Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008319.1 Hibiscus syriacus cultivar Beakdansim tig00111022_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4819703
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 21
Found at i:2610658 original size:2 final size:2
Alignment explanation
Indices: 2610651--2610682 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2610641 GAACATGTGA
2610651 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2610683 GTCTAAGAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2611679 original size:149 final size:149
Alignment explanation
Indices: 2611216--2611668 Score: 897
Period size: 149 Copynumber: 3.0 Consensus size: 149
2611206 GAGTCAAGGG
2611216 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
2611281 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
2611346 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
2611365 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
2611430 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
2611495 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
2611514 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
*
2611579 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
2611644 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
2611663 TCTACG
1 TCTACG
2611669 GGGCACTTCG
Statistics
Matches: 303, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
149 303 1.00
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:2611691 original size:23 final size:23
Alignment explanation
Indices: 2611647--2611691 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2611637 ATCATTATAT
*
2611647 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
2611670 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
2611692 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:2614993 original size:21 final size:21
Alignment explanation
Indices: 2614967--2615011 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2614957 GATTTCTGGG
* *
2614967 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
2614988 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
2615009 CAA
1 CAA
2615012 ACGACAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:2615615 original size:18 final size:18
Alignment explanation
Indices: 2615592--2615626 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2615582 CTAGGAGATT
2615592 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
2615610 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
2615627 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:2615712 original size:21 final size:22
Alignment explanation
Indices: 2615683--2615726 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2615673 GTTGTATGAT
2615683 AGAAAATTAT-GAAGTTATATG
1 AGAAAATTATAGAAGTTATATG
* *
2615704 AGAAGATTATAGGAGTTATATG
1 AGAAAATTATAGAAGTTATATG
2615726 A
1 A
2615727 AATTTAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (22 bp):
AGAAAATTATAGAAGTTATATG
Found at i:2615959 original size:2 final size:2
Alignment explanation
Indices: 2615952--2616003 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
2615942 GAACATGTGA
2615952 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2615994 AT AT AT AT AT
1 AT AT AT AT AT
2616004 GTCTAAGAGA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2617003 original size:149 final size:149
Alignment explanation
Indices: 2616540--2616992 Score: 888
Period size: 149 Copynumber: 3.0 Consensus size: 149
2616530 GAGTCGAGGG
2616540 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
2616605 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
2616670 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
2616689 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
2616754 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
2616819 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
2616838 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
* *
2616903 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGATATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
2616968 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
2616987 TCTACG
1 TCTACG
2616993 GGGCACTTCG
Statistics
Matches: 302, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 302 1.00
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:2617015 original size:23 final size:23
Alignment explanation
Indices: 2616971--2617015 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2616961 ATCATTATAT
*
