Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 165 of 226
Found at i:52628264 original size:52 final size:52
Alignment explanation
Indices: 52628202--52628306 Score: 192
Period size: 52 Copynumber: 2.0 Consensus size: 52
52628192 CAGCTGCTGG
* *
52628202 ACCTGCCAGGAAAAGTCTTTTGTTTGGACCCAAAATCTGGAAAAATATGTGT
1 ACCTGCCAGGAAAAGTCTTTGGTTTGGACCCAAAAACTGGAAAAATATGTGT
52628254 ACCTGCCAGGAAAAGTCTTTGGTTTGGACCCAAAAACTGGAAAAATATGTGT
1 ACCTGCCAGGAAAAGTCTTTGGTTTGGACCCAAAAACTGGAAAAATATGTGT
52628306 A
1 A
52628307 TCTCCAATGA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (52 bp):
ACCTGCCAGGAAAAGTCTTTGGTTTGGACCCAAAAACTGGAAAAATATGTGT
Found at i:52631500 original size:18 final size:18
Alignment explanation
Indices: 52631458--52631492 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
52631448 AAGAATCTGT
52631458 GATAGATGAGGAATTTCA
1 GATAGATGAGGAATTTCA
52631476 GATAGATGAGGAATTTC
1 GATAGATGAGGAATTTC
52631493 CGGTAGATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.37, C:0.06, G:0.29, T:0.29
Consensus pattern (18 bp):
GATAGATGAGGAATTTCA
Found at i:52631770 original size:64 final size:64
Alignment explanation
Indices: 52631669--52631792 Score: 230
Period size: 64 Copynumber: 1.9 Consensus size: 64
52631659 ATATATGTCC
*
52631669 AATATGAATAAATTTGAAGAGTACGTCTCCTTATCCATGTTTAAATATATATCCAACATGTTTA
1 AATATGAATAAATTTGAAGAGTACATCTCCTTATCCATGTTTAAATATATATCCAACATGTTTA
*
52631733 AATATGAATAAATTTGAAGAGTACATCTCCTTATCCATGTTTAAATATGTATCCAACATG
1 AATATGAATAAATTTGAAGAGTACATCTCCTTATCCATGTTTAAATATATATCCAACATG
52631793 GATACAAAGA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 58 1.00
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (64 bp):
AATATGAATAAATTTGAAGAGTACATCTCCTTATCCATGTTTAAATATATATCCAACATGTTTA
Found at i:52646316 original size:18 final size:18
Alignment explanation
Indices: 52646295--52646336 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
52646285 TCAAAAATTC
**
52646295 AAAAATTTATATTTTTTA
1 AAAAATTTATAAATTTTA
52646313 AAAAA-TTATAAATTTTA
1 AAAAATTTATAAATTTTA
52646330 AAAAATT
1 AAAAATT
52646337 CTAAAGAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AAAAATTTATAAATTTTA
Found at i:52646321 original size:17 final size:17
Alignment explanation
Indices: 52646308--52646341 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
52646298 AATTTATATT
52646308 TTTTAAAAAATTATAAA
1 TTTTAAAAAATTATAAA
*
52646325 TTTTAAAAAATTCTAAA
1 TTTTAAAAAATTATAAA
52646342 GAATATATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (17 bp):
TTTTAAAAAATTATAAA
Found at i:52653633 original size:18 final size:18
Alignment explanation
Indices: 52653591--52653625 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
52653581 AAGAATCTGT
52653591 GATAGATGAGGAATTTCA
1 GATAGATGAGGAATTTCA
52653609 GATAGATGAGGAATTTC
1 GATAGATGAGGAATTTC
52653626 CGGTAGATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.37, C:0.06, G:0.29, T:0.29
Consensus pattern (18 bp):
GATAGATGAGGAATTTCA
Found at i:52653884 original size:64 final size:64
Alignment explanation
Indices: 52653783--52653912 Score: 260
Period size: 64 Copynumber: 2.0 Consensus size: 64
52653773 GGGTGAGGGT
52653783 TAGGTAAGAATATATGTCCAATATGAATAAATTTGAAGAGTACATCTCCTTATCCATGTTTAAA
1 TAGGTAAGAATATATGTCCAATATGAATAAATTTGAAGAGTACATCTCCTTATCCATGTTTAAA
52653847 TAGGTAAGAATATATGTCCAATATGAATAAATTTGAAGAGTACATCTCCTTATCCATGTTTAAA
1 TAGGTAAGAATATATGTCCAATATGAATAAATTTGAAGAGTACATCTCCTTATCCATGTTTAAA
52653911 TA
1 TA
52653913 TGTACCCAAC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 66 1.00
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (64 bp):
TAGGTAAGAATATATGTCCAATATGAATAAATTTGAAGAGTACATCTCCTTATCCATGTTTAAA
Found at i:52656712 original size:22 final size:22
Alignment explanation
Indices: 52656687--52656729 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
52656677 TATCTTAATA
*
52656687 ATAACAACAAAATTGTAACAAC
1 ATAACAACAAAATAGTAACAAC
* *
52656709 ATAATAATAAAATAGTAACAA
1 ATAACAACAAAATAGTAACAA
52656730 AGTAGTGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.63, C:0.12, G:0.05, T:0.21
Consensus pattern (22 bp):
ATAACAACAAAATAGTAACAAC
Found at i:52662540 original size:72 final size:71
Alignment explanation
Indices: 52662461--52662669 Score: 222
Period size: 72 Copynumber: 2.9 Consensus size: 71
52662451 GAATTCATCA
* * *
52662461 ACTCAATTGGTTTCTTGACAAGCCTAATTGAGTGAGTTGCAATAGGTTTCCCAATGATTTTGGAA
1 ACTCAATTGG-TTCTTGACAAGCCTAAATGAGTGAGTTGCAAGAGGTTTCCCAATGATCTTGGAA
52662526 TCTGTCC
65 TCTGTCC
* * * * * **
52662533 ACTCAATTGGTTCTAATG-GAAGCTTAAATAAGTGAGTTGCAAGATGTTACCCAATGATCTTAAA
1 ACTCAATTGGTTCT--TGACAAGCCTAAATGAGTGAGTTGCAAGAGGTTTCCCAATGATCTTGGA
*
52662597 ATTTGTCC
64 ATCTGTCC
** * * * *
52662605 ACTCAATTGGTTCACCGACAAGTCTAAATGAGTGAGTTGCAAGAGATTTTCCAGTGATCTTGGAA
1 ACTCAATTGGTTC-TTGACAAGCCTAAATGAGTGAGTTGCAAGAGGTTTCCCAATGATCTTGGAA
52662670 CCGTTGTTGA
Statistics
Matches: 109, Mismatches: 24, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
71 5 0.05
72 102 0.94
73 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.33
Consensus pattern (71 bp):
ACTCAATTGGTTCTTGACAAGCCTAAATGAGTGAGTTGCAAGAGGTTTCCCAATGATCTTGGAAT
CTGTCC
Found at i:52665030 original size:11 final size:11
Alignment explanation
Indices: 52664993--52665066 Score: 50
Period size: 11 Copynumber: 6.8 Consensus size: 11
52664983 ATATTTTTTA
*
52664993 TTTTTAAAAAT
1 TTTTTAAAATT
*
52665004 ATTTTAAAATACT
1 TTTTTAAAAT--T
52665017 TTTTTAAAATT
1 TTTTTAAAATT
52665028 TTTTT---A--
1 TTTTTAAAATT
*
52665034 TTTTTAAAATA
1 TTTTTAAAATT
52665045 TTTTTAAAATACT
1 TTTTTAAAAT--T
52665058 TTTTTAAAA
1 TTTTTAAAA
52665067 ATTGTCTAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
6 5 0.10
8 1 0.02
9 1 0.02
11 24 0.48
13 19 0.38
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (11 bp):
TTTTTAAAATT
Found at i:52665039 original size:17 final size:17
Alignment explanation
Indices: 52665017--52665050 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
52665007 TTAAAATACT
*
52665017 TTTTTAAAATTTTTTTA
1 TTTTTAAAATATTTTTA
52665034 TTTTTAAAATATTTTTA
1 TTTTTAAAATATTTTTA
52665051 AAATACTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTTAAAATATTTTTA
Found at i:52665041 original size:41 final size:41
Alignment explanation
Indices: 52664986--52665066 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
52664976 TAAATATATA
52664986 TTTTTTATTTTTAAAA-ATATTTTAAAATACTTTTTTAAAAT
1 TTTTTTATTTTTAAAATAT-TTTTAAAATACTTTTTTAAAAT
52665027 TTTTTTATTTTTAAAATATTTTTAAAATACTTTTTTAAAA
1 TTTTTTATTTTTAAAATATTTTTAAAATACTTTTTTAAAA
52665067 ATTGTCTAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
41 37 0.95
42 2 0.05
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.59
Consensus pattern (41 bp):
TTTTTTATTTTTAAAATATTTTTAAAATACTTTTTTAAAAT
Found at i:52671524 original size:29 final size:31
Alignment explanation
Indices: 52671491--52671567 Score: 104
Period size: 29 Copynumber: 2.5 Consensus size: 31
52671481 TTTGGTTCAA
*
52671491 GTTACATTTTAGTCACTTATGTT-TGA-AAT
1 GTTACATTTTAGTCACTTATGTTATCATAAT
* *
52671520 GTTACGTTTTAGTCACTTATGTTATCATGAT
1 GTTACATTTTAGTCACTTATGTTATCATAAT
*
52671551 GTAACATTTTAGTCACT
1 GTTACATTTTAGTCACT
52671568 GAGCCGTTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
29 22 0.54
30 2 0.05
31 17 0.41
ACGTcount: A:0.26, C:0.13, G:0.14, T:0.47
Consensus pattern (31 bp):
GTTACATTTTAGTCACTTATGTTATCATAAT
Found at i:52672878 original size:21 final size:21
Alignment explanation
Indices: 52672824--52672879 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
52672814 TAATTTATAA
52672824 TTTTTTTTATATTTTGAAGAAT
1 TTTTTTTTA-ATTTTGAAGAAT
* * *
52672846 TTTTCTTGAATTTT-AAGATTT
1 TTTTTTTTAATTTTGAAGA-AT
52672867 TTTTTTTTAATTT
1 TTTTTTTTAATTT
52672880 CAAGTGCACA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 4 0.14
21 17 0.61
22 7 0.25
ACGTcount: A:0.23, C:0.02, G:0.07, T:0.68
Consensus pattern (21 bp):
TTTTTTTTAATTTTGAAGAAT
Found at i:52681400 original size:47 final size:47
Alignment explanation
Indices: 52681307--52681404 Score: 126
Period size: 47 Copynumber: 2.1 Consensus size: 47
52681297 TTATATGAAA
* * *
52681307 TATTTTTAAAAATTTTATCAAATAATAAAAAATATTTTACATATATT
1 TATTTTTAAAAATATTATCAAACAATAAAAAATATTTTACACATATT
* **
52681354 TATTTTTAGGAAATATT-TCAAACAATAAAAAATATTTTAGGCATATT
1 TATTTTTA-AAAATATTATCAAACAATAAAAAATATTTTACACATATT
52681401 TATT
1 TATT
52681405 CAAACACAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
47 38 0.86
48 6 0.14
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (47 bp):
TATTTTTAAAAATATTATCAAACAATAAAAAATATTTTACACATATT
Found at i:52682575 original size:63 final size:63
Alignment explanation
Indices: 52682476--52682601 Score: 243
Period size: 63 Copynumber: 2.0 Consensus size: 63
52682466 TATAGTACTG
52682476 TGATTGACTGTCTTTGTAAGAATGGGTTGGTAAAGGAGGCTCTCGATCTCTCTCGGAAATGAA
1 TGATTGACTGTCTTTGTAAGAATGGGTTGGTAAAGGAGGCTCTCGATCTCTCTCGGAAATGAA
*
52682539 TGATTGACTGTCTTTGTAAGAATGGGTTGGTAAAGGAGGCTCTTGATCTCTCTCGGAAATGAA
1 TGATTGACTGTCTTTGTAAGAATGGGTTGGTAAAGGAGGCTCTCGATCTCTCTCGGAAATGAA
52682602 GGATAAAGGC
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.25, C:0.13, G:0.29, T:0.33
Consensus pattern (63 bp):
TGATTGACTGTCTTTGTAAGAATGGGTTGGTAAAGGAGGCTCTCGATCTCTCTCGGAAATGAA
Found at i:52685628 original size:2 final size:2
Alignment explanation
Indices: 52685567--52685609 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
52685557 ATTTTCTAGT
52685567 TA TA TA 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
52685609 T
1 T
52685610 TAAAAGATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:52686942 original size:16 final size:16
Alignment explanation
Indices: 52686921--52686972 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
52686911 TTTGGTTCGC
52686921 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
52686937 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* *
52686953 TGTAATGGAATAGAGG
1 TGTATTGGATTAGAGG
52686969 TGTA
1 TGTA
52686973 ATAGCAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.29, C:0.00, G:0.37, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:52687019 original size:45 final size:44
Alignment explanation
Indices: 52686953--52687043 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 44
52686943 GGATTAGAGG
*
52686953 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAG-AAATCAACTGTTTGGTTGAA
* ***
52686998 TGTAATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
52687042 TG
1 TG
52687044 GAATAGATGT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 18 0.44
45 23 0.56
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.34
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
Found at i:52687559 original size:125 final size:121
Alignment explanation
Indices: 52687403--52687700 Score: 458
Period size: 125 Copynumber: 2.4 Consensus size: 121
52687393 ATCATATTTA
*
52687403 AACATAATTGTTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCCTTAAATAATT
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT-CTT-AATAATT
* * *
52687468 AATATTCTTATATGAATTTACTCAAATCATAAATATATGATACTGTAAAATATAAAATT-
64 AATATTCTCATATGAATTTACTCAAATCAT-AATATATGATACTATAAAAGA-AAAATTG
52687527 AACATAATTATTATTAAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
1 AACATAATTATTATT-AAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
