTCCA
1 TTTTTTCTTCTTTTTTCCA
20059292 TTTTTTCTTCTTTTTTTCC-
1 TTTTTTCTTC-TTTTTTCCA
*
20059311 --TTTTC--GTTTTTTCCA
1 TTTTTTCTTCTTTTTTCCA
**
20059326 TCATTT-TTCTTTTTTCTCA
1 TTTTTTCTTCTTTTTTC-CA
20059345 TTTTTTCTTCTTTT
1 TTTTTTCTTCTTTT
20059359 CTCTTTTATT
Statistics
Matches: 52, Mismatches: 7, Indels: 15
0.70 0.09 0.20
Matches are distributed among these distances:
14 8 0.15
17 8 0.15
18 7 0.13
19 16 0.31
20 13 0.25
ACGTcount: A:0.05, C:0.22, G:0.01, T:0.72
Consensus pattern (19 bp):
TTTTTTCTTCTTTTTTCCA
Found at i:20059321 original size:26 final size:29
Alignment explanation
Indices: 20059264--20059363 Score: 83
Period size: 26 Copynumber: 3.6 Consensus size: 29
20059254 TCTTTTTTCA
*
20059264 TTTTTCATTTTTTTTCTTCCCTTTTCCAT
1 TTTTTCATTCTTTTTCTTCCCTTTTCCAT
*
20059293 TTTTTC-TTCTTTTT-TT-CCTTTT-CGT
1 TTTTTCATTCTTTTTCTTCCCTTTTCCAT
20059318 TTTTTCCA-TCATTTTTCTT---TTTTCTCAT
1 TTTTT-CATTC-TTTTTCTTCCCTTTTC-CAT
20059346 TTTTTC-TTCTTTTCTCTT
1 TTTTTCATTCTTTT-TCTT
20059364 TTATTTCTTC
Statistics
Matches: 60, Mismatches: 3, Indels: 18
0.74 0.04 0.22
Matches are distributed among these distances:
25 7 0.12
26 17 0.28
27 14 0.23
28 16 0.27
29 6 0.10
ACGTcount: A:0.05, C:0.22, G:0.01, T:0.72
Consensus pattern (29 bp):
TTTTTCATTCTTTTTCTTCCCTTTTCCAT
Found at i:20059345 original size:16 final size:16
Alignment explanation
Indices: 20059231--20059365 Score: 68
Period size: 16 Copynumber: 8.3 Consensus size: 16
20059221 CCCCTCTTTT
* *
20059231 ATTTCTCTTTTTTTTC
1 ATTTTTCTTTTTTCTC
20059247 ATTTTTCTCTTTTT-TC
1 ATTTTTCT-TTTTTCTC
*
20059263 ATTTTTCATTTTT-T-
1 ATTTTTCTTTTTTCTC
* **
20059277 -TTCTTCCCTTTTC-C
1 ATTTTTCTTTTTTCTC
*
20059291 ATTTTTTCTTCTTTTTTTC
1 A-TTTTTC-T-TTTTTCTC
*
20059310 -CTTTTCGTTTTTTCCATC
1 ATTTTTC-TTTTTT-C-TC
20059328 ATTTTTCTTTTTTCTC
1 ATTTTTCTTTTTTCTC
20059344 ATTTTTTCTTCTTTTCTC
1 A-TTTTTCTT-TTTTCTC
20059362 -TTTT
1 ATTTT
20059366 ATTTCTTCTT
Statistics
Matches: 93, Mismatches: 13, Indels: 26
0.70 0.10 0.20
Matches are distributed among these distances:
13 9 0.10
15 6 0.06
16 33 0.35
17 20 0.22
18 19 0.20
19 6 0.06
ACGTcount: A:0.06, C:0.21, G:0.01, T:0.73
Consensus pattern (16 bp):
ATTTTTCTTTTTTCTC
Found at i:20059370 original size:19 final size:18
Alignment explanation
Indices: 20059232--20059375 Score: 78
Period size: 17 Copynumber: 8.1 Consensus size: 18
20059222 CCCTCTTTTA
20059232 TTTCTC-TTTTTT-TTCATT
1 TTTCTCATTTTTTCTTC--T
*
20059250 TTTCTC-TTTTTTCAT-T
1 TTTCTCATTTTTTCTTCT
*
20059266 TTTCAT-TTTTTTTCTTCCCT
1 TTTC-TCATTTTTTCTT--CT
20059286 TTTC-CATTTTTTCTTCT
1 TTTCTCATTTTTTCTTCT
20059303 TTT-T--TTCCTTTTCGTT-T
1 TTTCTCATT--TTTTC-TTCT
20059320 TTTC-CATCATTTTTCTT-T
1 TTTCTCAT--TTTTTCTTCT
20059338 TTTCTCATTTTTTCTTCT
1 TTTCTCATTTTTTCTTCT
*
20059356 TTTCTCTTTTATTTCTTCT
1 TTTCTCATTT-TTTCTTCT
20059375 T
1 T
20059376 CAAGCAAAAT
Statistics
Matches: 103, Mismatches: 4, Indels: 37
0.72 0.03 0.26
Matches are distributed among these distances:
15 2 0.02
16 5 0.05
17 31 0.30
18 31 0.30
19 28 0.27
20 5 0.05
21 1 0.01
ACGTcount: A:0.06, C:0.21, G:0.01, T:0.73
Consensus pattern (18 bp):
TTTCTCATTTTTTCTTCT
Found at i:20071108 original size:16 final size:16
Alignment explanation
Indices: 20071087--20071142 Score: 69
Period size: 16 Copynumber: 3.4 Consensus size: 16
20071077 TACCCAAAAG
20071087 AAATAATATAAAACCT
1 AAATAATATAAAACCT
20071103 AAATAA-ACTAAAACCT
1 AAATAATA-TAAAACCT
**
20071119 AAATAAGCTAAAACCT
1 AAATAATATAAAACCT
20071135 AAACTAAT
1 AAA-TAAT
20071143 TTAACTTCAC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
15 1 0.03
16 31 0.89
17 3 0.09
ACGTcount: A:0.61, C:0.16, G:0.02, T:0.21
Consensus pattern (16 bp):
AAATAATATAAAACCT
Found at i:20073573 original size:36 final size:34
Alignment explanation
Indices: 20073531--20073651 Score: 120
Period size: 35 Copynumber: 3.4 Consensus size: 34
20073521 GTTTAGCTCT
20073531 GATCAAGCTGGTAATTCCTTATATAGGTTCAACTC
1 GATCAAGCTGGTAATTCCTTATATAGGTTCAAC-C
* * *
20073566 TATTCAAGCTGGTAACTCCTTATACAGGTTCAGCACC
1 GA-TCAAGCTGGTAATTCCTTATATAGGTTCA--ACC
* *
20073603 GAT-GAGTTGGTAATTCCTTATATAGGTTCAACATC
1 GATCAAGCTGGTAATTCCTTATATAGGTTCAAC--C
*
20073638 GATC-AGCTGATAAT
1 GATCAAGCTGGTAAT
20073652 AATGTAATTA
Statistics
Matches: 70, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
33 2 0.03
35 36 0.51
36 28 0.40
37 2 0.03
38 2 0.03
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (34 bp):
GATCAAGCTGGTAATTCCTTATATAGGTTCAACC
Found at i:20077889 original size:24 final size:24
Alignment explanation
Indices: 20077862--20077910 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
20077852 CCCTTCTCTC
20077862 TAACAAAGTGACAATCGATCTCAA
1 TAACAAAGTGACAATCGATCTCAA
20077886 TAACAAAGTGACAATCGATCTCAA
1 TAACAAAGTGACAATCGATCTCAA
20077910 T
1 T
20077911 GTGCTTTGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.45, C:0.20, G:0.12, T:0.22
Consensus pattern (24 bp):
TAACAAAGTGACAATCGATCTCAA
Found at i:20078045 original size:18 final size:18
Alignment explanation
Indices: 20078019--20078058 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
20078009 ATTGTCTAAG
*
20078019 CAACGCTTTCAACCAAAC
1 CAACACTTTCAACCAAAC
20078037 CAACACTTTCAACCAAAC
1 CAACACTTTCAACCAAAC
20078055 CAAC
1 CAAC
20078059 TCCGCCACAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.42, C:0.40, G:0.03, T:0.15
Consensus pattern (18 bp):
CAACACTTTCAACCAAAC
Found at i:20084625 original size:2 final size:2
Alignment explanation
Indices: 20084620--20084650 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
20084610 TGTGTGTGTG
20084620 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
20084651 TTATGCCTGT
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:20089027 original size:30 final size:31
Alignment explanation
Indices: 20088983--20089041 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 31
20088973 ACTCGACAAG
*
20088983 ATCAGGCTGTAGTAG-GTCGTGGTCCAGCAAA
1 ATCAGGCTGCAGTAGTG-CGTGGTCCAGCAAA
20089014 ATCA-GCTGCAGTAGTGCGTGGTCCAGCA
1 ATCAGGCTGCAGTAGTGCGTGGTCCAGCA
20089042 GGGTCATCTG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.24, C:0.22, G:0.32, T:0.22
Consensus pattern (31 bp):
ATCAGGCTGCAGTAGTGCGTGGTCCAGCAAA
Found at i:20089053 original size:30 final size:30
Alignment explanation
Indices: 20089000--20089059 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
20088990 TGTAGTAGGT
*
20089000 CGTGGTCCAGCAAAATCAGCTGCAGTAGTG
1 CGTGGTCCAGCAAAATCAGCTGCAGCAGTG
*** *
20089030 CGTGGTCCAGCAGGGTCATCTGCAGCAGTG
1 CGTGGTCCAGCAAAATCAGCTGCAGCAGTG
20089060 TGTAGTACCC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.22, C:0.25, G:0.33, T:0.20
Consensus pattern (30 bp):
CGTGGTCCAGCAAAATCAGCTGCAGCAGTG
Found at i:20091553 original size:25 final size:25
Alignment explanation
Indices: 20091517--20091575 Score: 109
Period size: 25 Copynumber: 2.4 Consensus size: 25
20091507 AACACAGTGT
*
20091517 ACTTCAAATGGTCCTGACCATCGTG
1 ACTTCAATTGGTCCTGACCATCGTG
20091542 ACTTCAATTGGTCCTGACCATCGTG
1 ACTTCAATTGGTCCTGACCATCGTG
20091567 ACTTCAATT
1 ACTTCAATT
20091576 TTCCAGGGGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.24, C:0.27, G:0.17, T:0.32
Consensus pattern (25 bp):
ACTTCAATTGGTCCTGACCATCGTG
Found at i:20098361 original size:20 final size:20
Alignment explanation
Indices: 20098332--20098370 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
20098322 ATTCCACCAC
20098332 ATGCAACTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
*
20098352 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
20098371 CATGGGCTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:20099199 original size:86 final size:84
Alignment explanation
Indices: 20099054--20099225 Score: 254
Period size: 86 Copynumber: 2.0 Consensus size: 84
20099044 CCATGGTTTG
*
20099054 AACCGGAGACCCTTAGGTGGCGTTTGGTTCGCTTGAATGTTCATGAGAGAATTGAAATCTGTGAA
1 AACCGGAGACCCTTAGGTGGCGTTTGGTTCGCTGGAATGTTCATGAGAGAATTGAAATC--TGAA
*
20099119 GGAATTGGAATATGAATCTGA