2616971 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
2616994 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
2617016 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:2617864 original size:22 final size:22
Alignment explanation
Indices: 2617830--2617882 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
2617820 ATATTAGTCA
*
2617830 TTCGGAACATATCCAATGGTCC
1 TTCGGGACATATCCAATGGTCC
* *
2617852 TTCGGGACGTATCCAGTGGTCC
1 TTCGGGACATATCCAATGGTCC
*
2617874 TTCAGGACA
1 TTCGGGACA
2617883 AATACTGAAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (22 bp):
TTCGGGACATATCCAATGGTCC
Found at i:2624139 original size:66 final size:65
Alignment explanation
Indices: 2624032--2624195 Score: 167
Period size: 64 Copynumber: 2.5 Consensus size: 65
2624022 TTTGTTGAAG
* * * *
2624032 GTGCATCGATGCACATGGAGTGTATCGATGCA-CTCATTTAAAATAAATGAACATCGAATGTCA-
1 GTGCATCGATGCATAAGGAGTGCATCGATGCACCTCA-TTAAAATAAA--AACATCGAATATCAT
2624095 TTA
63 TTA
* * *
2624098 GTGCATTGATGCATAAGGAGTGCATCGATGCACCTGC-TTAAAATACAAACATCGAATATGATTT
1 GTGCATCGATGCATAAGGAGTGCATCGATGCACCT-CATTAAAATAAAAACATCGAATATCATTT
2624162 A
65 A
* *
2624163 -TGCACCGATGCAT-GGGTAGTGCATCGATGCACC
1 GTGCATCGATGCATAAGG-AGTGCATCGATGCACC
2624196 CGTCAAGGGA
Statistics
Matches: 84, Mismatches: 10, Indels: 10
0.81 0.10 0.10
Matches are distributed among these distances:
63 2 0.02
64 39 0.46
65 3 0.04
66 37 0.44
67 2 0.02
68 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (65 bp):
GTGCATCGATGCATAAGGAGTGCATCGATGCACCTCATTAAAATAAAAACATCGAATATCATTTA
Found at i:2624775 original size:22 final size:22
Alignment explanation
Indices: 2624742--2624819 Score: 129
Period size: 22 Copynumber: 3.5 Consensus size: 22
2624732 TGGTATATTA
*
2624742 GTCCTTAGGGACGTATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
* *
2624764 GTCTTTCAGGACGTATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
2624786 GTCCTTCGGGACGTATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
2624808 GTCCTTCGGGAC
1 GTCCTTCGGGAC
2624820 ATAGTGGTCC
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.15, C:0.26, G:0.31, T:0.28
Consensus pattern (22 bp):
GTCCTTCGGGACGTATCCAGTG
Found at i:2624827 original size:18 final size:19
Alignment explanation
Indices: 2624781--2624838 Score: 73
Period size: 22 Copynumber: 2.9 Consensus size: 19
2624771 AGGACGTATC
2624781 CAGTGGTCCTTCGGGACGTAT
1 CAGTGGTCCTTCGGGAC--AT
2624802 CCAGTGGTCCTTCGGGACAT
1 -CAGTGGTCCTTCGGGACAT
*
2624822 -AGTGGTCCTTCAGGACA
1 CAGTGGTCCTTCGGGACA
2624839 AATACTGAAC
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
18 16 0.46
20 2 0.06
22 17 0.49
ACGTcount: A:0.17, C:0.26, G:0.31, T:0.26
Consensus pattern (19 bp):
CAGTGGTCCTTCGGGACAT
Found at i:2627870 original size:3 final size:3
Alignment explanation
Indices: 2627862--2627898 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
2627852 TTATATATAT
*
2627862 TTA TTA TTA -TA TTA CTA TTA TTA TTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2627899 CAAATAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
2 4 0.13
3 26 0.87
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:2627872 original size:14 final size:15
Alignment explanation
Indices: 2627838--2627898 Score: 69
Period size: 14 Copynumber: 4.4 Consensus size: 15
2627828 TGTTCCCGTT
*
2627838 TTATTATA-ATATAA
1 TTATTATATATATTA
2627852 TTA-TATATAT-TTA
1 TTATTATATATATTA
*
2627865 TTATTATAT-TACTA
1 TTATTATATATATTA
2627879 TTATTAT-TATATTA
1 TTATTATATATATTA
2627893 TTATTA
1 TTATTA
2627899 CAAATAATTA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
13 11 0.28
14 29 0.73
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (15 bp):
TTATTATATATATTA
Found at i:2627874 original size:8 final size:8
Alignment explanation
Indices: 2627839--2627896 Score: 64
Period size: 8 Copynumber: 7.1 Consensus size: 8
2627829 GTTCCCGTTT
*
2627839 TATTATAA
1 TATTATTA
*
2627847 TATAATTA
1 TATTATTA
2627855 TATATATT-
1 TAT-TATTA
2627863 TATTATTA
1 TATTATTA
*
2627871 TATTACTA
1 TATTATTA
2627879 TTATTATTA
1 -TATTATTA
2627888 TATTATTA
1 TATTATTA
2627896 T
1 T
2627897 TACAAATAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
7 4 0.10
8 28 0.67
9 10 0.24
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (8 bp):
TATTATTA
Found at i:2627882 original size:11 final size:12
Alignment explanation
Indices: 2627866--2627899 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
2627856 ATATATTTAT
2627866 TATTA-TATTAC
1 TATTATTATTAC
2627877 TATTATTATTA-
1 TATTATTATTAC
2627888 TATTATTATTAC
1 TATTATTATTAC