*
52687592 ATATTCTCATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAAATTTG
65 ATATTCTCATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAAAATTG
* *
52687649 AA-ATAATTAATATTAAATATATCT-TAATTAAAATATATGATTTAATAAAATT
1 AACATAATTATTATTAAATATAT-TATAATTAAAATATATAATTTAATAAAATT
52687701 TAAAATAATT
Statistics
Matches: 164, Mismatches: 7, Indels: 10
0.91 0.04 0.06
Matches are distributed among these distances:
120 35 0.21
121 17 0.10
122 21 0.13
123 36 0.22
124 17 0.10
125 38 0.23
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (121 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTCATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAAAATTG
Found at i:52687574 original size:18 final size:16
Alignment explanation
Indices: 52687498--52687566 Score: 65
Period size: 16 Copynumber: 4.5 Consensus size: 16
52687488 CTCAAATCAT
* *
52687498 AAATATATGATACTGTA
1 AAATATATTATAAT-TA
52687515 AAATATA--A-AATTA
1 AAATATATTATAATTA
* *
52687528 ACATA-ATTATTATTA
1 AAATATATTATAATTA
52687543 AAATATATTATAATTA
1 AAATATATTATAATTA
52687559 AAATATAT
1 AAATATAT
52687567 AATTTAATAA
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
12 1 0.02
13 6 0.14
14 3 0.07
15 9 0.21
16 17 0.40
17 7 0.16
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (16 bp):
AAATATATTATAATTA
Found at i:52687638 original size:61 final size:61
Alignment explanation
Indices: 52687448--52687639 Score: 162
Period size: 61 Copynumber: 3.1 Consensus size: 61
52687438 ATATAATTTA
52687448 ATAAAATTCCTTAAATAATTAATATTCTTATATGAATTTACTCAAATCATAAATATATGATACT
1 ATAAAATT-CTT-AATAATTAATATTCTTATATGAATTTACTCAAATCAT-AATATATGATACT
* * * * * * * * * *
52687512 GTAAAA-T-ATAA-AATTAACATAATTATTAT-TAAAATATA-TTATAATTAAAATATATAAT-T
1 ATAAAATTCTTAATAATT-A-AT-ATTCTTATAT-GAATTTACTCA-AATCATAATATATGATAC
52687571 T
61 T
*
52687572 AATAAAATTCTTAATAATTAATATTCTCATATGAATTTACTCAAATCATAATATATGATACT
1 -ATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
52687634 ATAAAA
1 ATAAAA
52687640 GAAAATTTGA
Statistics
Matches: 95, Mismatches: 21, Indels: 27
0.66 0.15 0.19
Matches are distributed among these distances:
59 4 0.04
60 4 0.04
61 50 0.53
62 23 0.24
63 5 0.05
64 9 0.09
ACGTcount: A:0.49, C:0.08, G:0.03, T:0.40
Consensus pattern (61 bp):
ATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
Found at i:52687708 original size:120 final size:122
Alignment explanation
Indices: 52687403--52687711 Score: 448
Period size: 120 Copynumber: 2.5 Consensus size: 122
52687393 ATCATATTTA
**
52687403 AACATAATTGTTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCCTTAAATAATT
1 AACATAATTAATATTAAATATATTATAATTAAAATATATAATTTAATAAAATT-C-TAAATAATT
* * *
52687468 AATATTCTTATATGAATTTACTCAAATCATAAATATATGATACTGTAAAATATAAAATT
64 AATATTCTCATATGAATTTACTCAAATCATAAATATATGATACTATAAAAGATAAAATT
* *
52687527 AACATAATTATTATTAAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
1 AACATAATTAATATT-AAATATATTATAATTAAAATATATAATTTAATAAAATTCTAAATAATTA
*
52687592 ATATTCTCATATGAATTTACTCAAATCAT-AATATATGATACTATAAAAGA-AAATTT
65 ATATTCTCATATGAATTTACTCAAATCATAAATATATGATACTATAAAAGATAAAATT
*
52687648 GAA-ATAATTAATATTAAATATATCT-TAATTAAAATATATGATTTAATAAAATT-TAAAATAAT
1 -AACATAATTAATATTAAATATAT-TATAATTAAAATATATAATTTAATAAAATTCT-AAATAAT
52687710 TA
63 TA
52687712 TAACTAATAA
Statistics
Matches: 172, Mismatches: 9, Indels: 12
0.89 0.05 0.06
Matches are distributed among these distances:
119 1 0.01
120 43 0.25
121 17 0.10
122 21 0.12
123 37 0.22
124 15 0.09
125 38 0.22
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.41
Consensus pattern (122 bp):
AACATAATTAATATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTAAATAATTAA
TATTCTCATATGAATTTACTCAAATCATAAATATATGATACTATAAAAGATAAAATT
Found at i:52687810 original size:101 final size:93
Alignment explanation
Indices: 52687643--52687923 Score: 279
Period size: 91 Copynumber: 3.0 Consensus size: 93
52687633 TATAAAAGAA
* * *
52687643 AATTTGAAATAATTAATATTAAATAT-ATCTTAATTAA-AATATATGATTTAATAAAATT-TAAA
1 AATTTAAAATAATTAATATTAAATATAAT-TTAA-TAATAATATATAATTTCATAAAATTCT---
* * * *
52687705 ATAATTATAACTAATAAATTATATTTTATGAATTTGTAT
61 -T-A--ATAA-T-ATAAATTTTATTATATGAATTTATAC
* *
52687744 AATTTAAAATAA-TAATTATTACATATAATTTAATAATAATATATAATTTCATAAAATTCTTGAT
1 AATTTAAAATAATTAA-TATTAAATATAATTTAATAATAATATATAATTTCATAAAATTCTTAAT
*
52687808 -A-ATAAATTTTCTTATATGAATTTATAC
65 AATATAAATTTTATTATATGAATTTATAC
* *
52687835 AATTTAAAATAATTAATATTAAATATAATTTAATAGTGATATATAATTTCATAAAATTCTTAATA
1 AATTTAAAATAATTAATATTAAATATAATTTAATAATAATATATAATTTCATAAAATTCTTAATA
* *
52687900 ATA-AAATGTTCTTATATGAATTTA
66 ATATAAATTTTATTATATGAATTTA
52687924 CTAAAATCAA
Statistics
Matches: 158, Mismatches: 15, Indels: 23
0.81 0.08 0.12
Matches are distributed among these distances:
91 77 0.49
92 24 0.15
93 1 0.01
94 1 0.01
95 2 0.01
98 1 0.01
100 6 0.04
101 43 0.27
102 3 0.02
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (93 bp):
AATTTAAAATAATTAATATTAAATATAATTTAATAATAATATATAATTTCATAAAATTCTTAATA
ATATAAATTTTATTATATGAATTTATAC
Found at i:52687811 original size:91 final size:91
Alignment explanation
Indices: 52687716--52687923 Score: 285
Period size: 91 Copynumber: 2.3 Consensus size: 91
52687706 TAATTATAAC
* * * *
52687716 TAATAAATTATATTTTATGAATTTGTATAATTTAAAATAA-TAATTATTACATATAATTTAATAA
1 TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAA-TATTAAATATAATTTAATAA
*
52687780 TAATATATAATTTCATAAAATTCTTGA
65 TAATATATAATTTCATAAAATTCTTAA
* * *
52687807 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAGT
1 TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
52687872 GATATATAATTTCATAAAATTCTTAA
66 AATATATAATTTCATAAAATTCTTAA
*
52687898 TAATAAAATGT-TCTTATATGAATTTA
1 TAAT-AAAT-TATATTATATGAATTTA
52687924 CTAAAATCAA
Statistics
Matches: 105, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
91 82 0.78
92 22 0.21
93 1 0.01
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.46
Consensus pattern (91 bp):
TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
AATATATAATTTCATAAAATTCTTAA
Found at i:52688643 original size:15 final size:15
Alignment explanation
Indices: 52688623--52688658 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
52688613 GGTATATGTA
52688623 TAATTGACCTAAAAT
1 TAATTGACCTAAAAT
52688638 TAATTGACCTAAAAT
1 TAATTGACCTAAAAT
52688653 TAATTG
1 TAATTG
52688659 TTGGTATTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.36
Consensus pattern (15 bp):
TAATTGACCTAAAAT
Found at i:52688882 original size:6 final size:6
Alignment explanation
Indices: 52688871--52688899 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
52688861 GTTTGAACAT
52688871 TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
52688900 TTTCGTATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:52692984 original size:9 final size:9
Alignment explanation
Indices: 52692970--52693001 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
52692960 TATTCATGTA
52692970 TTATGTAAG
1 TTATGTAAG
*
52692979 TTATGTGAG
1 TTATGTAAG
52692988 TTATGTAAG
1 TTATGTAAG
52692997 TTATG
1 TTATG
52693002 ATATTTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.25, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:52695166 original size:28 final size:26
Alignment explanation
Indices: 52695076--52695169 Score: 75
Period size: 28 Copynumber: 3.5 Consensus size: 26
52695066 TAGCATTTAA
* *
52695076 TTAATTTTTTAAAATTTTAAAAAAAATT
1 TTAATTTTTT--AATTTTTAAAATAATT
* * *
52695104 ATAATTTTAT-ATTTTT-TAATAATT
1 TTAATTTTTTAATTTTTAAAATAATT
52695128 TTAATGATTTTTAATTTTTAAAAGTAATTT
1 TTAAT--TTTTTAATTTTTAAAA-TAA-TT
52695158 TTAATTTTTTAA
1 TTAATTTTTTAA
52695170 AATTAAAAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
24 10 0.19
25 5 0.10
26 4 0.08
27 6 0.12
28 17 0.33
29 3 0.06
30 7 0.13
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (26 bp):
TTAATTTTTTAATTTTTAAAATAATT
Found at i:52697388 original size:13 final size:14
Alignment explanation
Indices: 52697360--52697388 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
52697350 TCAGAAAAGT
52697360 AATTATTTTTTAGA
1 AATTATTTTTTAGA
52697374 AATTATTTTTT-GA
1 AATTATTTTTTAGA
52697387 AA
1 AA
52697389 ACTATTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (14 bp):
AATTATTTTTTAGA
Found at i:52697896 original size:43 final size:43
Alignment explanation
Indices: 52697844--52697981 Score: 161
Period size: 43 Copynumber: 3.2 Consensus size: 43
52697834 ACGGCACTAT
* * * * *
52697844 AGAATATGACCTTTAGCGGTGCTTTTCTCACAATCACTGCTAA
1 AGAACATGACATTTAGCGGTGCTTTTATCACAATCGCCGCTAA
52697887 AGAACATGACATTTAGCGGCT-CTTTTATCACAATCGCCGCTAA
1 AGAACATGACATTTAGCGG-TGCTTTTATCACAATCGCCGCTAA
* * * * *
52697930 AAAACATGACATTTAGCAGCGTTTTTATCACAAACGCCGCTAA
1 AGAACATGACATTTAGCGGTGCTTTTATCACAATCGCCGCTAA
*
52697973 AGAATATGA
1 AGAACATGA
52697982 TCTTTAGTGA
Statistics
Matches: 81, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
43 80 0.99
44 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.28
Consensus pattern (43 bp):
AGAACATGACATTTAGCGGTGCTTTTATCACAATCGCCGCTAA
Found at i:52697988 original size:43 final size:43
Alignment explanation
Indices: 52697812--52697981 Score: 148
Period size: 43 Copynumber: 4.0 Consensus size: 43
52697802 GTCGCTAAAT
* * * * *
52697812 TTTA-CAGCGTTTTT-TCACATAAACGGCACTATAGAATATGACC
1 TTTAGCAGCGTTTTTATCAC--AAACGCCGCTAAAGAACATGACA
* * * * * * *
52697855 TTTAGCGGTGCTTTTCTCACAATCACTGCTAAAGAACATGACA
1 TTTAGCAGCGTTTTTATCACAAACGCCGCTAAAGAACATGACA
* * *
52697898 TTTAGCGGC-TCTTTTATCACAATCGCCGCTAAAAAACATGACA
1 TTTAGCAGCGT-TTTTATCACAAACGCCGCTAAAGAACATGACA
*
52697941 TTTAGCAGCGTTTTTATCACAAACGCCGCTAAAGAATATGA
1 TTTAGCAGCGTTTTTATCACAAACGCCGCTAAAGAACATGA
52697982 TCTTTAGTGA
Statistics
Matches: 102, Mismatches: 21, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
43 90 0.88
44 8 0.08
45 4 0.04
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.30
Consensus pattern (43 bp):
TTTAGCAGCGTTTTTATCACAAACGCCGCTAAAGAACATGACA
Found at i:52700487 original size:9 final size:9
Alignment explanation
Indices: 52700473--52700511 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
52700463 TTTATGTATC
52700473 ATGTAAGTT
1 ATGTAAGTT
52700482 ATGTAAGTT
1 ATGTAAGTT
* *
52700491 ACGTGAGTT
1 ATGTAAGTT
52700500 ATGTAAGTT
1 ATGTAAGTT
52700509 ATG
1 ATG
52700512 ATATGATATA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.31, C:0.03, G:0.26, T:0.41
Consensus pattern (9 bp):
ATGTAAGTT
Found at i:52700589 original size:19 final size:19
Alignment explanation
Indices: 52700565--52700601 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
52700555 TTTAATTCTT
52700565 TAAAGTTATGTAAGTTATG
1 TAAAGTTATGTAAGTTATG
52700584 TAAAGTTATGTAAGTTAT
1 TAAAGTTATGTAAGTTAT
52700602 ATATTTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.43
Consensus pattern (19 bp):
TAAAGTTATGTAAGTTATG
Found at i:52700591 original size:10 final size:9
Alignment explanation
Indices: 52700567--52700601 Score: 61
Period size: 9 Copynumber: 3.8 Consensus size: 9
52700557 TAATTCTTTA
52700567 AAGTTATGT
1 AAGTTATGT
52700576 AAGTTATGT
1 AAGTTATGT
52700585 AAAGTTATGT
1 -AAGTTATGT
52700595 AAGTTAT
1 AAGTTAT
52700602 ATATTTTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 16 0.64
10 9 0.36
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.43
Consensus pattern (9 bp):
AAGTTATGT