64 GGAATTGCAATATGAATCTGA
* * * * *
20099140 AACCGGGGACCCTTAGGTGGCGTTTGGTTCGCTGGAATGTTCCTGAGGGAATTGGAATCTGAATG
1 AACCGGAGACCCTTAGGTGGCGTTTGGTTCGCTGGAATGTTCATGAGAGAATTGAAATCTGAAGG
*
20099205 AATTGCAATTTGAATCTGA
66 AATTGCAATATGAATCTGA
20099224 AA
1 AA
20099226 TCTGTTTGGT
Statistics
Matches: 78, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
84 24 0.31
86 54 0.69
ACGTcount: A:0.27, C:0.14, G:0.30, T:0.29
Consensus pattern (84 bp):
AACCGGAGACCCTTAGGTGGCGTTTGGTTCGCTGGAATGTTCATGAGAGAATTGAAATCTGAAGG
AATTGCAATATGAATCTGA
Found at i:20099831 original size:27 final size:28
Alignment explanation
Indices: 20099801--20099865 Score: 114
Period size: 27 Copynumber: 2.4 Consensus size: 28
20099791 CCTAAACCCG
*
20099801 AACCCGACCCGAATATCACACTT-AAAA
1 AACCCGACCCGAATATCACAATTAAAAA
20099828 AACCCGACCCGAATATCACAATTAAAAA
1 AACCCGACCCGAATATCACAATTAAAAA
20099856 AACCCGACCC
1 AACCCGACCC
20099866 AACCCGAACC
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 22 0.61
28 14 0.39
ACGTcount: A:0.45, C:0.35, G:0.08, T:0.12
Consensus pattern (28 bp):
AACCCGACCCGAATATCACAATTAAAAA
Found at i:20099871 original size:33 final size:31
Alignment explanation
Indices: 20099794--20099873 Score: 87
Period size: 27 Copynumber: 2.6 Consensus size: 31
20099784 TTTTCACCCT
*
20099794 AAACCCGAACCCGACCCGAATATCACACTTAAA
1 AAACCCG-ACCC-ACCCGAATATCACAATTAAA
20099827 AAACCCG----ACCCGAATATCACAATTAAAA
1 AAACCCGACCCACCCGAATATCACAATT-AAA
20099855 AAACCCGACCCAACCCGAA
1 AAACCCGACCC-ACCCGAA
20099874 CCCGAACCCG
Statistics
Matches: 40, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
27 16 0.40
28 10 0.25
33 14 0.35
ACGTcount: A:0.45, C:0.36, G:0.09, T:0.10
Consensus pattern (31 bp):
AAACCCGACCCACCCGAATATCACAATTAAA
Found at i:20099932 original size:34 final size:35
Alignment explanation
Indices: 20099873--20099940 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
20099863 CCCAACCCGA
*
20099873 ACCCGAACCCGATTTTTTTTATAAAAAAAAATCCG
1 ACCCGAACCCAATTTTTTTTATAAAAAAAAATCCG
*
20099908 ACCCGATCCCAATTTTTTTT-TAAAAAAAAATCC
1 ACCCGAACCCAATTTTTTTTATAAAAAAAAATCC
20099941 CACCTGACCC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 13 0.42
35 18 0.58
ACGTcount: A:0.40, C:0.24, G:0.06, T:0.31
Consensus pattern (35 bp):
ACCCGAACCCAATTTTTTTTATAAAAAAAAATCCG
Found at i:20099982 original size:32 final size:32
Alignment explanation
Indices: 20099931--20100004 Score: 114
Period size: 32 Copynumber: 2.3 Consensus size: 32
20099921 TTTTTTTTAA
20099931 AAAAAAATCCCACCTGACCCGAATATCACACTT
1 AAAAAAA-CCCACCTGACCCGAATATCACACTT
*
20099964 TAAAAAACCCGACC-GACCCGAATATCACACTT
1 AAAAAAACCC-ACCTGACCCGAATATCACACTT
20099996 AAAAAAACC
1 AAAAAAACC
20100005 TAACCCGACC
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
32 29 0.76
33 9 0.24
ACGTcount: A:0.46, C:0.32, G:0.07, T:0.15
Consensus pattern (32 bp):
AAAAAAACCCACCTGACCCGAATATCACACTT
Found at i:20100013 original size:33 final size:32
Alignment explanation
Indices: 20099931--20100015 Score: 109
Period size: 32 Copynumber: 2.6 Consensus size: 32
20099921 TTTTTTTTAA
20099931 AAAAAAATCCC-ACCTGACCCGAATATCACACTT
1 AAAAAAA-CCCAACC-GACCCGAATATCACACTT
* *
20099964 TAAAAAACCCGACCGACCCGAATATCACACTT
1 AAAAAAACCCAACCGACCCGAATATCACACTT
*
20099996 AAAAAAACCTAACCCGACCC
1 AAAAAAACCCAA-CCGACCC
20100016 TGAAATTTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
32 30 0.65
33 16 0.35
ACGTcount: A:0.44, C:0.35, G:0.07, T:0.14
Consensus pattern (32 bp):
AAAAAAACCCAACCGACCCGAATATCACACTT
Found at i:20100804 original size:2 final size:2
Alignment explanation
Indices: 20100797--20100827 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
20100787 GTTGTTTTTA
20100797 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20100828 ATACCTTTGT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20101354 original size:2 final size:2
Alignment explanation
Indices: 20101349--20101436 Score: 76
Period size: 2 Copynumber: 46.0 Consensus size: 2
20101339 ATATAATTTA
* * *
20101349 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT GT GT AT AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
20101390 AT AT A- AT AT AT AT -T AT TT TT AT AT TT TT AT AT AA 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
20101430 A- AT AT AT
1 AT AT AT AT
20101437 TTTTTAATAA
Statistics
Matches: 72, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
1 4 0.06
2 68 0.94
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
AT
Found at i:20105516 original size:26 final size:26
Alignment explanation
Indices: 20105472--20105534 Score: 99
Period size: 26 Copynumber: 2.4 Consensus size: 26
20105462 TATCGACTAA
*
20105472 TTGTATGTTTAGTTCAATGGATTTCC
1 TTGTATGTTTTGTTCAATGGATTTCC
* *
20105498 TTGTATGTTTTGTTGAATGGCTTTCC
1 TTGTATGTTTTGTTCAATGGATTTCC
20105524 TTGTATGTTTT
1 TTGTATGTTTT
20105535 TCTTTTTATG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.14, C:0.10, G:0.21, T:0.56
Consensus pattern (26 bp):
TTGTATGTTTTGTTCAATGGATTTCC
Found at i:20110738 original size:14 final size:15
Alignment explanation
Indices: 20110719--20110747 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
20110709 CCTTGGAGTG
20110719 TATTGGTGA-GATTT
1 TATTGGTGAGGATTT
20110733 TATTGGTGAGGATTT
1 TATTGGTGAGGATTT
20110748 AAATCTTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.21, C:0.00, G:0.31, T:0.48
Consensus pattern (15 bp):
TATTGGTGAGGATTT
Found at i:20113349 original size:30 final size:30
Alignment explanation
Indices: 20113312--20113377 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
20113302 TGGGTCAACT
*
20113312 CGTTGACTTTGACCGAGTCAACCTGTTGAC
1 CGTTGACTTTGACCGAGTCAACCCGTTGAC
*
20113342 TGTTGACTTTGACCGAGTCAACCCGTTGAC
1 CGTTGACTTTGACCGAGTCAACCCGTTGAC
20113372 CGTTGA
1 CGTTGA
20113378 TCGTTGACTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.20, C:0.26, G:0.24, T:0.30
Consensus pattern (30 bp):
CGTTGACTTTGACCGAGTCAACCCGTTGAC
Found at i:20116170 original size:43 final size:43
Alignment explanation
Indices: 20116109--20116442 Score: 481
Period size: 43 Copynumber: 7.7 Consensus size: 43
20116099 GTTACCGCAT
*
20116109 GTTCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAG
1 GTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAG
20116152 GTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAG
1 GTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAG
*
20116195 GTTCCTTTTCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAG
1 GTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAG
* * *
20116238 GTTCCTTTGTTGTGTGCAAGGGTAAACCTTACAGTTTCCACAG
1 GTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAG
*
20116281 GTTCTTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCTAG
1 GTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC-AG
* *
20116325 GTTCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCTAG
1 GTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAG
* * * *
20116368 GTTTCTTTGTTGTGTGCAAGGGTAAGCCCTTATAGTTT-CTCAG
1 GTTCCTTTGCTGTGTGCAAGGGTAAG-CCTTACAGTTTCCCCAG
* * * * *
20116411 GCTCTTTTTCTATGTGTAAGGGTAAGACCTTA
1 GTTCCTTTGCTGTGTGCAAGGGTAAG-CCTTA
20116443 TCGTTTTTGC
Statistics
Matches: 264, Mismatches: 25, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
43 214 0.81
44 50 0.19
ACGTcount: A:0.17, C:0.22, G:0.25, T:0.37
Consensus pattern (43 bp):
GTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAG
Found at i:20116391 original size:130 final size:129
Alignment explanation
Indices: 20116109--20116442 Score: 510
Period size: 130 Copynumber: 2.6 Consensus size: 129
20116099 GTTACCGCAT
* * *
20116109 GTTCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGCTGTGTGCAAGGG
1 GTTCCTTTGTTGTGTGCAAGGGTAAACCTTACAGTTTCCACAGGTTCTTTTGCTGTGTGCAAGGG
20116174 TAAGCCTTACAGTTTCCCCAGGTTCCTTTTCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAG
66 TAAGCCTTACAGTTTCCCCAGGTTCCTTTTCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAG
20116238 GTTCCTTTGTTGTGTGCAAGGGTAAACCTTACAGTTTCCACAGGTTCTTTTGCTGTGTGCAAGGG
1 GTTCCTTTGTTGTGTGCAAGGGTAAACCTTACAGTTTCCACAGGTTCTTTTGCTGTGTGCAAGGG
*
20116303 TAAGCCTTACAGTTTCCCCTAGGTTCCTTTGT-TGTGTGCAAGGGTAAGCCTTACAGTTTCCCTA
66 TAAGCCTTACAGTTTCCCC-AGGTTCCTTT-TCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCA
20116367 G
129 G
* * * * * * * *
20116368 GTTTCTTTGTTGTGTGCAAGGGTAAGCCCTTATAGTTT-CTCAGGCTCTTTTTCTATGTGTAAGG
1 GTTCCTTTGTTGTGTGCAAGGGTAA-ACCTTACAGTTTCCACAGGTTCTTTTGCTGTGTGCAAGG
20116432 GTAAGACCTTA
65 GTAAG-CCTTA
20116443 TCGTTTTTGC
Statistics
Matches: 189, Mismatches: 12, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
129 81 0.43
130 92 0.49
131 16 0.08
ACGTcount: A:0.17, C:0.22, G:0.25, T:0.37
Consensus pattern (129 bp):
GTTCCTTTGTTGTGTGCAAGGGTAAACCTTACAGTTTCCACAGGTTCTTTTGCTGTGTGCAAGGG
TAAGCCTTACAGTTTCCCCAGGTTCCTTTTCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAG
Found at i:20121275 original size:43 final size:43
Alignment explanation
Indices: 20121214--20121469 Score: 352
Period size: 43 Copynumber: 5.9 Consensus size: 43
20121204 ATCGTTACCG
* * * *
20121214 CAGGTTCCTTTGCTGTGTGCAAAGGTAAGCATTACAGTTTCCC
1 CAGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTATAGTTTCCC
20121257 CAGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTATAGTTTCCC
1 CAGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTATAGTTTCCC
20121300 CAGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTATAGTTTCCC
1 CAGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTATAGTTTCCC
* *
20121343 CAGGTTCCTTTGTTGTGTACAAGGGTAAGCCTTACAGTTTCCC
1 CAGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTATAGTTTCCC
* * *
20121386 TAGGTTTCTATGTTGTGTGCAAGGGTAAGACCTTATAGTTT-CC
1 CAGGTTCCTTTGTTGTGTGCAAGGGTAAG-CCTTATAGTTTCCC
* * * * * *
20121429 CAAGCTCTTTTGCTATGTGCAAGGGTAAGGCCTTATCGTTT
1 CAGGTTCCTTTGTTGTGTGCAAGGGTAA-GCCTTATAGTTT
20121470 TTGCATGCTC
Statistics
Matches: 191, Mismatches: 20, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
43 180 0.94
44 11 0.06
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (43 bp):
CAGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTATAGTTTCCC
Found at i:20122504 original size:17 final size:17
Alignment explanation
Indices: 20122464--20122525 Score: 72
Period size: 17 Copynumber: 3.6 Consensus size: 17
20122454 ATTCATGCAT
20122464 CTAGTTCATTGAA-TAAA
1 CTAGTTCATT-AATTAAA
20122481 GCTAGTTCATTAATTAAA
1 -CTAGTTCATTAATTAAA
* *
20122499 CTAGTTCATTCATCAAA
1 CTAGTTCATTAATTAAA
*
20122516 TTAGTTCATT
1 CTAGTTCATT
20122526 TACTAGACTA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
17 26 0.65
18 14 0.35
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (17 bp):
CTAGTTCATTAATTAAA
Found at i:20127777 original size:20 final size:20
Alignment explanation
Indices: 20127700--20127779 Score: 63
Period size: 20 Copynumber: 3.9 Consensus size: 20
20127690 AGAACCCCAG
* * *
20127700 GGGGGTATCGATTCCCCTGT
1 GGGGGAATCGATTCCCTTAT
* *
20127720 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGATT-CCCTT--AT
20127743 GGGGGAATC-AGTTCCCTTAT
1 GGGGGAATCGA-TTCCCTTAT
*
20127763 GGGGGGATCGATTCCCT
1 GGGGGAATCGATTCCCT
20127780 CTGTACCAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
20 26 0.55
21 5 0.11
22 5 0.11
23 11 0.23
ACGTcount: A:0.16, C:0.24, G:0.34, T:0.26
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTTAT
Found at i:20131633 original size:22 final size:21
Alignment explanation
Indices: 20131591--20131630 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
20131581 GAGTTTGTTT
*
20131591 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
20131612 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
20131631 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:20136757 original size:26 final size:26
Alignment explanation
Indices: 20136723--20136796 Score: 139
Period size: 26 Copynumber: 2.8 Consensus size: 26
20136713 CATGAAATTA
*
20136723 AAAATATTAGGCAGATATAGTTATTT
1 AAAATATTAGGCAGATATAGTTAGTT
20136749 AAAATATTAGGCAGATATAGTTAGTT
1 AAAATATTAGGCAGATATAGTTAGTT
20136775 AAAATATTAGGCAGATATAGTT
1 AAAATATTAGGCAGATATAGTT
20136797 GAATGGCCTA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 47 1.00
ACGTcount: A:0.43, C:0.04, G:0.18, T:0.35
Consensus pattern (26 bp):
AAAATATTAGGCAGATATAGTTAGTT
Found at i:20154092 original size:19 final size:18
Alignment explanation
Indices: 20154067--20154108 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
20154057 GTTATATGAC
*
20154067 TAGGGGTATTAGTACCCA
1 TAGGGGTATCAGTACCCA
*
20154085 TGAGGGGTATCGGTACCCA
1 T-AGGGGTATCAGTACCCA
20154104 TAGGG
1 TAGGG
20154109 CATTCTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.24, C:0.17, G:0.36, T:0.24
Consensus pattern (18 bp):
TAGGGGTATCAGTACCCA
Found at i:20156265 original size:13 final size:13
Alignment explanation
Indices: 20156247--20156281 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
20156237 ATGGGCAAAT
20156247 TTTGAAAACT-ATG
1 TTTGAAAA-TAATG
20156260 TTTGAAAATAATG
1 TTTGAAAATAATG
20156273 TTTGAAAAT
1 TTTGAAAAT
20156282 CAATATGTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 1 0.05
13 20 0.95
ACGTcount: A:0.43, C:0.03, G:0.14, T:0.40
Consensus pattern (13 bp):
TTTGAAAATAATG
Found at i:20160176 original size:9 final size:9
Alignment explanation
Indices: 20160162--20160238 Score: 59
Period size: 9 Copynumber: 8.4 Consensus size: 9
20160152 ATTAGGGTTA
*
20160162 AAATAAAGT
1 AAATAAAAT
20160171 AAAT-AAAT
1 AAATAAAAT
*
20160179 AATTAAAAT
1 AAATAAAAT
20160188 AACATAAAAT
1 AA-ATAAAAT
20160198 AAATATTAAAT
1 AAATA--AAAT
*
20160209 AAATAAAAG
1 AAATAAAAT
* *
20160218 AAA-GAAAG
1 AAATAAAAT
*
20160226 AAATAAAAG
1 AAATAAAAT
20160235 AAAT
1 AAAT
20160239 TTTAAATTAA
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
8 13 0.23
9 27 0.47
10 8 0.14
11 9 0.16
ACGTcount: A:0.71, C:0.01, G:0.06, T:0.21
Consensus pattern (9 bp):
AAATAAAAT
Found at i:20160186 original size:22 final size:20
Alignment explanation
Indices: 20160159--20160215 Score: 71
Period size: 22 Copynumber: 2.7 Consensus size: 20
20160149 AGCATTAGGG
20160159 TTAAAATAAAGTAAATAAATAA
1 TTAAAATAAA-TAAATAAAT-A
20160181 TTAAAATAACATAAAATAAATA
1 TTAAAATAA-AT-AAATAAATA
20160203 TT-AAATAAATAAA
1 TTAAAATAAATAAA
20160216 AGAAAGAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
19 3 0.09
20 2 0.06
21 6 0.18
22 13 0.39
23 9 0.27
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (20 bp):
TTAAAATAAATAAATAAATA
Found at i:20160673 original size:89 final size:89
Alignment explanation
Indices: 20160522--20160700 Score: 358
Period size: 89 Copynumber: 2.0 Consensus size: 89
20160512 CAATTTATTT
20160522 GTAACCAAATTCACAAAAAAAAAACTCTCCCATCTTCAAAAACCTCTCAACCCAATCCCCCAACT
1 GTAACCAAATTCACAAAAAAAAAACTCTCCCATCTTCAAAAACCTCTCAACCCAATCCCCCAACT
20160587 GCCCAAGTGTCGGCCAACTTCCCC
66 GCCCAAGTGTCGGCCAACTTCCCC
20160611 GTAACCAAATTCACAAAAAAAAAACTCTCCCATCTTCAAAAACCTCTCAACCCAATCCCCCAACT
1 GTAACCAAATTCACAAAAAAAAAACTCTCCCATCTTCAAAAACCTCTCAACCCAATCCCCCAACT
20160676 GCCCAAGTGTCGGCCAACTTCCCC
66 GCCCAAGTGTCGGCCAACTTCCCC
20160700 G
1 G
20160701 GTGGGACACC
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 90 1.00
ACGTcount: A:0.36, C:0.39, G:0.07, T:0.18
Consensus pattern (89 bp):
GTAACCAAATTCACAAAAAAAAAACTCTCCCATCTTCAAAAACCTCTCAACCCAATCCCCCAACT
GCCCAAGTGTCGGCCAACTTCCCC
Found at i:20161368 original size:5 final size:5
Alignment explanation
Indices: 20161358--20161440 Score: 65
Period size: 5 Copynumber: 17.4 Consensus size: 5
20161348 AATAAAAAAT
*
20161358 TAATA TAATA TAATA -AAAA TAATACA TAATA -AATA TAA-A -AATA TAATA
1 TAATA TAATA TAATA TAATA TAAT--A TAATA TAATA TAATA TAATA TAATA
20161406 T--TA TAATA T-ATGA T-ATA TATATA TAATA TAATA TA
1 TAATA TAATA TAAT-A TAATA TA-ATA TAATA TAATA TA
20161441 TAATAAAAAC
Statistics
Matches: 65, Mismatches: 2, Indels: 22
0.73 0.02 0.25
Matches are distributed among these distances:
3 5 0.08
4 13 0.20
5 37 0.57
6 5 0.08
7 5 0.08