2627900 AAATAATTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 16 0.76
12 5 0.24
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (12 bp):
TATTATTATTAC
Found at i:2627884 original size:17 final size:17
Alignment explanation
Indices: 2627862--2627898 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
2627852 TTATATATAT
2627862 TTATTATTATATTACTA
1 TTATTATTATATTACTA
*
2627879 TTATTATTATATTATTA
1 TTATTATTATATTACTA
2627896 TTA
1 TTA
2627899 CAAATAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
TTATTATTATATTACTA
Found at i:2627972 original size:24 final size:24
Alignment explanation
Indices: 2627913--2627969 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
2627903 TAATTACAAG
*
2627913 ACCCGAAGGCCCAAATACAATAGA
1 ACCCGAAGGCCCAAATACAAAAGA
* *
2627937 ACTCGAAGGCCCAAATACAAAATA
1 ACCCGAAGGCCCAAATACAAAAGA
2627961 ACCCTGAAG
1 ACCC-GAAG
2627970 CCCGATTACA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 24 0.86
25 4 0.14
ACGTcount: A:0.46, C:0.28, G:0.16, T:0.11
Consensus pattern (24 bp):
ACCCGAAGGCCCAAATACAAAAGA
Found at i:2631034 original size:60 final size:60
Alignment explanation
Indices: 2630925--2631041 Score: 155
Period size: 60 Copynumber: 1.9 Consensus size: 60
2630915 TTAGGTGCCA
* * * * *
2630925 ATTTTATAACTTTTAATAGTTGATTGACTCAACAAAGCAATAGTTTATAGTTGGGGGATC
1 ATTTTATAACTTTTAACAGTCGATAGACTCAACAAAGCAATAGTATATAGTCGGGGGATC
* *
2630985 ATTTTATAACTTTTAACAGTCGATAGACTCAATAAAGTAATA-TCATATAGTCGGGGG
1 ATTTTATAACTTTTAACAGTCGATAGACTCAACAAAGCAATAGT-ATATAGTCGGGGG
2631042 CCATTTGTGT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
59 1 0.02
60 48 0.98
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (60 bp):
ATTTTATAACTTTTAACAGTCGATAGACTCAACAAAGCAATAGTATATAGTCGGGGGATC
Found at i:2634353 original size:4 final size:4
Alignment explanation
Indices: 2634344--2634369 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
2634334 TTAAAACCCC
2634344 ATTA ATTA ATTA ATTA ATTA ATTA AT
1 ATTA ATTA ATTA ATTA ATTA ATTA AT
2634370 GTGAGTTTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
ATTA
Found at i:2636118 original size:27 final size:24
Alignment explanation
Indices: 2636070--2636117 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
2636060 ATCTTTGATC
2636070 TCTTCTTGAAGAATCCAAAAAAAA
1 TCTTCTTGAAGAATCCAAAAAAAA
2636094 TCTTCTTGAAGAATCCAAAAAAAA
1 TCTTCTTGAAGAATCCAAAAAAAA
2636118 ATTAGTAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.17, G:0.08, T:0.25
Consensus pattern (24 bp):
TCTTCTTGAAGAATCCAAAAAAAA
Found at i:2639586 original size:25 final size:24
Alignment explanation
Indices: 2639545--2639606 Score: 74
Period size: 25 Copynumber: 2.6 Consensus size: 24
2639535 TTTTCTATAT
2639545 TTTAATTATATTTATAACAATTAC
1 TTTAATTATATTTATAACAATTAC
* *
2639569 TTTAATATATTTTTATAAGAATTA-
1 TTTAAT-TATATTTATAACAATTAC
*
2639593 -TTAATTACATTTAT
1 TTTAATTATATTTAT
2639607 TTTTATATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
22 7 0.21
23 5 0.15
24 6 0.18
25 15 0.45
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (24 bp):
TTTAATTATATTTATAACAATTAC
Found at i:2651349 original size:22 final size:23
Alignment explanation
Indices: 2651323--2651374 Score: 77
Period size: 25 Copynumber: 2.2 Consensus size: 23
2651313 AATGAAAGTG
2651323 TTTTTCTAAGTTAAAGATTATTT
1 TTTTTCTAAGTTAAAGATTATTT
*
2651346 TTTTCTCATAAGTTAGAGATTATTT
1 TTTT-TC-TAAGTTAAAGATTATTT
2651371 TTTT
1 TTTT
2651375 CTCATAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 4 0.15
24 2 0.08
25 20 0.77
ACGTcount: A:0.27, C:0.06, G:0.10, T:0.58
Consensus pattern (23 bp):
TTTTTCTAAGTTAAAGATTATTT
Found at i:2651360 original size:25 final size:25
Alignment explanation
Indices: 2651329--2651381 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
2651319 AGTGTTTTTC
2651329 TAAGTTAAAGATTATTTTTTTCTCA
1 TAAGTTAAAGATTATTTTTTTCTCA
*
2651354 TAAGTTAGAGATTATTTTTTTCTCA
1 TAAGTTAAAGATTATTTTTTTCTCA
2651379 TAA
1 TAA
2651382 TAAATTAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.32, C:0.08, G:0.09, T:0.51
Consensus pattern (25 bp):
TAAGTTAAAGATTATTTTTTTCTCA
Found at i:2660491 original size:21 final size:21
Alignment explanation
Indices: 2660467--2660509 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
2660457 TCATTTTGGC
2660467 CACAAAGTTTGAATCTTTGAA
1 CACAAAGTTTGAATCTTTGAA
2660488 CACAAAGTTTGAATCTTTGAA
1 CACAAAGTTTGAATCTTTGAA
2660509 C
1 C
2660510 TTTTTCAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (21 bp):
CACAAAGTTTGAATCTTTGAA
Found at i:2661121 original size:27 final size:27