Found at i:52702697 original size:17 final size:19
Alignment explanation
Indices: 52702675--52702712 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
52702665 TTAAAAGATT
52702675 ATAATTTT-AT-ATTTTTA
1 ATAATTTTAATGATTTTTA
52702692 ATAATTTTAATGATTTTTA
1 ATAATTTTAATGATTTTTA
52702711 AT
1 AT
52702713 TTTTAAAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.42
18 2 0.11
19 9 0.47
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (19 bp):
ATAATTTTAATGATTTTTA
Found at i:52704596 original size:8 final size:7
Alignment explanation
Indices: 52704561--52704770 Score: 129
Period size: 7 Copynumber: 30.1 Consensus size: 7
52704551 TTAAAATCAG
52704561 ACCCTAA
1 ACCCTAA
*
52704568 ACACTAA
1 ACCCTAA
*
52704575 ACCATAA
1 ACCCTAA
52704582 ACCCTAA
1 ACCCTAA
52704589 ACCCCTAA
1 A-CCCTAA
*
52704597 ACCATAA
1 ACCCTAA
**
52704604 ACTTTAA
1 ACCCTAA
*
52704611 ACTCTAA
1 ACCCTAA
* *
52704618 ATCTTAA
1 ACCCTAA
*
52704625 GCCCCTAA
1 -ACCCTAA
*
52704633 ACCATAA
1 ACCCTAA
*
52704640 ACACTAA
1 ACCCTAA
*
52704647 ACACTAA
1 ACCCTAA
*
52704654 ACCATAA
1 ACCCTAA
*
52704661 ACACTAA
1 ACCCTAA
*
52704668 ACCATAA
1 ACCCTAA
*
52704675 A-CCTAC
1 ACCCTAA
52704681 ACCCTAA
1 ACCCTAA
*
52704688 ACCGTAA
1 ACCCTAA
*
52704695 ACACTAA
1 ACCCTAA
* *
52704702 ACTCT-T
1 ACCCTAA
*
52704708 ACACTAA
1 ACCCTAA
* *
52704715 ATCATAA
1 ACCCTAA
52704722 ACCCTAA
1 ACCCTAA
*
52704729 ACCTTAA
1 ACCCTAA
*
52704736 ACCCCAA
1 ACCCTAA
* *
52704743 ATCATAA
1 ACCCTAA
*
52704750 A-CCTAC
1 ACCCTAA
52704756 ACCCTAA
1 ACCCTAA
52704763 ACCCTAA
1 ACCCTAA
52704770 A
1 A
52704771 TATATATTAC
Statistics
Matches: 150, Mismatches: 48, Indels: 10
0.72 0.23 0.05
Matches are distributed among these distances:
6 12 0.08
7 127 0.85
8 11 0.07
ACGTcount: A:0.47, C:0.33, G:0.01, T:0.19
Consensus pattern (7 bp):
ACCCTAA
Found at i:52704696 original size:34 final size:34
Alignment explanation
Indices: 52704565--52704770 Score: 133
Period size: 36 Copynumber: 5.7 Consensus size: 34
52704555 AATCAGACCC
* * *
52704565 TAAACACTAAACCATAAACCCTAAACCCCTAAACCA
1 TAAAC-CTAAACCCTAAACCATAAA-CACTAAACCA
* * * * * *
52704601 TAAACTTTAAACTCTAAATCTTAAGCCCCTAAACCA
1 TAAAC-CTAAACCCTAAACCATAA-ACACTAAACCA
*
52704637 TAAACACTAAACACTAAACCATAAACACTAAACCA
1 TAAAC-CTAAACCCTAAACCATAAACACTAAACCA
* *
52704672 TAAACCTACACCCTAAACCGTAAACACTAAACTCTTACA
1 TAAACCTAAACCCTAAACCATAAACACTAAA--C---CA
* * * * *
52704711 CTAAATCATAAACCCTAAACCTTAAACCCCAAATCA
1 -TAAA-CCTAAACCCTAAACCATAAACACTAAACCA
* *
52704747 TAAACCTACACCCTAAACCCTAAA
1 TAAACCTAAACCCTAAACCATAAA
52704771 TATATATTAC
Statistics
Matches: 136, Mismatches: 26, Indels: 18
0.76 0.14 0.10
Matches are distributed among these distances:
34 40 0.29
35 18 0.13
36 50 0.37
39 2 0.01
40 4 0.03
41 22 0.16
ACGTcount: A:0.48, C:0.33, G:0.01, T:0.19
Consensus pattern (34 bp):
TAAACCTAAACCCTAAACCATAAACACTAAACCA
Found at i:52704714 original size:27 final size:26
Alignment explanation
Indices: 52704684--52704734 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
52704674 AACCTACACC
*
52704684 CTAAACCGTAAACACTAAACTCTTACA
1 CTAAACCATAAACACTAAAC-CTTACA
* *
52704711 CTAAATCATAAACCCTAAACCTTA
1 CTAAACCATAAACACTAAACCTTA
52704735 AACCCCAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 4 0.19
27 17 0.81
ACGTcount: A:0.45, C:0.29, G:0.02, T:0.24
Consensus pattern (26 bp):
CTAAACCATAAACACTAAACCTTACA
Found at i:52705303 original size:107 final size:106
Alignment explanation
Indices: 52705116--52705336 Score: 295
Period size: 107 Copynumber: 2.1 Consensus size: 106
52705106 CGCCACTATT
***
52705116 GCCACTAAAGCTCAACAACAAACGACGTCGTTTTCTCAACTTTTTTTGCAGCGTTTTGTGAAAAG
1 GCCACTAAAGCTCAACAACAAACGACGTCGTTTTCTCAACTTTTTTTGCAGCGTTTTCCAAAAAG
* * *
52705181 TGCCGCTAATTCTCGATCTATTGCGGCGTTATTTTATAAAA-C
66 CGCAGCTAATGCTCGATCTATTGCGGCGTT-TTTTA-AAAAGC
* *
52705223 GCCACTAAAGCTCAACAACAAACGTCGTTGTTTTGCTCAACTTTTTTGTG-A-CGTTTTCCAAAA
1 GCCACTAAAGCTCAACAACAAACGACGTCGTTTT-CTCAACTTTTTT-TGCAGCGTTTTCCAAAA
*
52705286 AGCGCAGCTAATGCTCGATCTATTGTGGCGTTTTTTAAAAAGC
64 AGCGCAGCTAATGCTCGATCTATTGCGGCGTTTTTTAAAAAGC
*
52705329 GCCGCTAA
1 GCCACTAA
52705337 TGCCACTAAA
Statistics
Matches: 101, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
105 4 0.04
106 13 0.13
107 69 0.68
108 13 0.13
109 2 0.02
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.33
Consensus pattern (106 bp):
GCCACTAAAGCTCAACAACAAACGACGTCGTTTTCTCAACTTTTTTTGCAGCGTTTTCCAAAAAG
CGCAGCTAATGCTCGATCTATTGCGGCGTTTTTTAAAAAGC
Found at i:52705450 original size:39 final size:40
Alignment explanation
Indices: 52705407--52705503 Score: 133
Period size: 40 Copynumber: 2.5 Consensus size: 40
52705397 CAAAGTGCTA
* * *
52705407 CTAATGCTCGATCTATAGCGGC-TTTTTCGAGAAGCGCCG
1 CTAATGCTCGATCTATAGCGACGTTTTTCAAAAAGCGCCG
*
52705446 CTAATGCTTGATCTATAGCGACGTTTTTCAAAAAGCGCCG
1 CTAATGCTCGATCTATAGCGACGTTTTTCAAAAAGCGCCG
* *
52705486 CTAATGCTCAACCTATAG
1 CTAATGCTCGATCTATAG
52705504 TGACATTTGT
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
39 20 0.40
40 30 0.60
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.29
Consensus pattern (40 bp):
CTAATGCTCGATCTATAGCGACGTTTTTCAAAAAGCGCCG
Found at i:52711382 original size:24 final size:23
Alignment explanation
Indices: 52711330--52711382 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 23
52711320 TATAAAGATC
*
52711330 ATGCATACCAACATAACCATATA
1 ATGCATACCAACACAACCATATA
*
52711353 AT-CATACCATCACAGACACATAT-
1 ATGCATACCAACACA-AC-CATATA
52711376 ATGCATA
1 ATGCATA
52711383 ACTAGATTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
22 10 0.40
23 6 0.24
24 9 0.36
ACGTcount: A:0.45, C:0.26, G:0.06, T:0.23
Consensus pattern (23 bp):
ATGCATACCAACACAACCATATA
Found at i:52712749 original size:3 final size:3
Alignment explanation
Indices: 52712741--52712772 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
52712731 GTCAGTCTGC
52712741 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
52712773 AACAGGTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:52713948 original size:17 final size:17
Alignment explanation
Indices: 52713926--52713960 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
52713916 ATAATCCAAA
*
52713926 AGAGTGAATTTAGGTTC
1 AGAGTGAACTTAGGTTC
52713943 AGAGTGAACTTAGGTTC
1 AGAGTGAACTTAGGTTC
52713960 A
1 A
52713961 AGCAGTGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.09, G:0.29, T:0.31
Consensus pattern (17 bp):
AGAGTGAACTTAGGTTC
Found at i:52718331 original size:3 final size:3
Alignment explanation
Indices: 52718323--52718356 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
52718313 TTAGTTTCTT
52718323 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
52718357 CTTTTAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:52722295 original size:25 final size:24
Alignment explanation
Indices: 52722251--52722307 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 24
52722241 GGAACTTTGA
52722251 ATTTGTTTGAAATTCTTATGTT-G
1 ATTTGTTTGAAATTCTTATGTTCG
* *
52722274 ATATTGTTGTGGAATTGTTATGTTCG
1 AT-TTGTT-TGAAATTCTTATGTTCG
52722300 ATTTGTTT
1 ATTTGTTT
52722308 AGATGTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
23 2 0.07
24 6 0.21
25 18 0.62
26 3 0.10
ACGTcount: A:0.19, C:0.04, G:0.21, T:0.56
Consensus pattern (24 bp):
ATTTGTTTGAAATTCTTATGTTCG
Found at i:52731720 original size:15 final size:15
Alignment explanation
Indices: 52731688--52731734 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
52731678 CTAATGTGTG
*
52731688 TATGGCTCCTCC-CTC
1 TATGGCTCCACCAC-C
52731703 TATGGCTCCACCACC
1 TATGGCTCCACCACC
* *
52731718 TATGGTTCCATCACC
1 TATGGCTCCACCACC
52731733 TA
1 TA
52731735 CTTGGACATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 27 0.96
16 1 0.04
ACGTcount: A:0.17, C:0.40, G:0.13, T:0.30
Consensus pattern (15 bp):
TATGGCTCCACCACC
Found at i:52738214 original size:13 final size:12
Alignment explanation
Indices: 52738176--52738225 Score: 59
Period size: 13 Copynumber: 4.2 Consensus size: 12
52738166 ATATTTTTGT
52738176 AATTAATTT-TA
1 AATTAATTTATA
*
52738187 AA-TAATATATCA
1 AATTAATTTAT-A
52738199 AATTAATTTAATA
1 AATTAATTT-ATA
52738212 AATTAATTTATA
1 AATTAATTTATA
52738224 AA
1 AA
52738226 AAAAATATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
10 5 0.15
11 3 0.09
12 8 0.24
13 15 0.45
14 2 0.06
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (12 bp):
AATTAATTTATA
Found at i:52740832 original size:32 final size:32
Alignment explanation
Indices: 52740791--52740854 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
52740781 TCTATGACTT
52740791 TCCCTTTTATCTTCTTATGTTTGTCATATATA
1 TCCCTTTTATCTTCTTATGTTTGTCATATATA
52740823 TCCCTTTTATCTTCTTATGTTTGTCATATATA
1 TCCCTTTTATCTTCTTATGTTTGTCATATATA
52740855 CGTCTTAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.19, C:0.19, G:0.06, T:0.56
Consensus pattern (32 bp):
TCCCTTTTATCTTCTTATGTTTGTCATATATA
Found at i:52756106 original size:12 final size:12
Alignment explanation
Indices: 52756089--52756122 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
52756079 TTATTTTTCT
52756089 TTACTTTATTTA
1 TTACTTTATTTA
52756101 TTACTTTATTTTA
1 TTACTTTA-TTTA
52756114 TTA-TTTATT
1 TTACTTTATT
52756123 ACTTATTTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 2 0.10
12 12 0.57
13 7 0.33
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (12 bp):
TTACTTTATTTA
Found at i:52756110 original size:8 final size:7
Alignment explanation
Indices: 52756049--52756129 Score: 50
Period size: 7 Copynumber: 12.0 Consensus size: 7
52756039 AGGCAACCCA
52756049 ATTT-TT
1 ATTTATT
52756055 ATTT-TT
1 ATTTATT
*
52756061 ATTTTTT
1 ATTTATT
52756068 A-TTAGTT
1 ATTTA-TT
52756075 A-TTATT
1 ATTTATT
52756081 ATTT-TT
1 ATTTATT
*
52756087 CTTTACTTT
1 ATTTA--TT
52756096 ATTTATT
1 ATTTATT
52756103 ACTTTA-T
1 A-TTTATT
52756110 -TTTATT
1 ATTTATT
52756116 ATTTATT
1 ATTTATT
*
52756123 ACTTATT
1 ATTTATT
52756130 TGGATATTAA
Statistics
Matches: 62, Mismatches: 4, Indels: 17
0.75 0.05 0.20
Matches are distributed among these distances:
5 4 0.06
6 21 0.34
7 27 0.44
8 4 0.06
9 6 0.10
ACGTcount: A:0.22, C:0.05, G:0.01, T:0.72
Consensus pattern (7 bp):
ATTTATT
Found at i:52782815 original size:21 final size:23
Alignment explanation
Indices: 52782777--52782824 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
52782767 TAGAAATAAT
* *
52782777 CAAAAAGAATTTATTCAAAAA-A
1 CAAAAAGAAATCATTCAAAAAGA
52782799 CAAAAAGAAATCA-TCAAAAAGA
1 CAAAAAGAAATCATTCAAAAAGA
52782821 CAAA
1 CAAA
52782825 CATGTCTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.67, C:0.12, G:0.06, T:0.15
Consensus pattern (23 bp):
CAAAAAGAAATCATTCAAAAAGA
Found at i:52785696 original size:98 final size:98
Alignment explanation
Indices: 52785522--52785718 Score: 349
Period size: 98 Copynumber: 2.0 Consensus size: 98
52785512 GTACAATAAA
* *
52785522 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCTAATACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
* * *
52785587 TCTTTAGAATCCCAAACTTGGAATATTTCCTTT
66 CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
52785620 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
52785685 CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
66 CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
52785718 A
1 A
52785719 TTATTTTTAA
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 94 1.00