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (5 bp):
TAATA
Found at i:20161374 original size:21 final size:21
Alignment explanation
Indices: 20161348--20161413 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
20161338 ATCTAGACCA
20161348 AATAAAAAATTAATATAATAT
1 AATAAAAAATTAATATAATAT
20161369 AAT-AAAAA-TAATACATAATA-
1 AATAAAAAATTAAT--ATAATAT
20161389 AATATAAAAATATAATAT--TAT
1 AATA-AAAAAT-TAATATAATAT
20161410 AATA
1 AATA
20161414 TATGATATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
19 4 0.11
20 10 0.26
21 13 0.34
22 7 0.18
24 4 0.11
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (21 bp):
AATAAAAAATTAATATAATAT
Found at i:20161401 original size:8 final size:9
Alignment explanation
Indices: 20161349--20161440 Score: 59
Period size: 8 Copynumber: 10.3 Consensus size: 9
20161339 TCTAGACCAA
*
20161349 ATAAAAAAT
1 ATAATAAAT
20161358 -TAATATAAT
1 ATAATA-AAT
*
20161367 ATAATAAAA
1 ATAATAAAT
*
20161376 ATAAT--AC
1 ATAATAAAT
20161383 ATAATAAAT
1 ATAATAAAT
20161392 ATAA-AAAT
1 ATAATAAAT
*
20161400 ATAAT-ATT
1 ATAATAAAT
*
20161408 ATAATATAT
1 ATAATAAAT
*
20161417 GATATATATAT
1 -ATA-ATAAAT
20161428 ATAATATAAT
1 ATAATA-AAT
20161438 ATA
1 ATA
20161441 TAATAAAAAC
Statistics
Matches: 66, Mismatches: 8, Indels: 17
0.73 0.09 0.19
Matches are distributed among these distances:
7 6 0.09
8 19 0.29
9 19 0.29
10 16 0.24
11 6 0.09
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (9 bp):
ATAATAAAT
Found at i:20161421 original size:28 final size:28
Alignment explanation
Indices: 20161360--20161464 Score: 82
Period size: 25 Copynumber: 3.9 Consensus size: 28
20161350 TAAAAAATTA
* *
20161360 ATATAATATAATAAAAATAATA-CAT-A-
1 ATATAATATAA-AAATATAATATTATAAT
20161386 ATA-AATATAAAAATATAATATTATAAT
1 ATATAATATAAAAATATAATATTATAAT
* * *
20161413 ATATGATAT--ATATAT-ATAATATAAT
1 ATATAATATAAAAATATAATATTATAAT
20161438 ATATAATA-AAAACTATATAATATTATA
1 ATATAATATAAAA--ATATAATATTATA
20161465 TTTTCGAAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 15
0.73 0.09 0.18
Matches are distributed among these distances:
24 9 0.15
25 25 0.40
26 10 0.16
27 3 0.05
28 8 0.13
29 7 0.11
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.37
Consensus pattern (28 bp):
ATATAATATAAAAATATAATATTATAAT
Found at i:20161430 original size:20 final size:20
Alignment explanation
Indices: 20161398--20161445 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
20161388 AAATATAAAA
20161398 ATATAATATTATAATATATG
1 ATATAATATTATAATATATG
20161418 ATAT-ATATATATAATATAAT-
1 ATATAATAT-TATAATAT-ATG
20161438 ATATAATA
1 ATATAATA
20161446 AAAACTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 4 0.16
20 16 0.64
21 5 0.20
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
ATATAATATTATAATATATG
Found at i:20161440 original size:38 final size:35
Alignment explanation
Indices: 20161349--20161438 Score: 91
Period size: 32 Copynumber: 2.7 Consensus size: 35
20161339 TCTAGACCAA
*
20161349 ATAAAAAAT-TAATATAATATAATAAAAATAATAC
1 ATAATAAATATAATATAATATAATAAAAATAATAC
** *
20161383 ATAATAAATATAA-A-AATATAAT-ATTATAATAT
1 ATAATAAATATAATATAATATAATAAAAATAATAC
* *
20161415 ATGATATATAT-ATATAATATAATA
1 ATAATAAATATAATATAATATAATA
20161439 TATAATAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
31 1 0.02
32 17 0.37
33 16 0.35
34 9 0.20
35 3 0.07
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (35 bp):
ATAATAAATATAATATAATATAATAAAAATAATAC
Found at i:20161599 original size:36 final size:35
Alignment explanation
Indices: 20161532--20161664 Score: 157
Period size: 36 Copynumber: 3.8 Consensus size: 35
20161522 ATTGTTTTAA
*
20161532 AAAACTATA-AATAT--GTTTTCCAAATATGTTTTT
1 AAAACTATATAATATACGTTTT-CAAAAATGTTTTT
*
20161565 AAAACTATATCATATACGTTTTCAAAAATCGTTTTT
1 AAAACTATATAATATACGTTTTCAAAAAT-GTTTTT
20161601 AAAACTATA-AATTATACGTTTTCAAAAATGTGTTTT
1 AAAACTATATAA-TATACGTTTTCAAAAATGT-TTTT
* *
20161637 CAAAAATATATAATATATGTTTTCAAAA
1 -AAAACTATATAATATACGTTTTCAAAA
20161665 CCGTATTATA
Statistics
Matches: 87, Mismatches: 5, Indels: 12
0.84 0.05 0.12
Matches are distributed among these distances:
33 9 0.10
34 4 0.05
35 9 0.10
36 41 0.47
37 22 0.25
38 2 0.02
ACGTcount: A:0.43, C:0.10, G:0.06, T:0.41
Consensus pattern (35 bp):
AAAACTATATAATATACGTTTTCAAAAATGTTTTT
Found at i:20161647 original size:73 final size:69
Alignment explanation
Indices: 20161532--20161664 Score: 178
Period size: 73 Copynumber: 1.9 Consensus size: 69
20161522 ATTGTTTTAA
* * *
20161532 AAAACTATAAATATGTTTTCCAAATATGTTTTTAAAACTATATCATATACGTTTTCAAAAATCGT
1 AAAACTATAAATATGTTTTCCAAAAATGTTTTTAAAAATATATAATATACGTTTTCAAAAATCGT
20161597 TTTT
66 TTTT
*
20161601 AAAACTATAAATTATACGTTTT-CAAAAATGTGTTTTCAAAAATATATAATATATGTTTTCAAAA
1 AAAACTATAAA-TAT--GTTTTCCAAAAATGT-TTTT-AAAAATATATAATATACGTTTTCAAAA
20161665 CCGTATTATA
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
69 11 0.20
70 3 0.05
71 8 0.15
72 9 0.16
73 24 0.44
ACGTcount: A:0.43, C:0.10, G:0.06, T:0.41
Consensus pattern (69 bp):
AAAACTATAAATATGTTTTCCAAAAATGTTTTTAAAAATATATAATATACGTTTTCAAAAATCGT
TTTT
Found at i:20161675 original size:23 final size:23
Alignment explanation
Indices: 20161631--20161687 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 23
20161621 TTCAAAAATG
*
20161631 TGTTTTCAAAAATATATAATATA
1 TGTTTTCAAAAACATATAATATA
* *
20161654 TGTTTTCAAAACCGTAT--TATA
1 TGTTTTCAAAAACATATAATATA
*
20161675 TATTTTCAAAAAC
1 TGTTTTCAAAAAC
20161688 CGATTTTTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
21 15 0.52
23 14 0.48
ACGTcount: A:0.42, C:0.11, G:0.05, T:0.42
Consensus pattern (23 bp):
TGTTTTCAAAAACATATAATATA
Found at i:20161778 original size:37 final size:37
Alignment explanation
Indices: 20161699--20161781 Score: 107
Period size: 39 Copynumber: 2.2 Consensus size: 37
20161689 GATTTTTTTT
*
20161699 AAAACTATATATTATATGTTTTTTTTAAAACGTTTTCTA
1 AAAACTATATATTATATG--TTTTTTAAAACATTTTCTA
20161738 AAAACTATATATTATATG-TTTTTAAAACATATTT-TCA
1 AAAACTATATATTATATGTTTTTTAAAACAT-TTTCT-A
20161775 AAAACTA
1 AAAACTA
20161782 CATTTTATTA
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
36 12 0.29
37 11 0.27
39 18 0.44
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (37 bp):
AAAACTATATATTATATGTTTTTTAAAACATTTTCTA
Found at i:20162958 original size:14 final size:14
Alignment explanation
Indices: 20162939--20162973 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
20162929 AAGTGAAAGA
20162939 ATAGTTATATAATT
1 ATAGTTATATAATT
20162953 ATAGTTATATAATT
1 ATAGTTATATAATT
20162967 AT-GTTAT
1 ATAGTTAT
20162974 GATTTTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.24
14 16 0.76
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (14 bp):
ATAGTTATATAATT
Found at i:20166644 original size:51 final size:53
Alignment explanation
Indices: 20166584--20166685 Score: 163
Period size: 54 Copynumber: 1.9 Consensus size: 53
20166574 TTTAGTGCAT
20166584 TTTTATCATATGCA-CCCATAGTGC-TATAATCAGCTTGGCACCTTTTATGCC
1 TTTTATCATATGCACCCCATAGTGCATATAATCAGCTTGGCACCTTTTATGCC
* *
20166635 TTTTATCATATGCACCCCATAGTGCTATATAATCAGTTTGGTACCTTTTAT
1 TTTTATCATATGCACCCCATAGTGC-ATATAATCAGCTTGGCACCTTTTAT
20166686 ATTTTTTATC
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
51 14 0.30
52 10 0.22
54 22 0.48
ACGTcount: A:0.25, C:0.23, G:0.13, T:0.40
Consensus pattern (53 bp):
TTTTATCATATGCACCCCATAGTGCATATAATCAGCTTGGCACCTTTTATGCC
Found at i:20166693 original size:54 final size:51
Alignment explanation
Indices: 20166583--20166697 Score: 158
Period size: 54 Copynumber: 2.2 Consensus size: 51
20166573 ATTTAGTGCA
*
20166583 TTTTTATCATATGCACCCATAGTGCTATAATCAGCTTGGCACCTTTTATGC
1 TTTTTATCATATGCACCCATAGTGCTATAATCAGCTTGGCACCTTTTATAC
* * * *
20166634 CTTTTATCATATGCACCCCATAGTGCTATATAATCAGTTTGGTACCTTTTATAT
1 TTTTTATCATATGCA-CCCATAGTGC--TATAATCAGCTTGGCACCTTTTATAC
20166688 TTTTTATCAT
1 TTTTTATCAT
20166698 TTGTGTAGAG
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
51 14 0.25
52 10 0.18
54 31 0.56