Alignment explanation
Indices: 2661083--2661136 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
2661073 GCTTGATGAT
2661083 TTCAAATATATTAATAATTATAAAACC
1 TTCAAATATATTAATAATTATAAAACC
2661110 TTCAAATATATTAATAATTATAAAACC
1 TTCAAATATATTAATAATTATAAAACC
2661137 ATTCTTTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (27 bp):
TTCAAATATATTAATAATTATAAAACC
Found at i:2662465 original size:16 final size:16
Alignment explanation
Indices: 2662444--2662514 Score: 124
Period size: 16 Copynumber: 4.4 Consensus size: 16
2662434 GGTATTACCC
*
2662444 GACCTGTTTTTAACTT
1 GACCTGTTTTTAACCT
*
2662460 GACCTGTTTTCAACCT
1 GACCTGTTTTTAACCT
2662476 GACCTGTTTTTAACCT
1 GACCTGTTTTTAACCT
2662492 GACCTGTTTTTAACCT
1 GACCTGTTTTTAACCT
2662508 GACCTGT
1 GACCTGT
2662515 AAATGATCCG
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 52 1.00
ACGTcount: A:0.18, C:0.25, G:0.14, T:0.42
Consensus pattern (16 bp):
GACCTGTTTTTAACCT
Found at i:2662751 original size:25 final size:22
Alignment explanation
Indices: 2662709--2662753 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 22
2662699 TGTATATAAA
2662709 ATTTAATAAAATTAATAAAATT
1 ATTTAATAAAATTAATAAAATT
2662731 ATTTAAATATAAATTAGATAAAA
1 ATTT-AATA-AAATTA-ATAAAA
2662754 CATTAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 4 0.20
23 4 0.20
24 6 0.30
25 6 0.30
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (22 bp):
ATTTAATAAAATTAATAAAATT
Found at i:2662799 original size:24 final size:23
Alignment explanation
Indices: 2662772--2662821 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
2662762 ATGCAAAGAA
2662772 AAATTAATATAGTTTAATTTATAT
1 AAATT-ATATAGTTTAATTTATAT
* *
2662796 AAATTTTATAGTTTTATTTATAT
1 AAATTATATAGTTTAATTTATAT
2662819 AAA
1 AAA
2662822 GAAAAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 19 0.79
24 5 0.21
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (23 bp):
AAATTATATAGTTTAATTTATAT
Found at i:2665318 original size:21 final size:20
Alignment explanation
Indices: 2665294--2665336 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 20
2665284 ATACTAATGA
2665294 ACTATATATATAGTTATATAT
1 ACTAT-TATATAGTTATATAT
2665315 AC---TATATAGTTATATAT
1 ACTATTATATAGTTATATAT
2665332 ACTAT
1 ACTAT
2665337 GAACTATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 7
0.73 0.00 0.27
Matches are distributed among these distances:
17 17 0.89
21 2 0.11
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.47
Consensus pattern (20 bp):
ACTATTATATAGTTATATAT
Found at i:2665322 original size:9 final size:9
Alignment explanation
Indices: 2665298--2665438 Score: 61
Period size: 9 Copynumber: 16.2 Consensus size: 9
2665288 TAATGAACTA
*
2665298 TATATATAGT
1 TATATATA-C
2665308 TATATATAC
1 TATATATAC
2665317 TATATAGT--
1 TATATA-TAC
2665325 TATATATAC
1 TATATATAC
*
2665334 TAT-GA-AC
1 TATATATAC
2665341 TATATA-A-
1 TATATATAC
*
2665348 TATATAGT-T
1 TATATA-TAC
2665357 TATATATAC
1 TATATATAC
2665366 TA-ATGA-AC
1 TATAT-ATAC
*
2665374 TATATATAA
1 TATATATAC
* *
2665383 TGTATAGT-T
1 TATATA-TAC
2665392 TATATATAC
1 TATATATAC
* *
2665401 CATATAGAC
1 TATATATAC
*
2665410 TATATATAT
1 TATATATAC
*
2665419 TATATAGT-T
1 TATATA-TAC
2665428 TATATATAC
1 TATATATAC
2665437 TA
1 TA
2665439 ATAAATTATA
Statistics
Matches: 101, Mismatches: 15, Indels: 31
0.69 0.10 0.21
Matches are distributed among these distances:
7 12 0.12
8 19 0.19
9 59 0.58
10 11 0.11
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (9 bp):
TATATATAC
Found at i:2665322 original size:52 final size:55
Alignment explanation
Indices: 2665203--2665367 Score: 162
Period size: 45 Copynumber: 3.2 Consensus size: 55
2665193 TTATAAATTA
* *
2665203 TATATTTA-TATATACTATATAGTTTATATATACTAATGAACTATAATATATAGT
1 TATATATACTATATACTATATAGTGTATATATACTAATGAACTATAATATATAGT
*
2665257 TGGTATAT-C-ATATACTATATAG-GT-TATATACTAATGAACTAT-ATATATAG-
1 T-ATATATACTATATACTATATAGTGTATATATACTAATGAACTATAATATATAGT
2665307 ----T-TA-TATATACTATATAGT-TATATATACT-ATGAACTATATAATATATAGTT
1 TATATATACTATATACTATATAGTGTATATATACTAATGAAC--TATAATATATAG-T
2665357 TATATATACTA
1 TATATATACTA
2665368 ATGAACTATA
Statistics
Matches: 91, Mismatches: 3, Indels: 32
0.72 0.02 0.25
Matches are distributed among these distances:
44 1 0.01
45 21 0.23
46 8 0.09
47 3 0.03
48 8 0.09
51 8 0.09
52 18 0.20
53 1 0.01
54 15 0.16
55 6 0.07
56 2 0.02
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44
Consensus pattern (55 bp):
TATATATACTATATACTATATAGTGTATATATACTAATGAACTATAATATATAGT
Found at i:2665412 original size:69 final size:68