ACGTcount: A:0.37, C:0.23, G:0.10, T:0.30
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
Found at i:52786449 original size:17 final size:17
Alignment explanation
Indices: 52786416--52786451 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
52786406 AAAATATAGG
* *
52786416 AAAATATTAGTTTAAAA
1 AAAATATTAGCTGAAAA
52786433 AAAATATTAGCTGAAAA
1 AAAATATTAGCTGAAAA
52786450 AA
1 AA
52786452 TAAGTATGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.61, C:0.03, G:0.08, T:0.28
Consensus pattern (17 bp):
AAAATATTAGCTGAAAA
Found at i:52787095 original size:19 final size:19
Alignment explanation
Indices: 52787071--52787183 Score: 172
Period size: 19 Copynumber: 5.8 Consensus size: 19
52787061 AATCATATAT
52787071 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
**
52787090 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
52787109 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
52787128 TCTAAGATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
**
52787149 TCTTGGATTGCATATCATA
1 TCTAAGATTGCATATCATA
52787168 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
52787184 CTCAAAAATT
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
19 67 0.80
21 17 0.20
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:52787158 original size:40 final size:40
Alignment explanation
Indices: 52787071--52787182 Score: 192
Period size: 40 Copynumber: 2.9 Consensus size: 40
52787061 AATCATATAT
52787071 TCTAAGATTGCATATCATATCTAAGATT--ATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
52787109 TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
**
52787149 TCTTGGATTGCATATCATATCTAAGATTGCATAT
1 TCTAAGATTGCATATCATATCTAAGATTGCATAT
52787183 CCTCAAAAAT
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
38 28 0.40
40 42 0.60
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (40 bp):
TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
Found at i:52787164 original size:59 final size:56
Alignment explanation
Indices: 52787064--52787183 Score: 170
Period size: 59 Copynumber: 2.1 Consensus size: 56
52787054 ATTACAAAAT
*
52787064 CATAT-ATTCTAAGATTGCATATCATATCTAAGATTATATATCATATCTAAGATTG
1 CATATCATTCTAAGATTGCATATCATATCTAAGATTACATATCATATCTAAGATTG
** *
52787119 CATATCATATCTAAGATTGCATATATCATATCTTGGATTGCATATCATATCTAAGATTG
1 CATATCAT-TCTAAGATTGC--ATATCATATCTAAGATTACATATCATATCTAAGATTG
52787178 CATATC
1 CATATC
52787184 CTCAAAAATT
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
55 5 0.09
56 2 0.04
57 11 0.19
59 39 0.68
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (56 bp):
CATATCATTCTAAGATTGCATATCATATCTAAGATTACATATCATATCTAAGATTG
Found at i:52787530 original size:44 final size:44
Alignment explanation
Indices: 52787398--52788092 Score: 414
Period size: 44 Copynumber: 15.8 Consensus size: 44
52787388 GACTTGCTTA
* * * *
52787398 TTTAGTCTGCTCCACTGTAACTTCAGGGAGATAAGACTA---GA
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATCGGC
*** * * * * *
52787439 TGCGATCTGCT-CTCTGTAACTTTAGAGAGATAAGATCTGA--GGT
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-T-ATCGGC
* * *
52787482 TTTAATCCGCTCCAATGCAACTTCAGGGAGATAGGATTATCGGC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATCGGC
* * **
52787526 TTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGACTTGTCATC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTATCGGC
* * *
52787571 TTTAGTCTGCCCCACTGCAACTTCA-GGAGGATAAGACTTAAGATCTGAGGT
1 TTTAATCTGCTCCACTGCAACTTCAGGGA-GATAAGA-TT---ATC---GGC
* *
52787622 TTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATCGGC
* ** **
52787666 TTTTATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCCATC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTATCGGC
* * * *
52787711 TTCAGTCTGCCCCACTGCAACTTCA-GGAGGATAAGACT-T--GC
1 TTTAATCTGCTCCACTGCAACTTCAGGGA-GATAAGATTATCGGC
* * *
52787752 TTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTA---GA
1 -T--TTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATCGGC
*** * *
52787796 TGCGATCTGCT-CTCTGCAACTTCAGGGAGATAGGATTATCGGC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATCGGC
** **
52787839 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCCATC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTATCGGC
* * * *
52787884 TTCAGTCTGCCCCACTGCAACTTCA-GGAGGATAAGACT-T--GC
1 TTTAATCTGCTCCACTGCAACTTCAGGGA-GATAAGATTATCGGC
* * * * *
52787925 TTACTTAGTCTGCCTCTAGTGCAACTTCAGGGAGATAAGACTA---GA
1 -T--TTAATCTG-CTCCACTGCAACTTCAGGGAGATAAGATTATCGGC
** ** * *
52787970 TGCAATCTGCT-TTCTGCAACTTCAGAGAGATAAGAATTGA--GGT
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAG-ATT-ATCGGC
* * *
52788013 TTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGAC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATCGGC
* *
52788057 TTTAATCTGCTCCACTACTACTTCAGGGAGATAAGA
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGA
52788093 CTTGTCATCT
Statistics
Matches: 510, Mismatches: 104, Indels: 77
0.74 0.15 0.11
Matches are distributed among these distances:
40 65 0.13
41 20 0.04
42 11 0.02
43 31 0.06
44 213 0.42
45 129 0.25
46 3 0.01
47 3 0.01
48 2 0.00
50 2 0.00
51 28 0.05
52 3 0.01
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.28
Consensus pattern (44 bp):
TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATCGGC
Found at i:52787770 original size:89 final size:89
Alignment explanation
Indices: 52787671--52787966 Score: 387
Period size: 89 Copynumber: 3.4 Consensus size: 89
52787661 TCGGCTTTTA
52787671 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCCATCTTCAGTCTGCCCCACTGCAACTTCA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCCATCTTCAGTCTGCCCCACTGCAACTTCA
52787736 GGAGGATAAGACTTGCTTACTTAG
66 GGAGGATAAGACTTGCTTACTTAG
* * * *
52787760 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTAG--A--TGC-GATCTG-CTCTCTGCAACTTC
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCCATCTTCAG-TCTGCCCCACTGCAACTTC
* * *
52787819 AGG-GAGATAGGATTATCGGC-T--TTAA
65 AGGAG-GATAAGACT-T--GCTTACTTAG
52787844 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCCATCTTCAGTCTGCCCCACTGCAACTTCA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCCATCTTCAGTCTGCCCCACTGCAACTTCA
52787909 GGAGGATAAGACTTGCTTACTTAG
66 GGAGGATAAGACTTGCTTACTTAG
* *
52787933 TCTGCCTCTAGTGCAACTTCAGGGAGATAAGACT
1 TCTG-CTCCACTGCAACTTCAGGGAGATAAGACT
52787967 AGATGCAATC
Statistics
Matches: 175, Mismatches: 16, Indels: 31
0.79 0.07 0.14
Matches are distributed among these distances:
83 1 0.01
84 60 0.34
85 7 0.04
86 4 0.02
87 4 0.02
88 7 0.04
89 64 0.37
90 28 0.16
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (89 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCCATCTTCAGTCTGCCCCACTGCAACTTCA
GGAGGATAAGACTTGCTTACTTAG
Found at i:52787925 original size:173 final size:172
Alignment explanation
Indices: 52787347--52788045 Score: 861
Period size: 173 Copynumber: 4.0 Consensus size: 172
52787337 TAGGAATTAG
* * *
52787347 TGCCATCTTCAGTCTGCCTCATTGCAACTTCAGGAGGATAAGACTTGCTTATTTAGTCTGCTCCA
1 TGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCA
* * * *
52787412 CTGTAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGTAACTTTAGAGAGATAAGATCT
66 CTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAGGAT-T
* * *
52787477 GAGGTTTTAATCCGCTCCAATGCAACTTCAGGGAGATAGGA-T
130 GAGGCTTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGACT
** ** * * * * *
52787519 TATCGGCTTTAATCTGCTCCACTGCAACTTCAAGGA-GATAAGACTTG-TCATCTTTAGTCTGCC
1 TGCCATCTTCAGTCTGCCCCACTGCAACTTC-AGGAGGATAAGACTTGCTTA-C-TTAGTCTGCT
* * *
52787582 CCACTGCAACTTCA-GGAGGATAAGACTTAAGATCTGAGGTTTTAATCCGCTCCACTGCAACTTC
63 CCACTGCAACTTCAGGGA-GATAAGAC-T-AGA--TG-CG-----ATCTGCT-CTCTGCAACTTC
* * *
52787646 AGGGAGATAGGATT-ATCGGCTTTTATCTGCTCCACTGCAACTTCAGGGAGATAAGACT
116 AGAGAGATAGGATTGA--GGCTTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGACT
52787704 TGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCA
1 TGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCA
*
52787769 CTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGGGAGATAGGATT-
66 CTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAGGATTG
*
52787833 ATCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGACT
131 A--GGCTTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGACT
*
52787877 TGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCCTCT
1 TGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTG-CTCC
* * * *
52787942 AGTGCAACTTCAGGGAGATAAGACTAGATGCAATCTGCTTTCTGCAACTTCAGAGAGATAAGAAT
65 ACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGAT-AGGAT
*
52788007 TGAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATA
129 TGAGGCTTTAATCCGCTCCACTGCAACTTCAGGGAGATA
52788046 GGATTATCGA
Statistics
Matches: 457, Mismatches: 46, Indels: 46
0.83 0.08 0.08
Matches are distributed among these distances:
171 2 0.00
172 36 0.08
173 162 0.35
174 99 0.22
175 8 0.02
176 1 0.00
177 2 0.00
178 1 0.00
179 1 0.00
180 2 0.00
182 4 0.01
183 8 0.02
184 89 0.19
185 40 0.09
186 2 0.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.29
Consensus pattern (172 bp):
TGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCA
CTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAGGATTG
AGGCTTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGACT
Found at i:52788033 original size:218 final size:216
Alignment explanation
Indices: 52787622--52788111 Score: 557
Period size: 218 Copynumber: 2.2 Consensus size: 216
52787612 GATCTGAGGT
* * * * * *
52787622 TTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGC-T-TTTATCTGCTCCACTGCA
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGACT-T-GCCATCTTCATCTGCCCCACTGCA
*
52787685 ACTTCAGGGAGATAAGACTTGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATAAGACTT
64 ACTTCAGGGAGATAAGACTTGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATAAGACTA
* * * * * *
52787750 GCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAA
129 GCATAC-TAATCTGCTCCACTGCAACTTCAGAGAGATAAGACTAGATGCAATCCGCTCACTGCAA
*
52787815 CTTCAGGGAGATAGGATTATCGGC
193 CTTCAGGGAGATAGGATTATCGAC
52787839 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCCATCTTCAGTCTGCCCCACTGCAA
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCCATCTTCA-TCTGCCCCACTGCAA
* * *
52787904 CTTCA-GGAGGATAAGACTTG-CTTACTT-AGTCTGCCTCTAGTGCAACTTCAGG-GAGATAAGA
65 CTTCAGGGA-GATAAGACTTGCCAT-CTTCAGTCTGCC-CCACTGCAACTTCAGGAG-GATAAGA
* ** * * **
52787965 CTAG-ATGC-AATCTGCT-TTCTGCAACTTCAGAGAGATAAGAATTGAGGTTTTAATCCGCTCCA
126 CTAGCATACTAATCTGCTCCACTGCAACTTCAGAGAGATAAG-ACT-A-GATGCAATCCGCT-CA
52788027 CTGCAACTTCAGGGAGATAGGATTATCGAC
187 CTGCAACTTCAGGGAGATAGGATTATCGAC
* * *
52788057 TTTAATCTGCTCCACTACTACTTCAGGGAGATAAGACTTGTCATCTTCGATCTGC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCCATCTTC-ATCTGC
52788112 TCCGCTCGAT
Statistics
Matches: 234, Mismatches: 27, Indels: 23
0.82 0.10 0.08
Matches are distributed among these distances:
214 20 0.09
215 11 0.05
216 3 0.01
217 62 0.26
218 137 0.59
219 1 0.00
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (216 bp):
TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCCATCTTCATCTGCCCCACTGCAAC
TTCAGGGAGATAAGACTTGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATAAGACTAGC
ATACTAATCTGCTCCACTGCAACTTCAGAGAGATAAGACTAGATGCAATCCGCTCACTGCAACTT
CAGGGAGATAGGATTATCGAC