ACGTcount: A:0.24, C:0.21, G:0.11, T:0.43
Consensus pattern (51 bp):
TTTTTATCATATGCACCCATAGTGCTATAATCAGCTTGGCACCTTTTATAC
Found at i:20168587 original size:8 final size:8
Alignment explanation
Indices: 20168576--20168604 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
20168566 TTATTTTATA
20168576 AAAAAAGC
1 AAAAAAGC
20168584 AAAAAAGC
1 AAAAAAGC
20168592 AAAAAAG-
1 AAAAAAGC
20168599 AAAAAA
1 AAAAAA
20168605 AATATTGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 6 0.29
8 15 0.71
ACGTcount: A:0.83, C:0.07, G:0.10, T:0.00
Consensus pattern (8 bp):
AAAAAAGC
Found at i:20169596 original size:16 final size:16
Alignment explanation
Indices: 20169575--20169620 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
20169565 ATTCTATGCG
20169575 ATGTTTTTTTATTTTT
1 ATGTTTTTTTATTTTT
* *
20169591 ATGTTTATTTAGTTTT
1 ATGTTTTTTTATTTTT
20169607 AT-TTTATTTTATTT
1 ATGTTT-TTTTATTT
20169621 ATTAACCATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
15 3 0.12
16 22 0.88
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (16 bp):
ATGTTTTTTTATTTTT
Found at i:20170002 original size:99 final size:96
Alignment explanation
Indices: 20169652--20170023 Score: 404
Period size: 97 Copynumber: 3.8 Consensus size: 96
20169642 TATCGCTCCT
* * * * * * *
20169652 AATTATTATACGATCTTGTGGTGACCCGATTCGGGCTATGATCCGCATTATTACGATCCGAACTT
1 AATTATTATACGACCTTGTGGTGACCCGATCCGGGGTATGATCCGCATTATTATGGTCTGGAC--
*
20169717 TACTAATTTCAAACT-CTAACCTTTTTATTAATTTGTTTG
64 T-CT-A-TT--AACTCCT-A-TTTTTTATTAATTTGTTTG
** *
20169756 AATTATTATACGACCTTGTGGTGACATGATACGGGGTATGATCCGCATTATTATGGTCTGGACTC
1 AATTATTATACGACCTTGTGGTGACCCGATCCGGGGTATGATCCGCATTATTATGGTCTGGACTC
20169821 TATTAACTCCTATTTTTTTATTAATTTGTTTG
66 TATTAACTCCTA-TTTTTTATTAATTTGTTTG
* * * * *
20169853 AATTATTATACGGCCTTATGGTGATCCGATCTGGGGTATGATCCACATTATTATGGTCTGGACTC
1 AATTATTATACGACCTTGTGGTGACCCGATCCGGGGTATGATCCGCATTATTATGGTCTGGACTC
20169918 TATTAACTCCTACATTTTTATATTAATTTGTTTG
66 TATTAACTCCT--ATTTTT-TATTAATTTGTTTG
* * * * * * * *
20169952 AATTATTATATGACCTCGCGGTGACCCGATCCGGGGTACGACCCGTATTATTACGGTCCGGACTC
1 AATTATTATACGACCTTGTGGTGACCCGATCCGGGGTATGATCCGCATTATTATGGTCTGGACTC
20170017 TATTAAC
66 TATTAAC
20170024 AACTAACTTT
Statistics
Matches: 232, Mismatches: 32, Indels: 13
0.84 0.12 0.05
Matches are distributed among these distances:
97 91 0.39
98 7 0.03
99 76 0.33
100 1 0.00
101 2 0.01
102 1 0.00
104 54 0.23
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.39
Consensus pattern (96 bp):
AATTATTATACGACCTTGTGGTGACCCGATCCGGGGTATGATCCGCATTATTATGGTCTGGACTC
TATTAACTCCTATTTTTTATTAATTTGTTTG
Found at i:20170286 original size:14 final size:14
Alignment explanation
Indices: 20170267--20170302 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
20170257 TTTTTATTTA
*
20170267 TTTAATTTCAGTCC
1 TTTAATTTCAGTAC
*
20170281 TTTAATTTCATTAC
1 TTTAATTTCAGTAC
20170295 TTTAATTT
1 TTTAATTT
20170303 ACTATTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.25, C:0.14, G:0.03, T:0.58
Consensus pattern (14 bp):
TTTAATTTCAGTAC
Found at i:20170709 original size:177 final size:177
Alignment explanation
Indices: 20170413--20170766 Score: 708
Period size: 177 Copynumber: 2.0 Consensus size: 177
20170403 TGTCCTTGAT
20170413 AGATCACCTTTTTTAGATTTAGTCCATAGTCTTTTAATTATTTGATTCATATTTAGTTATTAAAT
1 AGATCACCTTTTTTAGATTTAGTCCATAGTCTTTTAATTATTTGATTCATATTTAGTTATTAAAT
20170478 TAGAAGAATTCTTAATTTGGTCATCGTTTTTGCTCGAGGTTCCAATTTAATTATTCGAATTGTAA
66 TAGAAGAATTCTTAATTTGGTCATCGTTTTTGCTCGAGGTTCCAATTTAATTATTCGAATTGTAA
20170543 TATTGATTAAAATCAAGTAGCATTAATATTAGAGTCTGCATTTTTAG
131 TATTGATTAAAATCAAGTAGCATTAATATTAGAGTCTGCATTTTTAG
20170590 AGATCACCTTTTTTAGATTTAGTCCATAGTCTTTTAATTATTTGATTCATATTTAGTTATTAAAT
1 AGATCACCTTTTTTAGATTTAGTCCATAGTCTTTTAATTATTTGATTCATATTTAGTTATTAAAT
20170655 TAGAAGAATTCTTAATTTGGTCATCGTTTTTGCTCGAGGTTCCAATTTAATTATTCGAATTGTAA
66 TAGAAGAATTCTTAATTTGGTCATCGTTTTTGCTCGAGGTTCCAATTTAATTATTCGAATTGTAA
20170720 TATTGATTAAAATCAAGTAGCATTAATATTAGAGTCTGCATTTTTAG
131 TATTGATTAAAATCAAGTAGCATTAATATTAGAGTCTGCATTTTTAG
20170767 GTTTATACCT
Statistics
Matches: 177, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
177 177 1.00
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.45
Consensus pattern (177 bp):
AGATCACCTTTTTTAGATTTAGTCCATAGTCTTTTAATTATTTGATTCATATTTAGTTATTAAAT
TAGAAGAATTCTTAATTTGGTCATCGTTTTTGCTCGAGGTTCCAATTTAATTATTCGAATTGTAA
TATTGATTAAAATCAAGTAGCATTAATATTAGAGTCTGCATTTTTAG
Found at i:20175756 original size:95 final size:96
Alignment explanation
Indices: 20175583--20175851 Score: 389
Period size: 96 Copynumber: 2.8 Consensus size: 96
20175573 AGCAAAGATA
* * *
20175583 AAAAATTTCTCACTTGAGATGG-TTTTCTTAAAATCAATTTCATTTTTTTTGAAATACTTCCCCT
1 AAAAATTTATCACTTGAGATGGTTTTTCTTAAAATC-A----ATTTTTCTTGAAATAGTTCCCCT
20175647 TGGAACACATATTTTGAAATTTTTT-CACTCGAAAC
61 TGGAACACATATTTTGAAATTTTTTCCACTCGAAAC
*
20175682 AAAAATTTATCACTTGAGATGGTTTTTCTTAAAATCAATTTTGCTTGAAATAGTTCCCCTTGGAA
1 AAAAATTTATCACTTGAGATGGTTTTTCTTAAAATCAATTTTTCTTGAAATAGTTCCCCTTGGAA
* * *
20175747 CACAGATTTTGAATTTTTTTCCCCTCGAAAC
66 CACATATTTTGAAATTTTTTCCACTCGAAAC
* * *
20175778 AAAAATTTATCATTTGAAATGGTTTTTCTTAAAATCAATTTTTCTTGAGATAGTTCCCCTTGGAA
1 AAAAATTTATCACTTGAGATGGTTTTTCTTAAAATCAATTTTTCTTGAAATAGTTCCCCTTGGAA
20175843 CACATATTT
66 CACATATTT
20175852 GGAATTGTTT
Statistics
Matches: 156, Mismatches: 12, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
95 43 0.28
96 78 0.50
99 22 0.14
100 13 0.08
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42
Consensus pattern (96 bp):
AAAAATTTATCACTTGAGATGGTTTTTCTTAAAATCAATTTTTCTTGAAATAGTTCCCCTTGGAA
CACATATTTTGAAATTTTTTCCACTCGAAAC
Found at i:20177803 original size:4 final size:5
Alignment explanation
Indices: 20177747--20177800 Score: 56
Period size: 5 Copynumber: 10.6 Consensus size: 5
20177737 TGATTCTATG
** *
20177747 TTTT- TTTTA TTTTTA TGTTTA TTTGG TTCTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA -TTTTA T-TTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
20177798 TTT
1 TTT
20177801 ATTAATCATT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
4 4 0.10
5 27 0.66
6 10 0.24
ACGTcount: A:0.15, C:0.02, G:0.06, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:20177944 original size:102 final size:96
Alignment explanation
Indices: 20177832--20178180 Score: 329
Period size: 96 Copynumber: 3.6 Consensus size: 96
20177822 TATCGCTCCT
* * * *
20177832 AATTATTATACGATCTTGTGGTGACCCGATCTGGGGTATGACCCGCATTATTACAATCCAAACTT
1 AATTATTATACGACCTTGTGGTGACCCGATCCGGGGTATGATCCGCATTATTACAATCCAAACTC
* *
20177897 TACTTATTTCTAATCTAACCTTTTATTAATTTGTTAA
66 TA-TTA--ACT--CCT-ACCTTTTATTAATTTGTTAA
* * *** *
20177934 AATTATTATACGACCTTGTGGTGACCCGATCCAGGGTATGATCTGCATTATTATGGTCCGAACTC
1 AATTATTATACGACCTTGTGGTGACCCGATCCGGGGTATGATCCGCATTATTACAATCCAAACTC
* **
20177999 TATTAACTCCTACTTTTTATTAATTTGTTTG
66 TATTAACTCCTACCTTTTATTAATTTGTTAA
* *** **
20178030 AATTATTATACGACCTTGTGGTGACCCGATCCGGGGTATGATTCGCATTATTATGGTCCGGACTC
1 AATTATTATACGACCTTGTGGTGACCCGATCCGGGGTATGATCCGCATTATTACAATCCAAACTC
* ** **
20178095 TATGAACTCCTATTTTTTTTATTAATTTGTTTG
66 TATTAACTCCTA--CCTTTTATTAATTTGTTAA
* * * ** * *
20178128 AATTATTATATGACTTTGTGGTGACCCTATCCCAGGTATAACCCGCATTATTA
1 AATTATTATACGACCTTGTGGTGACCCGATCCGGGGTATGATCCGCATTATTA
20178181 TGGTATGGAC
Statistics
Matches: 216, Mismatches: 29, Indels: 8
0.85 0.11 0.03
Matches are distributed among these distances:
96 89 0.41
97 2 0.01
98 63 0.29
99 2 0.01
101 3 0.01
102 57 0.26
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.40
Consensus pattern (96 bp):
AATTATTATACGACCTTGTGGTGACCCGATCCGGGGTATGATCCGCATTATTACAATCCAAACTC
TATTAACTCCTACCTTTTATTAATTTGTTAA
Found at i:20178048 original size:96 final size:97
Alignment explanation
Indices: 20177917--20178199 Score: 392
Period size: 96 Copynumber: 2.9 Consensus size: 97
20177907 TAATCTAACC
**
20177917 TTTTATTAATTTGTTAAAATTATTATACGACCTTGTGGTGACCCGATCCAGGGTATGATCTGCAT