Alignment explanation
Indices: 2665308--2665462 Score: 212
Period size: 69 Copynumber: 2.3 Consensus size: 68
2665298 TATATATAGT
* *
2665308 TATATATACTATATAG-TTATATATACTATGAACTATATA-A-TATATAGTTTATATATACTAAT
1 TATATATAATGTATAGTTTATATATACTATGAACTATATATATTATATAGTTTATATATACTAAT
*
2665370 GAAC
66 -AAA
2665374 TATATATAATGTATAGTTTATATATACCATAT-AGACTATATATATTATATAGTTTATATATACT
1 TATATATAATGTATAGTTTATATATA-C-TATGA-ACTATATATATTATATAGTTTATATATACT
2665438 AATAAA
63 AATAAA
2665444 T-TATATAATGTATAGTTTA
1 TATATATAATGTATAGTTTA
2665463 GGGTTTATGA
Statistics
Matches: 80, Mismatches: 3, Indels: 9
0.87 0.03 0.10
Matches are distributed among these distances:
66 14 0.17
67 9 0.11
68 2 0.03
69 29 0.36
70 4 0.05
71 22 0.28
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (68 bp):
TATATATAATGTATAGTTTATATATACTATGAACTATATATATTATATAGTTTATATATACTAAT
AAA
Found at i:2665544 original size:36 final size:34
Alignment explanation
Indices: 2665477--2665545 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
2665467 TTATGATTTT
*
2665477 TATATATAGTTCATATGTAAATTATACTATATAG
1 TATATATAGTTCATATATAAATTATACTATATAG
** *
2665511 TATATATAGTTTTTATATATAATATATAGTATATA
1 TATATATAGTTCATATATA-AAT-TATACTATATA
2665546 AATATAAACC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
34 16 0.55
35 3 0.10
36 10 0.34
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.48
Consensus pattern (34 bp):
TATATATAGTTCATATATAAATTATACTATATAG
Found at i:2665550 original size:20 final size:20
Alignment explanation
Indices: 2665512--2665552 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2665502 ACTATATAGT
* * *
2665512 ATATATAGTTTTTATATATA
1 ATATATAGTATATAAATATA
2665532 ATATATAGTATATAAATATA
1 ATATATAGTATATAAATATA
2665552 A
1 A
2665553 ACCCTAAACC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (20 bp):
ATATATAGTATATAAATATA
Found at i:2665560 original size:7 final size:7
Alignment explanation
Indices: 2665550--2665667 Score: 110
Period size: 7 Copynumber: 16.9 Consensus size: 7
2665540 TATATAAATA
2665550 TAAACCC
1 TAAACCC
2665557 TAAACCC
1 TAAACCC
* *
2665564 TAAAACT
1 TAAACCC
2665571 TAAACCC
1 TAAACCC
*
2665578 TAAAACC
1 TAAACCC
*
2665585 TAAACAC
1 TAAACCC
* *
2665592 TAGACCA
1 TAAACCC
**
2665599 TAAACTA
1 TAAACCC
2665606 TAAACCC
1 TAAACCC
*
2665613 TAAATCC
1 TAAACCC
*
2665620 TAAACCA
1 TAAACCC
*
2665627 TAAACCA
1 TAAACCC
2665634 TAAACCC
1 TAAACCC
*
2665641 TAAATCC
1 TAAACCC
*
2665648 TAAACCA
1 TAAACCC
*
2665655 TAAACCA
1 TAAACCC
2665662 TAAACC
1 TAAACC
2665668 ATATATGTTC
Statistics
Matches: 90, Mismatches: 21, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
7 90 1.00
ACGTcount: A:0.50, C:0.31, G:0.01, T:0.18
Consensus pattern (7 bp):
TAAACCC
Found at i:2666365 original size:216 final size:215
Alignment explanation
Indices: 2665673--2666577 Score: 1420
Period size: 215 Copynumber: 4.2 Consensus size: 215
2665663 AAACCATATA
* *
2665673 TGTTCAATTTATTTAAATTTTATATTTGTAATTTCATATTTGTTCAATTTAGTCCTCAAAATTAT
1 TGTTTAATTTATTTAAATTTT-TATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTAT
* *
2665738 ATTTGCATTTGAAATTGACCTATACTTATTACTTATTTTATATTTTTTAATTGGCCCGTAACTTT
65 ATTTGCATCTGAAATTGACCTATACTTATTACTTA-TTTATATTTTTTAATTGGCCCATAACTTT
* **
2665803 TTAAATGGATATAATTTAGTACTTTTAATATTAATTTAAACCTCACAATTTAAAATTATTTCGAT
129 TTAAATGGGTATAATTTAGTACTTTTTGTATTAATTTAAACCTCACAATTTAAAATTATTTCGAT
2665868 TTGATCCCTCATCAATGTGTGT
194 TTGATCCCTCATCAATGTGTGT
* *
2665890 TGTTTAATTTATTTAAATTTTTATTT-TAAATTTCATATTT-ATCAATTTAGTCCTTCAAATTAT
1 TGTTTAATTTATTTAAATTTTTATTTGT-AATTTCATATTTGTTCAATTTAGTCCTCCAAATTAT
* * * *
2665953 ATTTGTATCTAAAATTGACCCATACTTATTACTTAGTTATATTTTTTTAATTGGCCCATAACTTT
65 ATTTGCATCTGAAATTGACCTATACTTATTACTTATTTATA-TTTTTTAATTGGCCCATAACTTT
*
2666018 TTAAAT-GGTATCATTTAGTACTTTTTTGTATTAATTTAAACCTCACAATTTAAAATTATTTCGA
129 TTAAATGGGTATAATTTAGTAC-TTTTTGTATTAATTTAAACCTCACAATTTAAAATTATTTCGA
*
2666082 TTTGAT---TC--C--TTTGTGT
193 TTTGATCCCTCATCAATGTGTGT
*
2666098 TGTTTAATTTATTTAATTTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTATA
1 TGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTATA
* *
2666163 TTTGCATCTGAAATTGACCTATACTTATTACTTATTTATATTTTTAAATTGGCCTATAACTTTTT
66 TTTGCATCTGAAATTGACCTATACTTATTACTTATTTATATTTTTTAATTGGCCCATAACTTTTT
* *
2666228 AAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACATCACAATTTAAAATTATTTCGATT
131 AAATGGGTATAATTTAGTAC-TTTTTGTATTAATTTAAACCTCACAATTTAAAATTATTTCGATT
2666293 TGATCCCTCATCAATGTGTGT
195 TGATCCCTCATCAATGTGTGT
*
2666314 TGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTA
1 TGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTATA
* * *
2666379 TTTGCATATGAAATTGATCC-ATACTTATTACTTAATTATA-TTTTTAATTAGCCCATAACTTTT
66 TTTGCATCTGAAATTGA-CCTATACTTATTACTTATTTATATTTTTTAATTGGCCCATAACTTTT
* *
2666442 TAAATGGGTATAATTTAGTACTTTTTGTATTAATATCAACCTCACAATTTAAAATTATTTCGATT
130 TAAATGGGTATAATTTAGTACTTTTTGTATTAATTTAAACCTCACAATTTAAAATTATTTCGATT
2666507 TGATCCCTCATCAATGTGTGT
195 TGATCCCTCATCAATGTGTGT
*
2666528 TATTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTA
1 TGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTA
2666578 ATTCTTAAAT
Statistics
Matches: 636, Mismatches: 38, Indels: 31
0.90 0.05 0.04
Matches are distributed among these distances:
208 70 0.11
209 120 0.19
210 1 0.00
212 4 0.01
214 131 0.21
215 167 0.26
216 121 0.19
217 22 0.03
ACGTcount: A:0.30, C:0.12, G:0.08, T:0.50
Consensus pattern (215 bp):
TGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTATA
TTTGCATCTGAAATTGACCTATACTTATTACTTATTTATATTTTTTAATTGGCCCATAACTTTTT
AAATGGGTATAATTTAGTACTTTTTGTATTAATTTAAACCTCACAATTTAAAATTATTTCGATTT
GATCCCTCATCAATGTGTGT
Found at i:2666467 original size:424 final size:425
Alignment explanation
Indices: 2665673--2666577 Score: 1426
Period size: 424 Copynumber: 2.1 Consensus size: 425
2665663 AAACCATATA
* *
2665673 TGTTCAATTTATTTAAATTTTATATTTGTAATTTCATATTTGTTCAATTTAGTCCTCAAAATTAT
1 TGTTTAATTTATTT-AATTTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCAAAATTAT
* * *
2665738 ATTTGCATTTGAAATTGACCTATACTTATTACTTATTTTATATTTTTTAATTGGCCCGTAACTTT
65 ATTTGCATCTGAAATTGACCTATACTTATTACTTATTTTATATTTTTAAATTGGCCCATAACTTT
*
2665803 TTAAATGGATATAATTTAGTACTTTTAATATTAATTTAAACCTCACAATTTAAAATTATTTCGAT
130 TTAAATGGATATAATTTAGTACTTTTAATATTAATTTAAACATCACAATTTAAAATTATTTCGAT
2665868 TTGATCCCTCATCAATGTGTGTTGTTTAATTTATTTAAATTTTTATTTTAAATTTCATATTTATC
195 TTGATCCCTCATCAATGTGTGTTGTTTAATTTATTTAAATTTTTATTTTAAATTTCATATTTATC
* * * *
2665933 AATTTAGTCCTTCAAATTATATTTGTATCTAAAATTGACCCATACTTATTACTTAGTTATATTTT
260 AATTTAGTCCTCCAAATTATATTTGCATATAAAATTGACCCATACTTATTACTTAATTATA-TTT
* * *
2665998 TTTAATTGGCCCATAACTTTTTAAATGGTATCATTTAGTACTTTTTTGTATTAATTTAAACCTCA
324 TTTAATTAGCCCATAACTTTTTAAATGGTATAATTTAGTAC-TTTTTGTATTAATATAAACCTCA
*
2666063 CAATTTAAAATTATTTCGATTTGAT-TC-C-TTTGTGT
388 CAATTTAAAATTATTTCGATTTGATCTCACATGTGTGT
*
2666098 TGTTTAATTTATTTAATTTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTATA
1 TGTTTAATTTATTTAATTTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCAAAATTATA
*
2666163 TTTGCATCTGAAATTGACCTATACTTATTACTTA-TTTATATTTTTAAATTGGCCTATAACTTTT
66 TTTGCATCTGAAATTGACCTATACTTATTACTTATTTTATATTTTTAAATTGGCCCATAACTTTT
* ** *
2666227 TAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACATCACAATTTAAAATTATTTCGAT
131 TAAATGGATATAATTTAGTAC-TTTTAATATTAATTTAAACATCACAATTTAAAATTATTTCGAT
*
2666292 TTGATCCCTCATCAATGTGTGTTGTTTAATTTATTTAAATTTTTATTTGT-AATTTCATATTTGT
195 TTGATCCCTCATCAATGTGTGTTGTTTAATTTATTTAAATTTTTATTT-TAAATTTCATATTT-A
* * *
2666356 TCAATTTAGTCCTCCAAATTTTATTTGCATATGAAATTGATCCATACTTATTACTTAATTATA-T
258 TCAATTTAGTCCTCCAAATTATATTTGCATATAAAATTGACCCATACTTATTACTTAATTATATT
*
2666420 TTTTAATTAGCCCATAACTTTTTAAATGGGTATAATTTAGTACTTTTTGTATTAATATCAACCTC
323 TTTTAATTAGCCCATAACTTTTTAAAT-GGTATAATTTAGTACTTTTTGTATTAATATAAACCTC
2666485 ACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGTGT
387 ACAATTTAAAATTATTTCGATTTGAT--CTCA-C-ATGTGTGT
* *
2666528 TATTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTA
1 TGTTTAATTTATTTAATTTTTTATTTGTAATTTCATATTTGTTCAATTTA
2666578 ATTCTTAAAT
Statistics
Matches: 442, Mismatches: 27, Indels: 17
0.91 0.06 0.03
Matches are distributed among these distances:
423 120 0.27
424 195 0.44
425 70 0.16
426 2 0.00
428 1 0.00
430 54 0.12
ACGTcount: A:0.30, C:0.12, G:0.08, T:0.50
Consensus pattern (425 bp):
TGTTTAATTTATTTAATTTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCAAAATTATA
TTTGCATCTGAAATTGACCTATACTTATTACTTATTTTATATTTTTAAATTGGCCCATAACTTTT
TAAATGGATATAATTTAGTACTTTTAATATTAATTTAAACATCACAATTTAAAATTATTTCGATT
TGATCCCTCATCAATGTGTGTTGTTTAATTTATTTAAATTTTTATTTTAAATTTCATATTTATCA
ATTTAGTCCTCCAAATTATATTTGCATATAAAATTGACCCATACTTATTACTTAATTATATTTTT
TAATTAGCCCATAACTTTTTAAATGGTATAATTTAGTACTTTTTGTATTAATATAAACCTCACAA
TTTAAAATTATTTCGATTTGATCTCACATGTGTGT
Found at i:2667263 original size:17 final size:17
Alignment explanation
Indices: 2667241--2667280 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
2667231 TTAAAAGAAT
2667241 TTGTTGTTCAACTCAAC
1 TTGTTGTTCAACTCAAC
** *
2667258 TTGTTGTTTGACTCGAC