Found at i:52793485 original size:98 final size:98
Alignment explanation
Indices: 52793311--52793507 Score: 358
Period size: 98 Copynumber: 2.0 Consensus size: 98
52793301 GTACAATAAA
*
52793311 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
* *
52793376 CCTTTAGAATCCCAAACTTGGAATATTTCCTTT
66 CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
*
52793409 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATATGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
52793474 CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
66 CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
52793507 A
1 A
52793508 TTATTTTTAA
Statistics
Matches: 95, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 95 1.00
ACGTcount: A:0.37, C:0.23, G:0.10, T:0.29
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
Found at i:52794882 original size:19 final size:19
Alignment explanation
Indices: 52794858--52794951 Score: 143
Period size: 19 Copynumber: 4.8 Consensus size: 19
52794848 AATCATATAT
52794858 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
52794877 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
52794896 TCTAAGATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
** *
52794917 TCTTGGATTGCATATCAAA
1 TCTAAGATTGCATATCATA
52794936 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
52794952 CTCAAAAATT
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
19 51 0.75
21 17 0.25
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:52794926 original size:40 final size:40
Alignment explanation
Indices: 52794851--52794950 Score: 145
Period size: 40 Copynumber: 2.6 Consensus size: 40
52794841 ATTACAAAAT
52794851 CATAT-AT-TCTAAGATTGC--ATATCATATCTAAGATTG
1 CATATCATATCTAAGATTGCATATATCATATCTAAGATTG
**
52794887 CATATCATATCTAAGATTGCATATATCATATCTTGGATTG
1 CATATCATATCTAAGATTGCATATATCATATCTAAGATTG
*
52794927 CATATCAAATCTAAGATTGCATAT
1 CATATCATATCTAAGATTGCATAT
52794951 CCTCAAAAAT
Statistics
Matches: 57, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
36 5 0.09
37 2 0.04
38 11 0.19
40 39 0.68
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (40 bp):
CATATCATATCTAAGATTGCATATATCATATCTAAGATTG
Found at i:52802390 original size:22 final size:22
Alignment explanation
Indices: 52802362--52802414 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
52802352 AACCAAAATT
52802362 ATCTCCTAAACTTTAGCATCTA
1 ATCTCCTAAACTTTAGCATCTA
*
52802384 ATCTCCTAAACTTTAGCATTTA
1 ATCTCCTAAACTTTAGCATCTA
52802406 ATCTCCTAA
1 ATCTCCTAA
52802415 TTAAAAGGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.32, C:0.26, G:0.04, T:0.38
Consensus pattern (22 bp):
ATCTCCTAAACTTTAGCATCTA
Found at i:52814307 original size:12 final size:12
Alignment explanation
Indices: 52814292--52814321 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
52814282 GTATATACGC
52814292 ATATATGTATAT
1 ATATATGTATAT
*
52814304 ATATATTTATAT
1 ATATATGTATAT
52814316 ATATAT
1 ATATAT
52814322 AAAATAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (12 bp):
ATATATGTATAT
Found at i:52814445 original size:20 final size:20
Alignment explanation
Indices: 52814409--52814468 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
52814399 ACATACGCGC
*
52814409 ATATAATGTAAGT-ATAATGA
1 ATATAATATAAGTAATAAT-A
52814429 ATATAATATAA-TAATAACTA
1 ATATAATATAAGTAATAA-TA
* *
52814449 ATATAATAAAATTAATAATA
1 ATATAATATAAGTAATAATA
52814469 TAAAAAAAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 1 0.03
20 27 0.77
21 7 0.20
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (20 bp):
ATATAATATAAGTAATAATA
Found at i:52814469 original size:17 final size:17
Alignment explanation
Indices: 52814422--52814476 Score: 58
Period size: 20 Copynumber: 3.1 Consensus size: 17
52814412 TAATGTAAGT
52814422 ATAATGAATATAATATAATA
1 ATAAT-AATATAATA-AA-A
52814442 ATAACTAATATAATAAAA
1 ATAA-TAATATAATAAAA
*
52814460 TTAATAATATAA-AAAA
1 ATAATAATATAATAAAA
52814476 A
1 A
52814477 ACTAAAACAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
16 4 0.12
17 8 0.25
18 4 0.12
19 2 0.06
20 13 0.41
21 1 0.03
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (17 bp):
ATAATAATATAATAAAA
Found at i:52819275 original size:23 final size:22
Alignment explanation
Indices: 52819243--52819288 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
52819233 AATCAAATTT
52819243 AATAAAAATAA-ATAACAAATAAA
1 AATAAAAATAATA-AACAAA-AAA
*
52819266 AATAATAATAATAAACAAAAAA
1 AATAAAAATAATAAACAAAAAA
52819288 A
1 A
52819289 GAGACTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 4 0.19
23 16 0.76
24 1 0.05
ACGTcount: A:0.78, C:0.04, G:0.00, T:0.17
Consensus pattern (22 bp):
AATAAAAATAATAAACAAAAAA
Found at i:52821609 original size:41 final size:40
Alignment explanation
Indices: 52821563--52821653 Score: 103
Period size: 40 Copynumber: 2.2 Consensus size: 40
52821553 AAACAGGCTT
52821563 TTAGCGGCG-TTTAGACAAAAAACGCCACTAAAAATCAAGCA
1 TTAGCGGCGCTTT-GA-AAAAAACGCCACTAAAAATCAAGCA
* * * ** *
52821604 TTAGCGGCGCTTTTATAAAAACGCCGCTAAATGTCGAGCA
1 TTAGCGGCGCTTTGAAAAAAACGCCACTAAAAATCAAGCA
52821644 TTAGCGGCGC
1 TTAGCGGCGC
52821654 CGCTAAAAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
40 30 0.70
41 10 0.23
42 3 0.07
ACGTcount: A:0.34, C:0.23, G:0.22, T:0.21
Consensus pattern (40 bp):
TTAGCGGCGCTTTGAAAAAAACGCCACTAAAAATCAAGCA
Found at i:52821801 original size:41 final size:41
Alignment explanation
Indices: 52821740--52821976 Score: 291
Period size: 41 Copynumber: 5.8 Consensus size: 41
52821730 TTTTTGGGGG
* *
52821740 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGGGC
1 CTTTAGCGGCGTTTTAGAAAAAGCGCCGCTAATGCTCTGGC
* * * *
52821781 CTTTAGCAGCGCTCTAGAAAAAGCGCCGCTAGTGCTCTGGC
1 CTTTAGCGGCGTTTTAGAAAAAGCGCCGCTAATGCTCTGGC
*
52821822 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTGGC
1 CTTTAGCGGCGTTTTAGAAAAAGCGCCGCTAATGCTCTGGC
* * **
52821863 CTTTAGTGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTTTC
1 CTTTAGCGGCGTTTTAGAAAAAGCGCCGCTAATGCTCTGGC
* *
52821904 CTTTAGCGGCGTTTTTA-AAAAAGCGCCGCTAAAGGTC-GAG-
1 CTTTAGCGGCG-TTTTAGAAAAAGCGCCGCTAATGCTCTG-GC
* * *
52821944 CATTAGCGGCGTTTTTGAAAAAGTGCCGCTAAT
1 CTTTAGCGGCGTTTTAGAAAAAGCGCCGCTAAT
52821977 AATAATAAAA
Statistics
Matches: 169, Mismatches: 24, Indels: 7
0.85 0.12 0.04
Matches are distributed among these distances:
39 4 0.02
40 24 0.14
41 137 0.81
42 4 0.02
ACGTcount: A:0.22, C:0.23, G:0.26, T:0.28
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTAGAAAAAGCGCCGCTAATGCTCTGGC
Found at i:52821883 original size:82 final size:81
Alignment explanation
Indices: 52821740--52821976 Score: 323
Period size: 82 Copynumber: 2.9 Consensus size: 81
52821730 TTTTTGGGGG
* * * *
52821740 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGGGCCTTTAGCAGCGCTCTAGAAAAAGC
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC-GGCCTTTAGCGGCGTTTTTGAAAAAGC
*
52821805 GCCGCTAGTGCTCTGGC
65 GCCGCTAATGCTCTGGC
*
52821822 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTGGCCTTTAGTGGCGTTTTTGAAAAAGC
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC-GGCCTTTAGCGGCGTTTTTGAAAAAGC
**
52821887 GCCGCTAATGCTCTTTC
65 GCCGCTAATGCTCTGGC
* * * * *
52821904 CTTTAGCGGCGTTTTTAAAAAAGCGCCGCTAAAGGTCGAG-CATTAGCGGCGTTTTTGAAAAAGT
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCG-GCCTTTAGCGGCGTTTTTGAAAAAGC
52821968 GCCGCTAAT
65 GCCGCTAAT
52821977 AATAATAAAA
Statistics
Matches: 139, Mismatches: 15, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
81 31 0.22
82 108 0.78
ACGTcount: A:0.22, C:0.23, G:0.26, T:0.28
Consensus pattern (81 bp):
CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGGCCTTTAGCGGCGTTTTTGAAAAAGCG
CCGCTAATGCTCTGGC
Found at i:52823045 original size:33 final size:33
Alignment explanation
Indices: 52822994--52823065 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 33
52822984 TTAAATAATA
* **
52822994 TTTAGGGGTTAGAAATTCAGGGTTGGGTTAGGG
1 TTTAGGGATTAGAAATTCAGGGTCAGGTTAGGG
** * *
52823027 TTTAGGGATTAGGGATTCATGGTCAGGTTTGGG
1 TTTAGGGATTAGAAATTCAGGGTCAGGTTAGGG
52823060 TTTAGG
1 TTTAGG
52823066 ATTTAGATTA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.19, C:0.04, G:0.40, T:0.36
Consensus pattern (33 bp):
TTTAGGGATTAGAAATTCAGGGTCAGGTTAGGG
Found at i:52823082 original size:115 final size:116
Alignment explanation
Indices: 52822950--52823224 Score: 333
Period size: 115 Copynumber: 2.4 Consensus size: 116
52822940 GTCAGGTTAT
*
52822950 GGTTTAGATTAATTAGTGTGTTTTAATTTATATATTAAATAATATTTAGGGGTTAGAAATTCAGG
1 GGTTTAGATTAATTAGTGT-TTTTAATTTATATATTAAATAAGATTTAGGGGTTAGAAATTCAGG
* * * * *
52823015 GTT-GGGTTAG-GGTTTAGGGATTAGGGATTCATGGTC-AGGTTTGGGTTT-A
65 GTTAGAGTTAGTGATTTAGGGATTAGAGATTCAGGGTCGA-GTTAGGGTTTAA
* *** **
52823064 GGATTTAGATTAATTAGTGTTTTTTAATTTATATATTAAATAAGGTTTAGGGGTTAGGGGTTTGG
1 GG-TTTAGATTAATTAGTG-TTTTTAATTTATATATTAAATAAGATTTAGGGGTTAGAAATTCAG
* *
52823129 GGTTAAGAGTTAGTGATTTAGGGTTTAGAGATTCGGGGTCGAGTTAGGGTTTAA
64 GGTT-AGAGTTAGTGATTTAGGGATTAGAGATTCAGGGTCGAGTTAGGGTTTAA
* *
52823183 GGTTTAGATTAATTAGTATTTTTAATTTATATACTAAATAAG
1 GGTTTAGATTAATTAGTGTTTTTAATTTATATATTAAATAAG
52823225 TTCTTATATA
Statistics
Matches: 138, Mismatches: 16, Indels: 11
0.84 0.10 0.07
Matches are distributed among these distances:
114 2 0.01
115 57 0.41
116 1 0.01
117 29 0.21
118 45 0.33
119 4 0.03
ACGTcount: A:0.28, C:0.02, G:0.27, T:0.43
Consensus pattern (116 bp):
GGTTTAGATTAATTAGTGTTTTTAATTTATATATTAAATAAGATTTAGGGGTTAGAAATTCAGGG
TTAGAGTTAGTGATTTAGGGATTAGAGATTCAGGGTCGAGTTAGGGTTTAA
Found at i:52824252 original size:16 final size:15
Alignment explanation
Indices: 52824231--52824263 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
52824221 CGCCATTTAT
*
52824231 AAAT-TTTCCCCCTG
1 AAATATTTCCCCCTA
52824245 AAATATTTCCCCCTA
1 AAATATTTCCCCCTA
52824260 AAAT
1 AAAT
52824264 CCCTAATTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.33, C:0.30, G:0.03, T:0.33
Consensus pattern (15 bp):
AAATATTTCCCCCTA
Found at i:52824453 original size:17 final size:17
Alignment explanation
Indices: 52824433--52824466 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
52824423 ATTTTTTCTG
*
52824433 ATATTATATGTATATAT
1 ATATTATATATATATAT
52824450 ATATTATATATATATAT
1 ATATTATATATATATAT
52824467 GGAGTAGCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
ATATTATATATATATAT
Found at i:52824457 original size:11 final size:12
Alignment explanation
Indices: 52824433--52824464 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
52824423 ATTTTTTCTG
52824433 ATAT-TATATGT
1 ATATATATATGT
52824444 ATATATATAT-T
1 ATATATATATGT
52824455 ATATATATAT
1 ATATATATAT
52824465 ATGGAGTAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 15 0.75
12 5 0.25
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (12 bp):
ATATATATATGT
Found at i:52824461 original size:15 final size:16
Alignment explanation
Indices: 52824433--52824466 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
52824423 ATTTTTTCTG
52824433 ATATTATATGTATATAT
1 ATATTATA-GTATATAT
52824450 ATATTATA-TATATAT
1 ATATTATAGTATATAT
52824465 AT
1 AT
52824467 GGAGTAGCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
ATATTATAGTATATAT
Found at i:52828123 original size:43 final size:43
Alignment explanation
Indices: 52828075--52828377 Score: 335
Period size: 43 Copynumber: 7.1 Consensus size: 43
52828065 ATGGCACTTT
* * *