1 TTTTATTAATTTGTTTGAATTATTATACGACCTTGTGGTGACCCGATCCAGGGTATGATCTGCAT
*
20177982 TATTATGGTCCGAACTCTATTAACTCCTA-CT
66 TATTATGGTCCGGACTCTATTAACTCCTATCT
*
20178013 TTTTATTAATTTGTTTGAATTATTATACGACCTTGTGGTGACCCGATCCGGGGTATGAT-TCGCA
1 TTTTATTAATTTGTTTGAATTATTATACGACCTTGTGGTGACCCGATCCAGGGTATGATCT-GCA
* *
20178077 TTATTATGGTCCGGACTCTATGAACTCCTATTTT
65 TTATTATGGTCCGGACTCTATTAACTCCTA-TCT
* * * * * *
20178111 TTTTATTAATTTGTTTGAATTATTATATGACTTTGTGGTGACCCTATCCCA-GGTATAACCCGCA
1 TTTTATTAATTTGTTTGAATTATTATACGACCTTGTGGTGACCCGAT-CCAGGGTATGATCTGCA
**
20178175 TTATTATGGTATGGACTCTATTAAC
65 TTATTATGGTCCGGACTCTATTAAC
20178200 AACTAACTTT
Statistics
Matches: 166, Mismatches: 16, Indels: 8
0.87 0.08 0.04
Matches are distributed among these distances:
95 1 0.01
96 87 0.52
98 76 0.46
99 2 0.01
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.41
Consensus pattern (97 bp):
TTTTATTAATTTGTTTGAATTATTATACGACCTTGTGGTGACCCGATCCAGGGTATGATCTGCAT
TATTATGGTCCGGACTCTATTAACTCCTATCT
Found at i:20181813 original size:19 final size:18
Alignment explanation
Indices: 20181789--20181824 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
20181779 TTGTCTGTTT
20181789 TATTTTTAATGATTTTATA
1 TATTTTTAAT-ATTTTATA
*
20181808 TATTTTTTATATTTTAT
1 TATTTTTAATATTTTAT
20181825 TTATGTGTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (18 bp):
TATTTTTAATATTTTATA
Found at i:20188362 original size:14 final size:14
Alignment explanation
Indices: 20188343--20188370 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
20188333 TGTTTGCAAG
20188343 TTATTAAATGTAGA
1 TTATTAAATGTAGA
20188357 TTATTAAATGTAGA
1 TTATTAAATGTAGA
20188371 GGTATTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (14 bp):
TTATTAAATGTAGA
Found at i:20191292 original size:17 final size:17
Alignment explanation
Indices: 20191270--20191342 Score: 83
Period size: 17 Copynumber: 4.2 Consensus size: 17
20191260 CAATTAAGAG
20191270 CTAGTTTAATAAATGAA
1 CTAGTTTAATAAATGAA
* *
20191287 CTAGTTTGATGAATGAA
1 CTAGTTTAATAAATGAA
*
20191304 CTAGTTTAATTAATGAA
1 CTAGTTTAATAAATGAA
* * *
20191321 CTAACTTTATTCAATGAA
1 CT-AGTTTAATAAATGAA
20191339 CTAG
1 CTAG
20191343 ATGCATGAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
17 33 0.70
18 14 0.30
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.37
Consensus pattern (17 bp):
CTAGTTTAATAAATGAA
Found at i:20194262 original size:182 final size:180
Alignment explanation
Indices: 20193832--20194269 Score: 467
Period size: 182 Copynumber: 2.4 Consensus size: 180
20193822 GTGCCAAATT
* * * * * *
20193832 AAAGGCATATAGTGACAAATTTTGTAACTAGAAGTTTTAGTAACTATGACAGAAAAAAATTGTCA
1 AAAGTCATATAGTGACAAATTTTGTAACTATAAG-TATAATAATTATTACA-AAAAAAATTGTCA
* **
20193897 CAACAAATAATGAGATTTAGATTTGTTGTGACAAAATTTTTTTTGTAATTATATATTTTAATTAT
64 CAACAAATAATGAGATTTAGATTTGTTGTGAAAAAATAGTTTTTGTAATTATATATTTTAATTAT
* *
20193962 AGTGACAAAATGTATATTCACAAATGATTATCTCCAAATTTTTGTACAAAAAAC
129 AGTGACAAAA-GTATATTCACAAA-GAATACCTCCAAATTTTTGTACAAAAAAC
* ** * * *
20194016 AAAATCATATAGTGACATGTTTTGTAACTATAAGCTATAATTATTGTTACAAAAAAAGTTGTCAC
1 AAAGTCATATAGTGACAAATTTTGTAACTATAAG-TATAATAATTATTACAAAAAAAATTGTCAC
**
20194081 AACAAATAATGAGATTTA-AGTTT-TTAGT-AAAAAATAGTTTTTGTTGTTATATATTTTAATTA
65 AACAAATAATGAGATTTAGA-TTTGTT-GTGAAAAAATAGTTTTTGTAATTATATATTTTAATTA
* * * * * *
20194143 TAGTGACAAAA-TATACTGTCACAAA-AATACCCCTCTATATTTTTTTGCGACAAA-
128 TAGTGACAAAAGTATA-T-TCACAAAGAATA--CCTCCAAATTTTTGTACAAAAAAC
* *
20194197 AAAGTCATATTGTGACAAATTTTGTAACTATAAGTGCTAATAATTATTACAAAAAAACATTGTCA
1 AAAGTCATATAGTGACAAATTTTGTAACTATAAGT-ATAATAATTATTACAAAAAAA-ATTGTCA
20194262 CAA-AAATA
64 CAACAAATA
20194270 TTACTATTCA
Statistics
Matches: 212, Mismatches: 34, Indels: 19
0.80 0.13 0.07
Matches are distributed among these distances:
180 8 0.04
181 54 0.25
182 75 0.35
183 36 0.17
184 39 0.18
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.36
Consensus pattern (180 bp):
AAAGTCATATAGTGACAAATTTTGTAACTATAAGTATAATAATTATTACAAAAAAAATTGTCACA
ACAAATAATGAGATTTAGATTTGTTGTGAAAAAATAGTTTTTGTAATTATATATTTTAATTATAG
TGACAAAAGTATATTCACAAAGAATACCTCCAAATTTTTGTACAAAAAAC
Found at i:20194825 original size:416 final size:415
Alignment explanation
Indices: 20194183--20194935 Score: 1118
Period size: 416 Copynumber: 1.8 Consensus size: 415
20194173 CCCTCTATAT
* * *
20194183 TTTTTTGCGACAAAAAAGTCATATTGTGACAAATTTTGTAACTATAAGTGCTAATAATTATTACA
1 TTTTTTGCGACAAAAAAATCATATAGTAACAAATTTTGTAACTATAAGTGCTAATAATTATTACA
* *** *
20194248 AAAAAACATTGTCACAAAAATATTACTATTCATGTTTTTGTGACAAATTATATTTATAGTTATAA
66 AAAAAACATTGTCACAAAAATAATACTATTCACACTTTTGTGACAAATTATATTTATAGCTATAA
* *
20194313 ATTTTAACTATAGTGATAGCATATATTGTCATAACTATTTTTTCTCAACTTTTTTATTTCAAAAG
131 ATTTTAACTATAGTGATAACATATATTGTCATAAATATTTTTTCTCAACTTTTTTATTTCAAAAG
* *
20194378 TTATATTGACAATTTTTATAATTATAATTTATAGTTATTGTTACAGAAAAAATTATTACATCAAA
196 TTATATTGACAAGTTTTATAATTATAATTTATAGTTATTGTTACAGAAAAAATTATCACATCAAA
* *
20194443 TAATAAAATTCAAGTTTTTTTGTAATAAATTATTTTTGTACTTAAATATTTTAATCATTATGAAA
261 TAATAAAAATCAAG-TTTTTGGTAATAAATTATTTTTGTACTTAAATATTTTAATCATTATGAAA
20194508 AATAATACTATCAGAACCATTTCTCCCTATCTTTAGTGTCAAAAATGTTATGTAGTAACAAAATA
325 AATAATACTATCAGAACCATTTCTCCCTATCTTTAGTGTCAAAAATGTTATGTAGTAACAAAATA
20194573 TATTGTCATAAAGGTTTTTCTCCATA
390 TATTGTCATAAAGGTTTTTCTCCATA
* * * *
20194599 TTTTTTGTGTCAAAAAAATCATATAGTAAC-AATTTTCGTAACTATAAGTGTTTATAATTATTA-
1 TTTTTTGCGACAAAAAAATCATATAGTAACAAATTTT-GTAACTATAAGTGCTAATAATTATTAC
** *
20194662 AAAAAAACATTGTCACGAAAAATAATGGTATTCACACTTTTGTGGCAAATTATACTTT-TAGCTA
65 AAAAAAACATTGTCAC-AAAAATAATACTATTCACACTTTTGTGACAAATTATA-TTTATAGCTA
* * * *
20194726 TAAATTTTAATTATAGTGATAACATATATTGTGATAAATA-TTTTTCTCCACTTTTTTGTTTCAA
128 TAAATTTTAACTATAGTGATAACATATATTGTCATAAATATTTTTTCTCAACTTTTTTATTTC-A
* * * *
20194790 AAATTTATATTGATAAGTTTTGTAATTATAATTTATAGTTATTGTTATAGAAAAAATTATCACAT
192 AAAGTTATATTGACAAGTTTTATAATTATAATTTATAGTTATTGTTACAGAAAAAATTATCACAT
* * * * *
20194855 TAGATAATAAAAATCAAGTTTTTGGTAATCAATTATTTTTGTAGTTATATATTTTAATCATTATG
257 CAAATAATAAAAATCAAGTTTTTGGTAATAAATTATTTTTGTACTTAAATATTTTAATCATTATG
*
20194920 AAAAATTATACTATCA
322 AAAAATAATACTATCA
20194936 ACAAAAATAA
Statistics
Matches: 298, Mismatches: 35, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
415 100 0.34
416 195 0.65
417 3 0.01
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (415 bp):
TTTTTTGCGACAAAAAAATCATATAGTAACAAATTTTGTAACTATAAGTGCTAATAATTATTACA
AAAAAACATTGTCACAAAAATAATACTATTCACACTTTTGTGACAAATTATATTTATAGCTATAA
ATTTTAACTATAGTGATAACATATATTGTCATAAATATTTTTTCTCAACTTTTTTATTTCAAAAG
TTATATTGACAAGTTTTATAATTATAATTTATAGTTATTGTTACAGAAAAAATTATCACATCAAA
TAATAAAAATCAAGTTTTTGGTAATAAATTATTTTTGTACTTAAATATTTTAATCATTATGAAAA
ATAATACTATCAGAACCATTTCTCCCTATCTTTAGTGTCAAAAATGTTATGTAGTAACAAAATAT
ATTGTCATAAAGGTTTTTCTCCATA
Found at i:20198686 original size:17 final size:16
Alignment explanation
Indices: 20198666--20198719 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 16
20198656 CCCTCTTTAA
20198666 TTTTTTT-ATTTCTTTT
1 TTTTTTTGATTT-TTTT
20198682 TTTTTTTGATTTTTTT
1 TTTTTTTGATTTTTTT
*
20198698 GATTTTTTGATTTTTATT
1 -TTTTTTTGATTTTT-TT
20198716 TTTT
1 TTTT
20198720 ACTAACCGGG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
16 11 0.33
17 20 0.61
18 2 0.06
ACGTcount: A:0.09, C:0.02, G:0.06, T:0.83
Consensus pattern (16 bp):
TTTTTTTGATTTTTTT
Found at i:20198694 original size:8 final size:8
Alignment explanation
Indices: 20198683--20198712 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
20198673 ATTTCTTTTT
20198683 TTTTTTGA
1 TTTTTTGA
20198691 TTTTTTTGA
1 -TTTTTTGA
20198700 TTTTTTGA
1 TTTTTTGA
20198708 TTTTT
1 TTTTT
20198713 ATTTTTTACT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.10, C:0.00, G:0.10, T:0.80
Consensus pattern (8 bp):
TTTTTTGA
Found at i:20198719 original size:8 final size:8
Alignment explanation
Indices: 20198665--20198712 Score: 53
Period size: 9 Copynumber: 5.8 Consensus size: 8
20198655 ACCCTCTTTA
20198665 ATTTTTTT
1 ATTTTTTT
20198673 ATTTCTTTT