1 TTGTTGTTCAACTCAAC
2667275 TTGTTG
1 TTGTTG
2667281 GTTGTTATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.17, G:0.20, T:0.47
Consensus pattern (17 bp):
TTGTTGTTCAACTCAAC
Found at i:2667867 original size:29 final size:30
Alignment explanation
Indices: 2667818--2667874 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
2667808 ATACAATTTT
*
2667818 TAAATTTGATAGCACAAAATAAATTTTCCC
1 TAAATTTAATAGCACAAAATAAATTTTCCC
* *
2667848 TAAATTTAATA-CCCAAAATAATTTTTC
1 TAAATTTAATAGCACAAAATAAATTTTC
2667875 TAGCTCCACC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 14 0.58
30 10 0.42
ACGTcount: A:0.44, C:0.16, G:0.04, T:0.37
Consensus pattern (30 bp):
TAAATTTAATAGCACAAAATAAATTTTCCC
Found at i:2670507 original size:20 final size:20
Alignment explanation
Indices: 2670478--2670519 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2670468 GATAAATCAA
2670478 AATAAGAAAAAGAAAA-AAAT
1 AATAAG-AAAAGAAAAGAAAT
*
2670498 AATAATAAAAGAAAAGAAAT
1 AATAAGAAAAGAAAAGAAAT
2670518 AA
1 AA
2670520 ATATATTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.79, C:0.00, G:0.10, T:0.12
Consensus pattern (20 bp):
AATAAGAAAAGAAAAGAAAT
Found at i:2670521 original size:24 final size:22
Alignment explanation
Indices: 2670469--2670522 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 22
2670459 AACCACAAAG
*
2670469 ATAAATCAAAATAAGAAAAAGAA
1 ATAAAT-AAAATAAAAAAAAGAA
*
2670492 AAAAATAATAATAAAAGAAAAGAA
1 ATAAATAA-AATAAAA-AAAAGAA
2670516 ATAAATA
1 ATAAATA
2670523 TATTGAATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 2 0.08
23 11 0.42
24 13 0.50
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.15
Consensus pattern (22 bp):
ATAAATAAAATAAAAAAAAGAA
Found at i:2675781 original size:20 final size:20
Alignment explanation
Indices: 2675756--2675802 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
2675746 TTAGGATCCT
2675756 GCTAAAAAGTAGGTTTTGAA
1 GCTAAAAAGTAGGTTTTGAA
2675776 GCTAAAAAGTAGGTTTTGAA
1 GCTAAAAAGTAGGTTTTGAA
2675796 GCTAAAA
1 GCTAAAA
2675803 TTCCTAGCTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.43, C:0.06, G:0.23, T:0.28
Consensus pattern (20 bp):
GCTAAAAAGTAGGTTTTGAA
Found at i:2677658 original size:18 final size:19
Alignment explanation
Indices: 2677625--2677661 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
2677615 TGGTTATAAC
2677625 TATATGTGATTATATGTAT
1 TATATGTGATTATATGTAT
*
2677644 TATAT-TGATTGTATGTAT
1 TATATGTGATTATATGTAT
2677662 GCATGACTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.54
Consensus pattern (19 bp):
TATATGTGATTATATGTAT
Found at i:2678837 original size:103 final size:103
Alignment explanation
Indices: 2678612--2678829 Score: 409
Period size: 103 Copynumber: 2.1 Consensus size: 103
2678602 GTCGAGGGTC
2678612 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
2678677 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
2678715 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
2678780 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
2678818 TATGTGGTCCTT
1 TATGTGGTCCTT
2678830 ATGGACATTA
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 112 1.00
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:2678879 original size:23 final size:23
Alignment explanation
Indices: 2678846--2678913 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
2678836 ATTATTATAT
2678846 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
2678869 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* *
2678892 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
2678914 AGCTGTGGTG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.21, C:0.28, G:0.26, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:2680627 original size:14 final size:15
Alignment explanation
Indices: 2680597--2680636 Score: 73
Period size: 14 Copynumber: 2.7 Consensus size: 15
2680587 GGTATCTCTC
2680597 TTTTCATCTTCTCCA
1 TTTTCATCTTCTCCA
2680612 TTTTCATCTT-TCCA
1 TTTTCATCTTCTCCA
2680626 TTTTCATCTTC
1 TTTTCATCTTC
2680637 CTTGACCTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 14 0.58
15 10 0.42
ACGTcount: A:0.12, C:0.30, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTTCATCTTCTCCA
Found at i:2682058 original size:17 final size:16
Alignment explanation
Indices: 2682025--2682071 Score: 51
Period size: 18 Copynumber: 2.9 Consensus size: 16
2682015 TTTGATGTAC
*
2682025 TTATAAAAATACAAATTT
1 TTATAAAAATA-TAA-TT
2682043 TTATAAAAATATAATT
1 TTATAAAAATATAATT
*
2682059 ATATAAAAA-ATAA
1 TTATAAAAATATAA