52828075 TAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAAGTTATGATCTA
1 TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTTCTGATCTA
* * * * *
52828118 TAGCGGCGTTCGTGAGAGAAGCGTCGCTAAAGGTCCTGATATA
1 TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTTCTGATCTA
* * *
52828161 TAGCAGCGTTTGTGGGAAAAGCGACGCTAAAGG-TCTTGATCTA
1 TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTTC-TGATCTA
** * *
52828204 TAGCGGCGTTTGTGCCAAAAACGCCACTAAAGG-TCTTGATCTA
1 TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTTC-TGATCTA
* ** *
52828247 TAGCGGCGTTTGT-ATAAAAAGCATCGCTAAAGGTCCTGATCTA
1 TAGCGGCGTTTGTGA-GAAAAGCGCCGCTAAAGGTTCTGATCTA
* *
52828290 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
1 TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTTCTGATCTA
* * *
52828333 TAGCGGCGTTTGTG-GGAAAGCGCTGCTAAAGGTTTTGATCTA
1 TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTTCTGATCTA
52828375 TAG
1 TAG
52828378 TTCCTGATCT
Statistics
Matches: 220, Mismatches: 36, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
42 28 0.13
43 191 0.87
44 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (43 bp):
TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTTCTGATCTA
Found at i:52828234 original size:86 final size:86
Alignment explanation
Indices: 52828075--52828377 Score: 371
Period size: 86 Copynumber: 3.5 Consensus size: 86
52828065 ATGGCACTTT
* * * * *
52828075 TAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAAGT-TATGATCTATAGCGGCGTTCGTGAGAGAAG
1 TAGCGGCGTTTGTGGAAAAAGCGACGCTAAAGGTCT-TGATCTATAGCGGCGTTTGTGAGAAAAG
* *
52828139 CGTCGCTAAAGGTCCTGATATA
65 CGCCGCTAAAGGTCCTGATCTA
* * ** *
52828161 TAGCAGCGTTTGTGGGAAAAGCGACGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGCCAAAAAC
1 TAGCGGCGTTTGTGGAAAAAGCGACGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGAGAAAAGC
* *
52828226 GCCACTAAAGGTCTTGATCTA
66 GCCGCTAAAGGTCCTGATCTA
** * *
52828247 TAGCGGCGTTTGTATAAAAAGC-ATCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGGAAAAG
1 TAGCGGCGTTTGTGGAAAAAGCGA-CGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGAGAAAAG
52828311 CGCCGCTAAAGGTCCTGATCTA
65 CGCCGCTAAAGGTCCTGATCTA
* *
52828333 TAGCGGCGTTTGTGG-GAAAGCG-CTGCTAAAGGTTTTGATCTATAG
1 TAGCGGCGTTTGTGGAAAAAGCGAC-GCTAAAGGTCTTGATCTATAG
52828378 TTCCTGATCT
Statistics
Matches: 184, Mismatches: 29, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
84 1 0.01
85 25 0.14
86 157 0.85
87 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (86 bp):
TAGCGGCGTTTGTGGAAAAAGCGACGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGAGAAAAGC
GCCGCTAAAGGTCCTGATCTA
Found at i:52828305 original size:129 final size:127
Alignment explanation
Indices: 52828075--52828377 Score: 410
Period size: 129 Copynumber: 2.3 Consensus size: 127
52828065 ATGGCACTTT
* * *
52828075 TAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAAGTTATGATCTATAGCGGCGTTCGTGAGAGAAGC
1 TAGCGGCGTTTGTGAAAAAA-CGCCGCTAAAGGTT-TGATCTATAGCGGCGTTCGTGAAAAAAGC
* *
52828140 GTCGCTAAAGGTCCTGATATATAGCAGCGTTTGTGGGAAAAGCGACGCTAAAGGTCTTGATCTA
64 ATCGCTAAAGGTCCTGATATATAGCAGCGTTTGTGGGAAAAGCGACGCTAAAGGTCCTGATCTA
* * *
52828204 TAGCGGCGTTTGTGCCAAAAACGCCACTAAAGGTCTTGATCTATAGCGGCGTTTGT-ATAAAAAG
1 TAGCGGCGTTTGTG-AAAAAACGCCGCTAAAGGT-TTGATCTATAGCGGCGTTCGTGA-AAAAAG
* * *
52828268 CATCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
63 CATCGCTAAAGGTCCTGATATATAGCAGCGTTTGTGGGAAAAGCGACGCTAAAGGTCCTGATCTA
** * *
52828333 TAGCGGCGTTTGTGGGAAAGCGCTGCTAAAGGTTTTGATCTATAG
1 TAGCGGCGTTTGTGAAAAAACGCCGCTAAAGG-TTTGATCTATAG
52828378 TTCCTGATCT
Statistics
Matches: 154, Mismatches: 16, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
128 25 0.16
129 123 0.80
130 6 0.04
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (127 bp):
TAGCGGCGTTTGTGAAAAAACGCCGCTAAAGGTTTGATCTATAGCGGCGTTCGTGAAAAAAGCAT
CGCTAAAGGTCCTGATATATAGCAGCGTTTGTGGGAAAAGCGACGCTAAAGGTCCTGATCTA
Found at i:52829470 original size:38 final size:38
Alignment explanation
Indices: 52829419--52829494 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
52829409 ACCCCCTGAC
52829419 ATCAAACAATTTCATGTTCAACACATGCTGCCTGGGAT
1 ATCAAACAATTTCATGTTCAACACATGCTGCCTGGGAT
52829457 ATCAAACAATTTCATGTTCAACACATGCTGCCTGGGAT
1 ATCAAACAATTTCATGTTCAACACATGCTGCCTGGGAT
52829495 TTCCGGGTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.29
Consensus pattern (38 bp):
ATCAAACAATTTCATGTTCAACACATGCTGCCTGGGAT
Found at i:52838902 original size:74 final size:74
Alignment explanation
Indices: 52838746--52838892 Score: 269
Period size: 75 Copynumber: 2.0 Consensus size: 74
52838736 CAAAAACAGA
52838746 GATGCTTTAAAATTAGAAAAAAAACTTTTTTATGGTATTCATATATTTATTTCCTATCTTTATAG
1 GATGCTTTAAAATTAGAAAAAAAACTTTTTTATGGTATTCATATATTTATTTCCTATCTTTATAG
52838811 AAATATTCT
66 AAATATTCT
52838820 GATGCTTTAAAATTAGAAAAAAAAAAC-TTTTTATGGTATTCATATATTTATTTCCTATCTTTAT
1 GATGCTTTAAAATTAG--AAAAAAAACTTTTTTATGGTATTCATATATTTATTTCCTATCTTTAT
52838884 AGAAATATT
64 AGAAATATT
52838893 TCTATCTTTA
Statistics
Matches: 71, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
74 16 0.23
75 46 0.65
76 9 0.13
ACGTcount: A:0.38, C:0.09, G:0.08, T:0.45
Consensus pattern (74 bp):
GATGCTTTAAAATTAGAAAAAAAACTTTTTTATGGTATTCATATATTTATTTCCTATCTTTATAG
AAATATTCT
Found at i:52844720 original size:24 final size:24
Alignment explanation
Indices: 52844675--52844720 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
52844665 TAATTTTATG
*
52844675 ATTTTTTATATTTTTTAAATTTCA
1 ATTTTTTATATTTTTGAAATTTCA
52844699 ATTTTTTAT-TTTTTGAATATTT
1 ATTTTTTATATTTTTGAA-ATTT
52844721 TTATAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (24 bp):
ATTTTTTATATTTTTGAAATTTCA
Found at i:52852305 original size:2 final size:2
Alignment explanation
Indices: 52852294--52852326 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
52852284 ACTTTAATGA
52852294 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52852327 GTTTACGTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:52862709 original size:284 final size:284
Alignment explanation
Indices: 52862367--52863183 Score: 1598
Period size: 284 Copynumber: 2.9 Consensus size: 284
52862357 TTTCAATTCA
*
52862367 ATTAATTTAATTTACCCACAATTTTCTTCTTCAGTTTCATACGAAGCAAACGAACAATGGGTCTT
1 ATTAATTTAATTTACCCACAATTTTCTTCTTCAGTTTCATTCGAAGCAAACGAACAATGGGTCTT
52862432 GAATTCTTCAATAATATGAATCAGAAATTACCTTGCAATTGATGTGTCGAATTACTTTTTCACAA
66 GAATTCTTCAATAATATGAATCAGAAATTACCTTGCAATTGATGTGTCGAATTACTTTTTCACAA
52862497 TAACCACTAATTAAGGCCTGTTTTGCTTCTGTTCTAAATTCCACTTCAGCTTTACAATGTAATTT
131 TAACCACTAATTAAGGCCTGTTTTGCTTCTGTTCTAAATTCCACTTCAGCTTTACAATGTAATTT
52862562 TTCAATTTTCCACACTAGACTTACTTTTTGTGTTAATTTTTCAATGATAATGGTCAATTATTTCT
196 TTCAATTTTCCACACTAGACTTACTTTTTGTGTTAATTTTTCAATGATAATGGTCAATTATTTCT
52862627 ACCTATTTAAGTGTTCTTTAACAG
261 ACCTATTTAAGTGTTCTTTAACAG
52862651 ATTAATTTAATTTACCCACAATTTTCTTCTTCAGTTTCATTCGAAGCAAACGAACAATGGGTCTT
1 ATTAATTTAATTTACCCACAATTTTCTTCTTCAGTTTCATTCGAAGCAAACGAACAATGGGTCTT
52862716 GAATTCTTCAATAATATGAATCAGAAATTACCTTGCAATTGATGTGTCGAATTACTTTTTCACAA
66 GAATTCTTCAATAATATGAATCAGAAATTACCTTGCAATTGATGTGTCGAATTACTTTTTCACAA
52862781 TAACCACTAATTAAGGCCTGTTTTGCTTCTGTTCTAAATTCCACTTCAGCTTTACAATGTAATTT
131 TAACCACTAATTAAGGCCTGTTTTGCTTCTGTTCTAAATTCCACTTCAGCTTTACAATGTAATTT
52862846 TTCAATTTTCCACACTAGACTTACTTTTTGTGTTAATTTTTCAATGATAATGGTCAATTATTTCT
196 TTCAATTTTCCACACTAGACTTACTTTTTGTGTTAATTTTTCAATGATAATGGTCAATTATTTCT
52862911 ACCTATTTAAGTGTTCTTTAACAG
261 ACCTATTTAAGTGTTCTTTAACAG
52862935 ATTAATTTAATTTACCCACAATTTTCTTCTTCAGTTTCATTCGAAGCAAACGAACAATGGGTCTT
1 ATTAATTTAATTTACCCACAATTTTCTTCTTCAGTTTCATTCGAAGCAAACGAACAATGGGTCTT
52863000 GAATTCTTCAATAATATGAATCAGAAATTACCTTGCAATTGATGTGTCGAATTACTTTTTCACAA
66 GAATTCTTCAATAATATGAATCAGAAATTACCTTGCAATTGATGTGTCGAATTACTTTTTCACAA
*
52863065 TAACCACTAATTAAGGCCTGTTTTGCTTCTGTTCTAAATTCCACTTCAGCTTCACAATGTAATTT
131 TAACCACTAATTAAGGCCTGTTTTGCTTCTGTTCTAAATTCCACTTCAGCTTTACAATGTAATTT
* *
52863130 TTCAATTTTCCACACTAGACTTACTTTTTGTGTTAATTTTTCAACGATACTGGT
196 TTCAATTTTCCACACTAGACTTACTTTTTGTGTTAATTTTTCAATGATAATGGT
52863184 AAAATATTAT
Statistics
Matches: 529, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
284 529 1.00
ACGTcount: A:0.30, C:0.18, G:0.11, T:0.41
Consensus pattern (284 bp):
ATTAATTTAATTTACCCACAATTTTCTTCTTCAGTTTCATTCGAAGCAAACGAACAATGGGTCTT
GAATTCTTCAATAATATGAATCAGAAATTACCTTGCAATTGATGTGTCGAATTACTTTTTCACAA
TAACCACTAATTAAGGCCTGTTTTGCTTCTGTTCTAAATTCCACTTCAGCTTTACAATGTAATTT
TTCAATTTTCCACACTAGACTTACTTTTTGTGTTAATTTTTCAATGATAATGGTCAATTATTTCT
ACCTATTTAAGTGTTCTTTAACAG
Found at i:52877692 original size:22 final size:20
Alignment explanation
Indices: 52877647--52877693 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
52877637 TTAATTAACT
* *
52877647 TATTTTCAGGAAAAGTTTCT
1 TATTTTCAGCAAAAGTTTCA
52877667 TATTTTCAGCAAAATGGTTTCA
1 TATTTTCAGCAAAA--GTTTCA
52877689 TATTT
1 TATTT
52877694 AATACATGCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 13 0.57
22 10 0.43
ACGTcount: A:0.30, C:0.11, G:0.13, T:0.47
Consensus pattern (20 bp):
TATTTTCAGCAAAAGTTTCA
Found at i:52878878 original size:56 final size:56
Alignment explanation
Indices: 52878792--52878904 Score: 226
Period size: 56 Copynumber: 2.0 Consensus size: 56
52878782 TTCAAAATAC
52878792 CAAAAGAGTGTTGACAGTGTGGATGGATCTCCAATGATATCCGTACCCCGAGCTAG
1 CAAAAGAGTGTTGACAGTGTGGATGGATCTCCAATGATATCCGTACCCCGAGCTAG
52878848 CAAAAGAGTGTTGACAGTGTGGATGGATCTCCAATGATATCCGTACCCCGAGCTAG
1 CAAAAGAGTGTTGACAGTGTGGATGGATCTCCAATGATATCCGTACCCCGAGCTAG
52878904 C
1 C
52878905 TTAGTGACAC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.23
Consensus pattern (56 bp):
CAAAAGAGTGTTGACAGTGTGGATGGATCTCCAATGATATCCGTACCCCGAGCTAG
Found at i:52880617 original size:18 final size:19
Alignment explanation
Indices: 52880581--52880617 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
52880571 GTTAAAATTG
52880581 AAACGAAATTAAAAGAAAA
1 AAACGAAATTAAAAGAAAA
*
52880600 AAACGAAA-TAAAATAAAA
1 AAACGAAATTAAAAGAAAA
52880618 TAATGGGACG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.76, C:0.05, G:0.08, T:0.11
Consensus pattern (19 bp):
AAACGAAATTAAAAGAAAA
Found at i:52884340 original size:113 final size:113
Alignment explanation
Indices: 52884140--52884803 Score: 1096
Period size: 113 Copynumber: 5.9 Consensus size: 113
52884130 AATAAGCAAC
* * *
52884140 AGCGGCGTTTTTTAAAAAGCACCGCAAAAAACCTAATCCAAAACGACGCAGTTTTGTGAGCTTTG
1 AGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAATCCAAAACGACGCAGTTTTGTGAGCTTTG
52884205 TGGATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTCAGGGCTTT
66 TGGATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTCAGGGCTTT
*
52884253 AACGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAATCCAAAACGACGCAGTTTTGTGAGCTTTG
1 AGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAATCCAAAACGACGCAGTTTTGTGAGCTTTG
* *
52884318 TGGATTTAGCGGCGTTTTTAAGGTAGCGCCGCTAATGCTCAGGGCTGT
66 TGGATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTCAGGGCTTT
52884366 AGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAATCCAAAACGACGCAGTTTTGTGAGCTTTG
1 AGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAATCCAAAACGACGCAGTTTTGTGAGCTTTG
*
52884431 TGGATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTCAGGGATTT
66 TGGATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTCAGGGCTTT
52884479 AGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAATCCAAAACGACGCAGTTTTGTGAGCTTTG
1 AGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAATCCAAAACGACGCAGTTTTGTGAGCTTTG
*
52884544 TGGATTTAGCGGTGTTTTTAAGGAAGCGCCGCTAATGCTCAGGGCTTT
66 TGGATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTCAGGGCTTT
* ** *
52884592 AGCGGCGTTTTTGAGATAGCGCCGCAAAAAACCTAATGTAAAATGACGCAGTTTTGTGAGCTTTC
1 AGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAATCCAAAACGACGCAGTTTTGTGAGCTTT-
* * * * *
52884657 GGGGATTTAGCAGCATTTTTAAGAAAGCGCCGCTAATGTTCAGGGCTTT
65 GTGGATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTCAGGGCTTT
* *
52884706 AGCGGCGTTTTTGGGAAAGCGCCGCAAAAAACCTAATCCAAAACGACGCCGTTTTGTGAGCTTTC
1 AGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAATCCAAAACGACGCAGTTTTGTGAGCTTT-
* * *
52884771 GGGGATTTAGTGGCGTTGTTT-AGAAAGCGCCGC
65 GTGGATTTAGCGGCGTT-TTTAAGGAAGCGCCGC
52884804 AAAAAACATA
Statistics
Matches: 518, Mismatches: 31, Indels: 3
0.94 0.06 0.01
Matches are distributed among these distances:
113 387 0.75
114 128 0.25
115 3 0.01
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (113 bp):
AGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAATCCAAAACGACGCAGTTTTGTGAGCTTTG
TGGATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTCAGGGCTTT
Found at i:52884822 original size:73 final size:73
Alignment explanation
Indices: 52884703--52884935 Score: 317
Period size: 73 Copynumber: 3.2 Consensus size: 73
52884693 TGTTCAGGGC
** *
52884703 TTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAACCTAATCCAAAACGACGCCGTTTTGTGAGCT
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGCCGTTTTGTGAGCT
52884768 TTCGGGGA
66 TTCGGGGA
* * * * *
52884776 TTTAGTGGCGTTGTTT-AGAAAGCGCCGCAAAAAACATAAGGCAAAACGACTCCGTTTTGTGCGC
1 TTTAGCGGCGTT-TTTAAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGCCGTTTTGTGAGC
52884840 TTTCGGGGA
65 TTTCGGGGA
* * *
52884849 TTTAGCGGCGTTTTTAAGGAAGCGCCGCAAAAAAAACCTAAGCCAAAACGACGCC-TTTTTTGTG
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGC--AAAAAACCTAAGCCAAAACGACGCCGTTTTGTGAG
52884913 CTTTCGGGGA
64 CTTTCGGGGA
*
52884923 TTTAGCGGTGTTT
1 TTTAGCGGCGTTT
52884936 AATTGATTTA
Statistics
Matches: 141, Mismatches: 15, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
72 3 0.02
73 84 0.60
74 32 0.23
75 22 0.16
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (73 bp):
TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGCCGTTTTGTGAGCT
TTCGGGGA
Found at i:52914908 original size:50 final size:50
Alignment explanation
Indices: 52914773--52915208 Score: 309
Period size: 48 Copynumber: 8.9 Consensus size: 50
52914763 CTGACAGCGG
* * * *
52914773 ATCTCACTTCCCCGACACTGCAATTTAAAAGATCGAAGCCACAGCGGCGA
1 ATCTCACTTCCCAGACATTGCAATTTAAAAGATTGAAGCCACAACGGCGA
* * ** **** ** * *
52914823 ATCTCAC-TACTAGTGA-TGCAGCGGAGCAGATTGAAGCTACAACGGCAA
1 ATCTCACTTCCCAGACATTGCAATTTAAAAGATTGAAGCCACAACGGCGA
52914871 ATCTCACTTCCCAGACATTGCAATTTAAAAGATTGAAGCCACAACGGCGA
1 ATCTCACTTCCCAGACATTGCAATTTAAAAGATTGAAGCCACAACGGCGA
* * * **** ** * *
52914921 ATCTTACTT--CTGGCGA-TGCAGCGGAGCAGATTGAAGCTACAACGGCAA
1 ATCTCACTTCCCAGAC-ATTGCAATTTAAAAGATTGAAGCCACAACGGCGA
52914969 ATCTCACTTCCCAGACATTGCAATTTAAAAGATTGAAGCCACAACGGCGA
1 ATCTCACTTCCCAGACATTGCAATTTAAAAGATTGAAGCCACAACGGCGA
* * * **** ** * *
52915019 ATCTTACTT--CTGGCGA-TGCAGCGGAGCAGATTGAAGCTACAACGGCAA
1 ATCTCACTTCCCAGAC-ATTGCAATTTAAAAGATTGAAGCCACAACGGCGA
52915067 ATCTCACTTCCCAGACATTGCAATTTAAAAGATTGAAGCCACAACGGCGA
1 ATCTCACTTCCCAGACATTGCAATTTAAAAGATTGAAGCCACAACGGCGA
* * * * *** * *
52915117 ATCTTACTT--CTGGCAATGC-AGCGAAGAAGATTGAAGCTACAACAGCGA
1 ATCTCACTTCCCAGACATTGCAATTTAA-AAGATTGAAGCCACAACGGCGA
* * * *
52915165 ATCTCATTTCCCCGATATTGCAATTTAAAAGATCGAAGCCACAA
1 ATCTCACTTCCCAGACATTGCAATTTAAAAGATTGAAGCCACAA
52915209 TGGTAGATTT
Statistics
Matches: 281, Mismatches: 91, Indels: 28
0.70 0.23 0.07
Matches are distributed among these distances:
47 3 0.01
48 133 0.47
49 13 0.05
50 129 0.46
51 3 0.01
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.21
Consensus pattern (50 bp):
ATCTCACTTCCCAGACATTGCAATTTAAAAGATTGAAGCCACAACGGCGA
Found at i:52915224 original size:98 final size:98
Alignment explanation
Indices: 52914773--52915208 Score: 719
Period size: 98 Copynumber: 4.4 Consensus size: 98
52914763 CTGACAGCGG
* * * * * * * *
52914773 ATCTCACTTCCCCGACACTGCAATTTAAAAGATCGAAGCCACAGCGGCGAATCTCACTACTAGTG
1 ATCTCACTTCCCAGACATTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCTGGCG
52914838 ATGCAGCGGAGCAGATTGAAGCTACAACGGCAA
66 ATGCAGCGGAGCAGATTGAAGCTACAACGGCAA
52914871 ATCTCACTTCCCAGACATTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCTGGCG
1 ATCTCACTTCCCAGACATTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCTGGCG
52914936 ATGCAGCGGAGCAGATTGAAGCTACAACGGCAA
66 ATGCAGCGGAGCAGATTGAAGCTACAACGGCAA
52914969 ATCTCACTTCCCAGACATTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCTGGCG
1 ATCTCACTTCCCAGACATTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCTGGCG
52915034 ATGCAGCGGAGCAGATTGAAGCTACAACGGCAA
66 ATGCAGCGGAGCAGATTGAAGCTACAACGGCAA
*
52915067 ATCTCACTTCCCAGACATTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCTGGCA
1 ATCTCACTTCCCAGACATTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCTGGCG
* * * *
52915132 ATGCAGCGAAGAAGATTGAAGCTACAACAGCGA
66 ATGCAGCGGAGCAGATTGAAGCTACAACGGCAA
* * * *
52915165 ATCTCATTTCCCCGATATTGCAATTTAAAAGATCGAAGCCACAA
1 ATCTCACTTCCCAGACATTGCAATTTAAAAGATTGAAGCCACAA
52915209 TGGTAGATTT
Statistics
Matches: 321, Mismatches: 17, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 321 1.00
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.21
Consensus pattern (98 bp):
ATCTCACTTCCCAGACATTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCTGGCG
ATGCAGCGGAGCAGATTGAAGCTACAACGGCAA
Found at i:52915763 original size:5 final size:5
Alignment explanation
Indices: 52915740--52915775 Score: 56
Period size: 5 Copynumber: 7.2 Consensus size: 5
52915730 CTTACATTGC
52915740 TATTT TA-TT TATTT CTATTT TATTT TATTT TATTT T
1 TATTT TATTT TATTT -TATTT TATTT TATTT TATTT T
52915776 TTGTTTGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 4 0.14
5 20 0.69
6 5 0.17
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (5 bp):
TATTT
Found at i:52916519 original size:3 final size:3
Alignment explanation
Indices: 52916511--52916575 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
52916501 GAATTAGTCC
52916511 TAT TAT 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 TAT TAT
52916559 TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
52916576 CCTATTTATT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:52918838 original size:21 final size:23
Alignment explanation
Indices: 52918800--52918847 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
52918790 TAGAAATAAT
* *
52918800 CAAAAAGAATTTATTCAAAAA-A
1 CAAAAAGAAATCATTCAAAAAGA
52918822 CAAAAAGAAATCA-TCAAAAAGA
1 CAAAAAGAAATCATTCAAAAAGA
52918844 CAAA
1 CAAA
52918848 CATGTATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.67, C:0.12, G:0.06, T:0.15
Consensus pattern (23 bp):
CAAAAAGAAATCATTCAAAAAGA
Found at i:52919622 original size:3 final size:3
Alignment explanation
Indices: 52919547--52919604 Score: 75
Period size: 3 Copynumber: 19.7 Consensus size: 3
52919537 TGTAGCATTT
* *
52919547 TTA TTA TT- TTG TTCA TTA TT- CTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
52919591 TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TT
52919605 TAATGTTATT
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
2 3 0.06
3 44 0.90
4 2 0.04
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:52919622 original size:9 final size:9
Alignment explanation
Indices: 52919543--52919622 Score: 61
Period size: 9 Copynumber: 8.2 Consensus size: 9
52919533 CCTTTGTAGC
52919543 ATTTTTATT
1 ATTTTTATT
52919552 ATTTTGTTCATT
1 A-TTT-TT-ATT
52919564 ATTCTATTATT
1 ATT-T-TTATT
*
52919575 ATTATTATT
1 ATTTTTATT
*
52919584 ATTATTATT
1 ATTTTTATT
*
52919593 ATTATTATT
1 ATTTTTATT
* *
52919602 ATTTAATGTT
1 ATTT-TTATT
52919612 ATTTTTATT
1 ATTTTTATT
52919621 AT
1 AT
52919623 CATCGCATTT
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
9 32 0.54
10 10 0.17
11 10 0.17
12 7 0.12
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.68
Consensus pattern (9 bp):
ATTTTTATT
Found at i:52920700 original size:108 final size:109
Alignment explanation
Indices: 52920507--52920927 Score: 700
Period size: 108 Copynumber: 3.8 Consensus size: 109
52920497 CAAATTATTG
* *
52920507 AGGCAATATTTAGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
52920572 CGTTCAACCAAATGGCTTAATATCCTTTTAAAAATTTTAAAATA
66 CGTTCAACCAAATGGCTTAATATCCTTTTAAAAATTTTAAAATA
* *
52920616 AGGCAATGTTTTGCATTTAGAAATTCGAGAAAACATG-CCTAAGGTGCTGGGTGTCGATTTTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
* *
52920680 CGTTCAACCAAAGGGATTAATATCCTTTTAAAAATTTTAAAATA
66 CGTTCAACCAAATGGCTTAATATCCTTTTAAAAATTTTAAAATA
52920724 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
*
52920789 CGTTCAACCAAATGGCTTAATATCCTTTTAAAAAAAATTTCAAAATA
66 CGTTCAACCAAATGGCTTAATATCCTTTT---AAAAATTTTAAAATA
52920836 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
* * * *
52920901 CATTTAACCAAATTGCTAAAATATCCT
66 CGTTCAACCAAATGGCT-TAATATCCT
52920928 CTTGAATTTT
Statistics
Matches: 292, Mismatches: 15, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
108 104 0.36
109 87 0.30
112 93 0.32
113 8 0.03
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.34
Consensus pattern (109 bp):
AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
CGTTCAACCAAATGGCTTAATATCCTTTTAAAAATTTTAAAATA
Found at i:52927802 original size:51 final size:52
Alignment explanation
Indices: 52927747--52927867 Score: 158
Period size: 52 Copynumber: 2.3 Consensus size: 52
52927737 CGGTGGCATA
** *
52927747 CACATAGTACCAC-CGTTGT-AGCCAAAGTTA-CCTTCTTCACAAAGTGGCGTT
1 CACATAGTACCACAC-TTGTGA-CCAAAACTATCCTTCTTCACAAAGTGGCCTT
*
52927798 CACATAGTACCACACTTGTGACCAAAACTATCTTTCTTCACAAAGTGGCCTT
1 CACATAGTACCACACTTGTGACCAAAACTATCCTTCTTCACAAAGTGGCCTT
*
52927850 CACTTAGTACCACACTTG
1 CACATAGTACCACACTTG
52927868 AGTCACTAGT
Statistics
Matches: 62, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
51 24 0.39
52 38 0.61
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.28
Consensus pattern (52 bp):
CACATAGTACCACACTTGTGACCAAAACTATCCTTCTTCACAAAGTGGCCTT
Found at i:52929906 original size:3 final size:3
Alignment explanation
Indices: 52929898--52929955 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
52929888 TTTGTTTGGT
52929898 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
52929946 TTA TTA TTA T
1 TTA TTA TTA T
52929956 CTTTTAAATT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:52935892 original size:40 final size:41
Alignment explanation
Indices: 52935847--52935935 Score: 103
Period size: 41 Copynumber: 2.2 Consensus size: 41
52935837 GGCTTTAATG
*
52935847 GCGTTTTTCAAAAAGCGTCACT-A-G-TGCATGGGCTTTAGCA
1 GCGTTTTTCAAAAAGCGCCACTAACGCT-CA-GGGCTTTAGCA
** *
52935887 GCGTTTTTGGAAAAGCGCCGCTAACGCTCAGGGCTTTAGCA
1 GCGTTTTTCAAAAAGCGCCACTAACGCTCAGGGCTTTAGCA
52935928 GCGTTTTT
1 GCGTTTTT
52935936 TTGAAAAGTG
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
40 18 0.43
41 20 0.48
42 3 0.07
43 1 0.02
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.30
Consensus pattern (41 bp):