1 ATTT-TTTT
20198682 -TTTTTTT
1 ATTTTTTT
20198689 GATTTTTTT
1 -ATTTTTTT
*
20198698 GATTTTTTG
1 -ATTTTTTT
20198707 ATTTTT
1 ATTTTT
20198713 ATTTTTTACT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
7 4 0.11
8 13 0.36
9 19 0.53
ACGTcount: A:0.10, C:0.02, G:0.06, T:0.81
Consensus pattern (8 bp):
ATTTTTTT
Found at i:20200213 original size:17 final size:17
Alignment explanation
Indices: 20200191--20200262 Score: 81
Period size: 17 Copynumber: 4.2 Consensus size: 17
20200181 GATTAAGAAG
20200191 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* *
20200208 TAGTTTGATGAATGAAC
1 TAGTTTAATAAATGAAC
*
20200225 TAGTTTAATTAATGAAC
1 TAGTTTAATAAATGAAC
* * *
20200242 TAATTTTATTCAATGAAC
1 T-AGTTTAATAAATGAAC
20200260 TAG
1 TAG
20200263 ATGCATGAAT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
17 32 0.70
18 14 0.30
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.39
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:20200230 original size:34 final size:35
Alignment explanation
Indices: 20200191--20200262 Score: 101
Period size: 34 Copynumber: 2.1 Consensus size: 35
20200181 GATTAAGAAG
* *
20200191 TAGTTTAATAAATGAACTAGTTTGA-TGAATGAAC
1 TAGTTTAATAAATGAACTAATTTGATTCAATGAAC
* *
20200225 TAGTTTAATTAATGAACTAATTTTATTCAATGAAC
1 TAGTTTAATAAATGAACTAATTTGATTCAATGAAC
20200260 TAG
1 TAG
20200263 ATGCATGAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
34 22 0.67
35 11 0.33
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.39
Consensus pattern (35 bp):
TAGTTTAATAAATGAACTAATTTGATTCAATGAAC
Found at i:20202307 original size:29 final size:29
Alignment explanation
Indices: 20202219--20202308 Score: 90
Period size: 29 Copynumber: 3.0 Consensus size: 29
20202209 CCAAAATATA
*
20202219 TAACTTTTAAAATTTATATTTTTGGTCCCT
1 TAACTTTTAAAATTTATA-TTTTGGTCACT
* * * * *
20202249 AAACTTTTTAAATTTTATACTTTAGCCACT
1 TAAC-TTTTAAAATTTATATTTTGGTCACT
* *
20202279 TAACTTTTAAAAATTACATTTTGGTCACT
1 TAACTTTTAAAATTTATATTTTGGTCACT
20202308 T
1 T
20202309 TTCAAATTTG
Statistics
Matches: 46, Mismatches: 13, Indels: 3
0.74 0.21 0.05
Matches are distributed among these distances:
29 20 0.43
30 13 0.28
31 13 0.28
ACGTcount: A:0.31, C:0.14, G:0.06, T:0.49
Consensus pattern (29 bp):
TAACTTTTAAAATTTATATTTTGGTCACT
Found at i:20203969 original size:3 final size:3
Alignment explanation
Indices: 20203963--20204021 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
20203953 ACTACTACTG
20203963 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
20204011 CTT CTT CTT CT
1 CTT CTT CTT CT
20204022 AGCTTGAAGT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:20206725 original size:27 final size:28
Alignment explanation
Indices: 20206657--20206725 Score: 74
Period size: 27 Copynumber: 2.5 Consensus size: 28
20206647 GATACTAACT
20206657 TTTA-AAATTTA-TAAAGTAATTATTGAA
1 TTTATAAATTTATTAAAG-AATTATTGAA
* *
20206684 TTTATTAAA-TGATTAAA-AATTATTTAA
1 TTTA-TAAATTTATTAAAGAATTATTGAA
20206711 TTTATAAATTTATTA
1 TTTATAAATTTATTA
20206726 TAACATTTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
26 4 0.11
27 22 0.63
28 2 0.06
29 7 0.20
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.49
Consensus pattern (28 bp):
TTTATAAATTTATTAAAGAATTATTGAA
Found at i:20207822 original size:12 final size:13
Alignment explanation
Indices: 20207797--20207833 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
20207787 AACCACATTC
*
20207797 TATTTTTATTTTA
1 TATTTTTATATTA
20207810 TATTTTTA-ATTA
1 TATTTTTATATTA
20207822 T-TTTTTATATTA
1 TATTTTTATATTA
20207834 AATTAATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
11 6 0.27
12 8 0.36
13 8 0.36
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (13 bp):
TATTTTTATATTA
Found at i:20208010 original size:31 final size:33
Alignment explanation
Indices: 20207958--20208033 Score: 88
Period size: 31 Copynumber: 2.4 Consensus size: 33
20207948 AATAACATAT
*
20207958 GAGAGAAAATAT-TGTTTAGTGACT-AAAATAC
1 GAGAGAAAATATATGTTCAGTGACTAAAAATAC
* *
20207989 GAGAGAAAATATAT-TTCAGTGAGTAAAAATAT
1 GAGAGAAAATATATGTTCAGTGACTAAAAATAC
20208021 GAGA-AAAAGTATA
1 GAGAGAAAA-TATA
20208034 GTTAAATGAG
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
31 24 0.62
32 15 0.38
ACGTcount: A:0.50, C:0.04, G:0.20, T:0.26
Consensus pattern (33 bp):
GAGAGAAAATATATGTTCAGTGACTAAAAATAC
Found at i:20208044 original size:32 final size:32
Alignment explanation
Indices: 20207958--20208046 Score: 83
Period size: 31 Copynumber: 2.8 Consensus size: 32
20207948 AATAACATAT
* * * *
20207958 GAGAGAAAATATTGTTTAGTGACT-AAAATAC
1 GAGAGAAAATATAGTTAAATGAGTAAAAATAC
* * * *
20207989 GAGAGAAAATATATTTCAGTGAGTAAAAATAT
1 GAGAGAAAATATAGTTAAATGAGTAAAAATAC
20208021 GAGA-AAAAGTATAGTTAAATGAGTAA
1 GAGAGAAAA-TATAGTTAAATGAGTAA
20208047 CTCTGTAATT
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
31 24 0.50
32 24 0.50
ACGTcount: A:0.49, C:0.03, G:0.20, T:0.27
Consensus pattern (32 bp):
GAGAGAAAATATAGTTAAATGAGTAAAAATAC
Found at i:20215071 original size:2 final size:2
Alignment explanation
Indices: 20215064--20215100 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
20215054 ATAAAATGTA
20215064 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20215101 ACGGTTAAAA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20216026 original size:15 final size:15
Alignment explanation
Indices: 20216006--20216036 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
20215996 ACTTTATCAA
20216006 AGTTTCGAAACTTTC
1 AGTTTCGAAACTTTC
*
20216021 AGTTTCGATACTTTC
1 AGTTTCGAAACTTTC
20216036 A
1 A
20216037 CAAAGTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.42
Consensus pattern (15 bp):
AGTTTCGAAACTTTC
Found at i:20217387 original size:18 final size:19
Alignment explanation
Indices: 20217366--20217407 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
20217356 GAGGAAGATC
*
20217366 AAGAATAAGAA-AAGAAAG
1 AAGAATAAGAACAAGAAAA
*
20217384 AAG-AGAAGAACAAGAAAA
1 AAGAATAAGAACAAGAAAA
20217402 AAGAAT
1 AAGAAT
20217408 GAGGTGGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 3
0.76 0.12 0.12
Matches are distributed among these distances:
17 6 0.32
18 12 0.63
19 1 0.05
ACGTcount: A:0.71, C:0.02, G:0.21, T:0.05
Consensus pattern (19 bp):
AAGAATAAGAACAAGAAAA
Found at i:20217913 original size:18 final size:17
Alignment explanation
Indices: 20217883--20217927 Score: 72
Period size: 19 Copynumber: 2.5 Consensus size: 17
20217873 GAAAATGATT
20217883 TGATTTTGAAAAACAAAA
1 TGATTTTGAAAAA-AAAA
20217901 TGAATTTTGAAAAAAAAA
1 TG-ATTTTGAAAAAAAAA
20217919 TGATTTTGA
1 TGATTTTGA
20217928 GCTTTCAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.27
18 8 0.31
19 11 0.42
ACGTcount: A:0.51, C:0.02, G:0.13, T:0.33
Consensus pattern (17 bp):
TGATTTTGAAAAAAAAA
Found at i:20227122 original size:26 final size:26
Alignment explanation
Indices: 20227093--20227146 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
20227083 CTAATTCTAG
* **
20227093 TAGTTGGTTTGATCAACTAATTTGAT
1 TAGTTGATTTGAAAAACTAATTTGAT
*
20227119 TAGTTGATTTGAAAAATTAATTTGAT
1 TAGTTGATTTGAAAAACTAATTTGAT
20227145 TA
1 TA
20227147 ACTGTTTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (26 bp):
TAGTTGATTTGAAAAACTAATTTGAT
Found at i:20228131 original size:16 final size:16
Alignment explanation
Indices: 20228119--20228159 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
20228109 TGAGCAATGG
20228119 GCTTAACGAGCAACGA
1 GCTTAACGAGCAACGA
20228135 GCTTAACGAGCAACGA
1 GCTTAACGAGCAACGA
20228151 GCTTAACGA
1 GCTTAACGA
20228160 ACACGAGTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (16 bp):
GCTTAACGAGCAACGA
Found at i:20228144 original size:9 final size:9
Alignment explanation
Indices: 20228119--20228159 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 9
20228109 TGAGCAATGG
20228119 GCTTAACGA
1 GCTTAACGA
20228128 GC--AACGA
1 GCTTAACGA
20228135 GCTTAACGA
1 GCTTAACGA
20228144 GC--AACGA
1 GCTTAACGA
20228151 GCTTAACGA
1 GCTTAACGA