GCGTTTTTCAAAAAGCGCCACTAACGCTCAGGGCTTTAGCA
Found at i:52936533 original size:15 final size:14
Alignment explanation
Indices: 52936480--52936529 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
52936470 ACTATTTTAA
*
52936480 GGTTTAGAGGAGTAT
1 GGTTTAG-GGATTAT
*
52936495 GGATTTAGGAATTAT
1 GG-TTTAGGGATTAT
*
52936510 GGATTAGGGATTAT
1 GGTTTAGGGATTAT
52936524 GGTTTA
1 GGTTTA
52936530 AGGGTTGGGA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
14 15 0.52
15 9 0.31
16 5 0.17
ACGTcount: A:0.28, C:0.00, G:0.34, T:0.38
Consensus pattern (14 bp):
GGTTTAGGGATTAT
Found at i:52936550 original size:21 final size:20
Alignment explanation
Indices: 52936516--52936554 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
52936506 TTATGGATTA
*
52936516 GGGATTATGGTTTAAGGGTT
1 GGGATTAAGGTTTAAGGGTT
52936536 GGGATTTAAGGTTTAAGGG
1 GGGA-TTAAGGTTTAAGGG
52936555 ATTAGGGGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.23, C:0.00, G:0.41, T:0.36
Consensus pattern (20 bp):
GGGATTAAGGTTTAAGGGTT
Found at i:52940591 original size:19 final size:19
Alignment explanation
Indices: 52940567--52940605 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
52940557 TGATGATCAA
52940567 ACTCATGAATCAAATGAAG
1 ACTCATGAATCAAATGAAG
52940586 ACTCATGAATCAAATGAAG
1 ACTCATGAATCAAATGAAG
52940605 A
1 A
52940606 TTTTACCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.15, G:0.15, T:0.21
Consensus pattern (19 bp):
ACTCATGAATCAAATGAAG
Found at i:52940701 original size:26 final size:26
Alignment explanation
Indices: 52940672--52940724 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
52940662 TTTTTCTTAC
52940672 ATAGTTTTAATTTTAATTTTACGACT
1 ATAGTTTTAATTTTAATTTTACGACT
52940698 ATAGTTTTAATTTTAATTTTACGACT
1 ATAGTTTTAATTTTAATTTTACGACT
52940724 A
1 A
52940725 GCTAATTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.53
Consensus pattern (26 bp):
ATAGTTTTAATTTTAATTTTACGACT
Found at i:52944167 original size:91 final size:91
Alignment explanation
Indices: 52944012--52944187 Score: 316
Period size: 91 Copynumber: 1.9 Consensus size: 91
52944002 CTTCCAGGCC
52944012 AAGGAAGTAGGACATTTGTCCTAAATCAAACATCTCAAACTTTTTCTCCATTTTACCTTTGAAAC
1 AAGGAAGTAGGACATTTGTCCTAAATCAAACATCTCAAACTTTTTCTCCATTTTACCTTTGAAAC
* *
52944077 CAGCCAGTAATTCATAACTTGCCTGG
66 CAACCAGCAATTCATAACTTGCCTGG
* *
52944103 AAGGAAGTAGGACATTTGTCCTAAATCAGACATCTCAAACTTTTTCTCCATTTTGCCTTTGAAAC
1 AAGGAAGTAGGACATTTGTCCTAAATCAAACATCTCAAACTTTTTCTCCATTTTACCTTTGAAAC
52944168 CAACCAGCAATTCATAACTT
66 CAACCAGCAATTCATAACTT
52944188 TCTCCTGTCA
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
91 81 1.00
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.32
Consensus pattern (91 bp):
AAGGAAGTAGGACATTTGTCCTAAATCAAACATCTCAAACTTTTTCTCCATTTTACCTTTGAAAC
CAACCAGCAATTCATAACTTGCCTGG
Found at i:52954550 original size:5 final size:6
Alignment explanation
Indices: 52954533--52954557 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
52954523 CTGTTATCTC
52954533 TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT T
52954558 TGAATTTTTA
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:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:52960049 original size:20 final size:20
Alignment explanation
Indices: 52960024--52960061 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
52960014 TGGTTTTAGC
*
52960024 CTTCTGGTAAGCTACTCTTT
1 CTTCTGCTAAGCTACTCTTT
52960044 CTTCTGCTAAGCTACTCT
1 CTTCTGCTAAGCTACTCT
52960062 ATTGATGGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.29, G:0.13, T:0.42
Consensus pattern (20 bp):
CTTCTGCTAAGCTACTCTTT
Found at i:52968575 original size:20 final size:20
Alignment explanation
Indices: 52968550--52968588 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
52968540 GTTTTTACAT
52968550 ATATTAATAAATTTATATAC
1 ATATTAATAAATTTATATAC
*
52968570 ATATTAATAAATTTTTATA
1 ATATTAATAAATTTATATA
52968589 TTTTAAATTG
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:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATTAATAAATTTATATAC
Found at i:52969357 original size:108 final size:108
Alignment explanation
Indices: 52969137--52969355 Score: 275
Period size: 108 Copynumber: 2.0 Consensus size: 108
52969127 TACTTTGAAG
* * * *
52969137 TTTTAAGAGGATATTTGACTATTTGGTCAAACGAAAAATCGAAACACAGCACGTTAGGAAACTCT
1 TTTTAAAAGGATACTCGACTATTTGGTCAAACGAAAAATCAAAACACAGCACGTTAGGAAACTCT
* *
52969202 TTCTCGAATTTTTCAAATGTAAAATATTGTCTTTATTTTAAAA
66 TTCTCGAATTTCTCAAATGCAAAATATTGTCTTTATTTTAAAA
* * * **
52969245 TTTTAAAAGGATACTCGGCTATTTGGTCAAACGAGAAGA-CAAAACCCAGCACGTTAGGGCACGT
1 TTTTAAAAGGATACTCGACTATTTGGTCAAACGA-AAAATCAAAACACAGCACGTTAGGAAAC-T
*
52969309 -TTTCTCGAATTTCT-AAATGCAAAATATTG-CTTTTATTTTGAAA
64 CTTTCTCGAATTTCTCAAATGCAAAATATTGTC-TTTATTTTAAAA
52969352 TTTT
1 TTTT
52969356 TATTTCTTTG
Statistics
Matches: 96, Mismatches: 12, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
106 1 0.01
107 29 0.30
108 62 0.65
109 4 0.04
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Consensus pattern (108 bp):
TTTTAAAAGGATACTCGACTATTTGGTCAAACGAAAAATCAAAACACAGCACGTTAGGAAACTCT
TTCTCGAATTTCTCAAATGCAAAATATTGTCTTTATTTTAAAA
Found at i:52976517 original size:26 final size:27
Alignment explanation
Indices: 52976488--52976542 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
52976478 ACAATTAATT
*
52976488 AAAATATAAAAGAT-TAAAAAT-TAAAA
1 AAAATA-AAAAAATCTAAAAATCTAAAA
*
52976514 AAAATAAAAAAATCTGAAAATCTAAAA
1 AAAATAAAAAAATCTAAAAATCTAAAA
52976541 AA
1 AA
52976543 TACCATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 6 0.24
26 12 0.48
27 7 0.28
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.20
Consensus pattern (27 bp):
AAAATAAAAAAATCTAAAAATCTAAAA
Found at i:52978604 original size:18 final size:18
Alignment explanation
Indices: 52978581--52978635 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
52978571 TTTAGAATCT
52978581 TTTTAAAATTATTATAAA
1 TTTTAAAATTATTATAAA
*
52978599 TTTTAAAA-AATATATAAA
1 TTTTAAAATTAT-TATAAA
*
52978617 -TTTAAGAATTTTTATAAA
1 TTTTAA-AATTATTATAAA
52978635 T
1 T
52978636 AATTTGAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
17 7 0.23
18 22 0.73
19 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TTTTAAAATTATTATAAA
Found at i:52982455 original size:40 final size:41
Alignment explanation
Indices: 52982411--52982601 Score: 266
Period size: 40 Copynumber: 4.7 Consensus size: 41
52982401 AAATATATTT
* *
52982411 ATTTTTTTTAATTTTAAAATATTTTTTACATAC-TTTTTTA
1 ATTTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
*
52982451 ATTTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTA
1 ATTTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
52982492 A-TTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
1 ATTTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
**
52982532 A-TTTTTTTAATTTTAAAATATTTTTAAAATA-TTTTTAAA
1 ATTTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
*
52982571 ATATATTTTTTAATTTTTTAAA-ATTTTTAAA
1 AT-T-TTTTTTAA-TTTTAAAATATTTTTAAA
52982602 TAAAAATGGG
Statistics
Matches: 139, Mismatches: 7, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
39 7 0.05
40 99 0.71
41 9 0.06
42 17 0.12
43 7 0.05
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (41 bp):
ATTTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
Found at i:52982457 original size:10 final size:10
Alignment explanation
Indices: 52982444--52982598 Score: 58
Period size: 11 Copynumber: 15.4 Consensus size: 10
52982434 TTTTACATAC
52982444 TTTTTT-AAT
1 TTTTTTAAAT
52982453 TTTTTTAAA-
1 TTTTTTAAAT
*
52982462 -TTTTAAAAT
1 TTTTTTAAAT
*
52982471 ATTTTTAAAAT
1 -TTTTTTAAAT
*
52982482 ACTTTTTTTAAT
1 --TTTTTTAAAT
52982494 TTTTTT-AA-
1 TTTTTTAAAT
*
52982502 -TTTTAAAAT
1 TTTTTTAAAT
*
52982511 ATTTTTAAAAT
1 -TTTTTTAAAT
*
52982522 ACTTTTTTTAAT
1 --TTTTTTAAAT
52982534 TTTTTT-AA-
1 TTTTTTAAAT
*
52982542 -TTTTAAAAT
1 TTTTTTAAAT
*
52982551 ATTTTTAAAAT
1 -TTTTTTAAAT
*
52982562 ATTTTTAAAAT
1 -TTTTTTAAAT
*
52982573 ATATTTTTTAAT
1 -T-TTTTTAAAT
*
52982585 TTTTTAAAAT
1 TTTTTTAAAT
52982595 TTTT
1 TTTT
52982599 AAATAAAAAT
Statistics
Matches: 118, Mismatches: 13, Indels: 29
0.74 0.08 0.18
Matches are distributed among these distances:
7 8 0.07
8 11 0.09
9 10 0.08
10 25 0.21
11 41 0.35
12 23 0.19
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.63
Consensus pattern (10 bp):
TTTTTTAAAT
Found at i:52982578 original size:13 final size:11
Alignment explanation
Indices: 52982462--52982598 Score: 91
Period size: 11 Copynumber: 13.3 Consensus size: 11
52982452 TTTTTTTAAA
52982462 TTTTAAAATAT
1 TTTTAAAATAT
52982473 TTTTAAAATACT
1 TTTTAAAATA-T
**
52982485 TTTTTTAAT-T
1 TTTTAAAATAT
*
52982495 TTTT----TAA
1 TTTTAAAATAT
52982502 TTTTAAAATAT
1 TTTTAAAATAT
52982513 TTTTAAAATACT
1 TTTTAAAATA-T
**
52982525 TTTTTTAAT-T
1 TTTTAAAATAT
*
52982535 TTTT----TAA
1 TTTTAAAATAT
52982542 TTTTAAAATAT
1 TTTTAAAATAT
52982553 TTTTAAAATAT
1 TTTTAAAATAT
52982564 TTTTAAAATAT
1 TTTTAAAATAT
**
52982575 ATTTTTTAAT-T
1 -TTTTAAAATAT
52982586 TTTTAAAAT-T
1 TTTTAAAATAT
52982596 TTT
1 TTT
52982599 AAATAAAAAT
Statistics
Matches: 101, Mismatches: 12, Indels: 27
0.72 0.09 0.19
Matches are distributed among these distances:
6 2 0.02
7 8 0.08
10 21 0.21
11 47 0.47
12 23 0.23
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:52982581 original size:51 final size:52
Alignment explanation
Indices: 52982502--52982603 Score: 163
Period size: 51 Copynumber: 2.0 Consensus size: 52
52982492 ATTTTTTTAA
*
52982502 TTTTAAAATATTTTTAAAATACTTTTTTTAATTTTTT-TAATTTTAAAATAT
1 TTTTAAAATATTTTTAAAATACTTTTTTTAATTTTTTAAAATTTTAAAATAT
*
52982553 TTTTAAAATATTTTTAAAATA-TATTTTTTAATTTTTTAAAATTTTTAAATA
1 TTTTAAAATATTTTTAAAATACT-TTTTTTAATTTTTTAAAATTTTAAAATA
52982604 AAAATGGGCC
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
50 1 0.02
51 35 0.74
52 11 0.23
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (52 bp):
TTTTAAAATATTTTTAAAATACTTTTTTTAATTTTTTAAAATTTTAAAATAT
Found at i:52983514 original size:2 final size:2
Alignment explanation
Indices: 52983507--52983537 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
52983497 TTGACCATTG
52983507 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
52983538 TAATAATTAC
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:52984245 original size:32 final size:32
Alignment explanation
Indices: 52984199--52984263 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
52984189 ACACAATTTG
*
52984199 AGTTATCCGGAAATTCAAATAATAAAAGACAA
1 AGTTATCCGAAAATTCAAATAATAAAAGACAA
52984231 AGTTATCCGAAAATTCAAATAATAAAAGACAA
1 AGTTATCCGAAAATTCAAATAATAAAAGACAA
52984263 A
1 A
52984264 ACTACGTCGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.55, C:0.12, G:0.11, T:0.22
Consensus pattern (32 bp):
AGTTATCCGAAAATTCAAATAATAAAAGACAA
Found at i:52985128 original size:15 final size:15
Alignment explanation
Indices: 52985093--52985146 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
52985083 ATTCGGAGGA
* *
52985093 GGAGAGGAGGAGGAG
1 GGAGAGGAAGAGAAG
*
52985108 GAAGAGGAAGAGAAG
1 GGAGAGGAAGAGAAG
52985123 GGAGAGAGAAGA-AAG
1 GGAGAG-GAAGAGAAG
*
52985138 GGAAAGGAA
1 GGAGAGGAA
52985147 AAGGAGGAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
14 3 0.09
15 25 0.76
16 5 0.15
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (15 bp):
GGAGAGGAAGAGAAG
Done.