20228160 ACACGAGTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
7 14 0.50
9 14 0.50
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (9 bp):
GCTTAACGA
Found at i:20229621 original size:21 final size:20
Alignment explanation
Indices: 20229597--20229923 Score: 354
Period size: 21 Copynumber: 15.8 Consensus size: 20
20229587 CATATTCGTA
20229597 TTGCGATAG-TCCAAGTTCGCG
1 TTGCGATAGCTCCAAGTT--CG
**
20229618 TTGCGAT-TTTCCAAGTTCG
1 TTGCGATAGCTCCAAGTTCG
20229637 TTGCGATAGTCTCCAAGTTCG
1 TTGCGATAG-CTCCAAGTTCG
20229658 TTGCGATAGTCTCCAAGTTCG
1 TTGCGATAG-CTCCAAGTTCG
*
20229679 TTGCGATAGTCTCCAAATTCG
1 TTGCGATAG-CTCCAAGTTCG
* *
20229700 TTGCGACAGTCTCCAAGTTCA
1 TTGCGATAG-CTCCAAGTTCG
*
20229721 TTGCGATAGTCTCCAAATTCG
1 TTGCGATAG-CTCCAAGTTCG
* *
20229742 TTGCGATAATCTCCAAATTCG
1 TTGCGAT-AGCTCCAAGTTCG
*
20229763 TTGTGATAGTCTCCAAGTTCG
1 TTGCGATAG-CTCCAAGTTCG
20229784 TTGCGATAGTCTCCAAGTTCG
1 TTGCGATAG-CTCCAAGTTCG
*
20229805 TTGAGATAGTCTCCAAGTTCG
1 TTGCGATAG-CTCCAAGTTCG
* **
20229826 TTGTGATAGTCTCCAAGTGAG
1 TTGCGATAG-CTCCAAGTTCG
*
20229847 TTGCGATAGTCTCCAAGTGCG
1 TTGCGATAG-CTCCAAGTTCG
*
20229868 TTGCGATAGTCTCCAAGTGCG
1 TTGCGATAG-CTCCAAGTTCG
*
20229889 TTGCGATAGTCTCCAAATTCG
1 TTGCGATAG-CTCCAAGTTCG
20229910 TTGCGATAG-TCCAA
1 TTGCGATAGCTCCAA
20229924 AATCGCAACG
Statistics
Matches: 278, Mismatches: 23, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
19 14 0.05
20 1 0.00
21 262 0.94
22 1 0.00
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.33
Consensus pattern (20 bp):
TTGCGATAGCTCCAAGTTCG
Found at i:20229674 original size:63 final size:62
Alignment explanation
Indices: 20229597--20229920 Score: 447
Period size: 63 Copynumber: 5.2 Consensus size: 62
20229587 CATATTCGTA
*
20229597 TTGCGATAG--TCCAAGTTCGCGTTGCGAT-TTTCCAAGTTCGTTGCGATAGTCTCCAAGTTCG
1 TTGCGATAGTCTCCAAGTT--CGTTGCGATATCTCCAAGTTCGTTGCGATAGTCTCCAAGTTCG
* * *
20229658 TTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAATTCGTTGCGACAGTCTCCAAGTTCA
1 TTGCGATAGTCTCCAAGTTCGTTGCGATA-TCTCCAAGTTCGTTGCGATAGTCTCCAAGTTCG
* * *
20229721 TTGCGATAGTCTCCAAATTCGTTGCGATAATCTCCAAATTCGTTGTGATAGTCTCCAAGTTCG
1 TTGCGATAGTCTCCAAGTTCGTTGCGAT-ATCTCCAAGTTCGTTGCGATAGTCTCCAAGTTCG
* * **
20229784 TTGCGATAGTCTCCAAGTTCGTTGAGATAGTCTCCAAGTTCGTTGTGATAGTCTCCAAGTGAG
1 TTGCGATAGTCTCCAAGTTCGTTGCGATA-TCTCCAAGTTCGTTGCGATAGTCTCCAAGTTCG
* * *
20229847 TTGCGATAGTCTCCAAGTGCGTTGCGATAGTCTCCAAGTGCGTTGCGATAGTCTCCAAATTCG
1 TTGCGATAGTCTCCAAGTTCGTTGCGATA-TCTCCAAGTTCGTTGCGATAGTCTCCAAGTTCG
20229910 TTGCGATAGTC
1 TTGCGATAGTC
20229921 CAAAATCGCA
Statistics
Matches: 237, Mismatches: 20, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
61 18 0.08
62 1 0.00
63 217 0.92
64 1 0.00
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.33
Consensus pattern (62 bp):
TTGCGATAGTCTCCAAGTTCGTTGCGATATCTCCAAGTTCGTTGCGATAGTCTCCAAGTTCG
Found at i:20229918 original size:42 final size:42
Alignment explanation
Indices: 20229597--20229920 Score: 467
Period size: 42 Copynumber: 7.8 Consensus size: 42
20229587 CATATTCGTA
*
20229597 TTGCGATAG--TCCAAGTTCGCGTTGCGAT--TTTCCAAGTTCG
1 TTGCGATAGTCTCCAAGTT--CGTTGCGATAGTCTCCAAGTTCG
20229637 TTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAGTTCG
1 TTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAGTTCG
* * *
20229679 TTGCGATAGTCTCCAAATTCGTTGCGACAGTCTCCAAGTTCA
1 TTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAGTTCG
* * *
20229721 TTGCGATAGTCTCCAAATTCGTTGCGATAATCTCCAAATTCG
1 TTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAGTTCG
*
20229763 TTGTGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAGTTCG
1 TTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAGTTCG
* * **
20229805 TTGAGATAGTCTCCAAGTTCGTTGTGATAGTCTCCAAGTGAG
1 TTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAGTTCG
* *
20229847 TTGCGATAGTCTCCAAGTGCGTTGCGATAGTCTCCAAGTGCG
1 TTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAGTTCG
*
20229889 TTGCGATAGTCTCCAAATTCGTTGCGATAGTC
1 TTGCGATAGTCTCCAAGTTCGTTGCGATAGTC
20229921 CAAAATCGCA
Statistics
Matches: 258, Mismatches: 22, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
40 18 0.07
42 240 0.93
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.33
Consensus pattern (42 bp):
TTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAGTTCG
Found at i:20230038 original size:6 final size:6
Alignment explanation
Indices: 20230029--20230059 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
20230019 GACACGTATT
*
20230029 ACCACG ACCACG ACCACG ACCACA ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG A
20230060 GACGGACGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.39, C:0.48, G:0.13, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:20230040 original size:16 final size:16
Alignment explanation
Indices: 20230003--20230034 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
20229993 ACGTGTCGAA
20230003 GACACGTATTACCACG
1 GACACGTATTACCACG
20230019 GACACGTATTACCACG
1 GACACGTATTACCACG
20230035 ACCACGACCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.31, G:0.19, T:0.19
Consensus pattern (16 bp):
GACACGTATTACCACG
Found at i:20230545 original size:6 final size:6
Alignment explanation
Indices: 20230534--20230558 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
20230524 TCGTCTCGTC
20230534 TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG T
20230559 AATACGTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.48, T:0.36
Consensus pattern (6 bp):
TCGTGG
Found at i:20230671 original size:21 final size:21
Alignment explanation
Indices: 20230645--20230691 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
20230635 CTTGGAGAAG
*
20230645 TTGGAGACTATCGCAACGCAC
1 TTGGAGACTATCGCAACGAAC
*
20230666 TTGGAGACTATCGCAATGAAC
1 TTGGAGACTATCGCAACGAAC
20230687 TTGGA
1 TTGGA
20230692 AAATCGCAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.23
Consensus pattern (21 bp):
TTGGAGACTATCGCAACGAAC
Found at i:20230902 original size:41 final size:40
Alignment explanation
Indices: 20230828--20230906 Score: 106
Period size: 41 Copynumber: 1.9 Consensus size: 40
20230818 TGTTTTAAGG
* * *
20230828 GTATCGATACCATCCATCAGGTATCGGTTCTACCCTTACA
1 GTATCGATACCATCAATCAGGTATCGATACTACCCTTACA
20230868 GTATCGATACCACTTCAAT-AGGTATCGATACTACCCTTA
1 GTATCGATACCA--TCAATCAGGTATCGATACTACCCTTA
20230907 ATAATTTCAC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
40 12 0.35
41 18 0.53
42 4 0.12
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (40 bp):
GTATCGATACCATCAATCAGGTATCGATACTACCCTTACA
Found at i:20237058 original size:23 final size:23
Alignment explanation
Indices: 20237028--20237071 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
20237018 CAGCTCGTAA
20237028 TTTGCACCGAAGTGCCACATAGG
1 TTTGCACCGAAGTGCCACATAGG
*
20237051 TTTGCACCGTAGTGCCACATA
1 TTTGCACCGAAGTGCCACATA
20237072 TTTTTCCCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (23 bp):
TTTGCACCGAAGTGCCACATAGG
Found at i:20237091 original size:21 final size:21
Alignment explanation
Indices: 20237065--20237113 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
20237055 CACCGTAGTG
* *
20237065 CCACATATTTTTCCCGAATGA
1 CCACATATTTATCCCGAAGGA
20237086 CCACATATTTATCCCGAAGGA
1 CCACATATTTATCCCGAAGGA
20237107 CCACATA
1 CCACATA
20237114 AGACCCTCGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.33, C:0.31, G:0.10, T:0.27
Consensus pattern (21 bp):
CCACATATTTATCCCGAAGGA
Found at i:20237273 original size:21 final size:21
Alignment explanation
Indices: 20237247--20237328 Score: 137
Period size: 21 Copynumber: 3.9 Consensus size: 21
20237237 CATAGGGTCT
*
20237247 GTTCACATTCACTGATTCAAA
1 GTTCACATTTACTGATTCAAA
* *
20237268 GTTCACATTTGCTGATTTAAA
1 GTTCACATTTACTGATTCAAA
20237289 GTTCACATTTACTGATTCAAA
1 GTTCACATTTACTGATTCAAA
20237310 GTTCACATTTACTGATTCA
1 GTTCACATTTACTGATTCA
20237329 TATGATCATA
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (21 bp):
GTTCACATTTACTGATTCAAA
Done.