2682072 AATGAACCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 4 0.15
16 10 0.37
17 2 0.07
18 11 0.41
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (16 bp):
TTATAAAAATATAATT
Found at i:2683197 original size:31 final size:31
Alignment explanation
Indices: 2683154--2683220 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
2683144 GTTAAAGTCG
* * *
2683154 AGTGTTTGTTTTGTTATAAATCGATAACGTT
1 AGTGATTGTTTTGTTACAAATCGATAACATT
*
2683185 AGTGATTGTTTTGTTACAAATTGATAACATT
1 AGTGATTGTTTTGTTACAAATCGATAACATT
2683216 AGTGA
1 AGTGA
2683221 CCAATTTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.30, C:0.06, G:0.19, T:0.45
Consensus pattern (31 bp):
AGTGATTGTTTTGTTACAAATCGATAACATT
Found at i:2692922 original size:94 final size:93
Alignment explanation
Indices: 2692730--2692900 Score: 245
Period size: 95 Copynumber: 1.8 Consensus size: 93
2692720 GACTCTTCGC
* ** * * *
2692730 TCGCCGCCGTCGTCTACTCGGAGATGAGGATCGACTTCCAGTTCTCGTCCATTTTGATTGGACTT
1 TCGCCGCCGTCGACTACTCCAAGATGAGGATAGACTTCCAGTTCTCGGCCATTTTAATTGGACTT
2692795 CCTTTAGAGAAAGAAATCAGAACTGGAA
66 CCTTTAGAGAAAGAAATCAGAACTGGAA
*
2692823 TCGCCGCCGTCGACTACTACACAAGATGAGGATAGACTTCCGGTTCTCGGCCA-TTTAATTGGAC
1 TCGCCGCCGTCGACTACT-C-CAAGATGAGGATAGACTTCCAGTTCTCGGCCATTTTAATTGGAC
*
2692887 TTCGTTTAGAGAAA
64 TTCCTTTAGAGAAA
2692901 AGGATCAAGG
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
93 17 0.25
94 24 0.35
95 27 0.40
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.27
Consensus pattern (93 bp):
TCGCCGCCGTCGACTACTCCAAGATGAGGATAGACTTCCAGTTCTCGGCCATTTTAATTGGACTT
CCTTTAGAGAAAGAAATCAGAACTGGAA
Found at i:2702740 original size:53 final size:53
Alignment explanation
Indices: 2702641--2702830 Score: 193
Period size: 53 Copynumber: 3.5 Consensus size: 53
2702631 ATTGTATGAG
* * *
2702641 TGTGTATCGGTACACTGAGGAGTGTATTGGTACCCTCAAAACATCGAATACCATT
1 TGTGTATCGGT--ACTGAGGAGTGTATCGATACACTCAAAACATCGAATACCATT
* * * * * *
2702696 TGTGTATCGGTACTGAGAAGTGTATCGATACATTTAAAATATCGAATGCTATT
1 TGTGTATCGGTACTGAGGAGTGTATCGATACACTCAAAACATCGAATACCATT
* * * *
2702749 TGTGTATCGGTACATTGAGGAGTGTATCGATACCCTC-AAACATCGAGTGCTATT
1 TGTGTATCGGTAC--TGAGGAGTGTATCGATACACTCAAAACATCGAATACCATT
*
2702803 TGTGTATCGTTACACTGAGGAGTGTATC
1 TGTGTATCGGT--ACTGAGGAGTGTATC
2702831 AATATCCCTA
Statistics
Matches: 115, Mismatches: 16, Indels: 9
0.82 0.11 0.06
Matches are distributed among these distances:
53 46 0.40
54 38 0.33
55 29 0.25
56 2 0.02
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (53 bp):
TGTGTATCGGTACTGAGGAGTGTATCGATACACTCAAAACATCGAATACCATT
Found at i:2702806 original size:54 final size:54
Alignment explanation
Indices: 2702641--2702839 Score: 240
Period size: 54 Copynumber: 3.7 Consensus size: 54
2702631 ATTGTATGAG
* * * *
2702641 TGTGTATCGGTACACTGAGGAGTGTATTGGTACCCTCAAAACATCGAATACCATT
1 TGTGTATCGGTACACTGAGGAGTGTATCGATACCCTC-AAACATCGAATGCTATT
* ** * *
2702696 TGTGTATCGGT--ACTGAGAAGTGTATCGATACATTTAAAATATCGAATGCTATT
1 TGTGTATCGGTACACTGAGGAGTGTATCGATAC-CCTCAAACATCGAATGCTATT
* *
2702749 TGTGTATCGGTACATTGAGGAGTGTATCGATACCCTCAAACATCGAGTGCTATT
1 TGTGTATCGGTACACTGAGGAGTGTATCGATACCCTCAAACATCGAATGCTATT
* *
2702803 TGTGTATCGTTACACTGAGGAGTGTATCAATATCCCT
1 TGTGTATCGGTACACTGAGGAGTGTATCGATA-CCCT
2702840 AACTATGAAA
Statistics
Matches: 121, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
53 42 0.35
54 46 0.38
55 33 0.27
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (54 bp):
TGTGTATCGGTACACTGAGGAGTGTATCGATACCCTCAAACATCGAATGCTATT
Found at i:2703365 original size:21 final size:21
Alignment explanation
Indices: 2703330--2703445 Score: 87
Period size: 21 Copynumber: 5.4 Consensus size: 21
2703320 AGTTGAGGGT
*
2703330 CTATGTAGTCATTCGGGATAA
1 CTATGTGGTCATTCGGGATAA
* *
2703351 TTATGTGGTCTTTCGGGATAA
1 CTATGTGGTCATTCGGGATAA
* *
2703372 ATATATGG-CACTTCGGTG-TAA
1 CTATGTGGTCA-TTCGG-GATAA
2703393 CCCTATGTGGT-ACTTCGGTG-TAAA
1 --CTATGTGGTCA-TTCGG-GAT-AA
2703417 CTATGTGGTCATTCGGGATAA
1 CTATGTGGTCATTCGGGATAA
*
2703438 TTATGTGG
1 CTATGTGG
2703446 CACTTCAGTG
Statistics
Matches: 78, Mismatches: 9, Indels: 16
0.76 0.09 0.16
Matches are distributed among these distances:
20 1 0.01
21 42 0.54
22 16 0.21
23 17 0.22
24 2 0.03
ACGTcount: A:0.23, C:0.14, G:0.27, T:0.36
Consensus pattern (21 bp):
CTATGTGGTCATTCGGGATAA
Found at i:2703408 original size:23 final size:22
Alignment explanation
Indices: 2703352--2703425 Score: 73
Period size: 23 Copynumber: 3.4 Consensus size: 22
2703342 TCGGGATAAT
2703352 TATGTGGT-CTTTCGG-GATAAA-
1 TATGTGGTAC-TTCGGTG-TAAAC
* * *
2703373 TATATGGCACTTCGGTGTAACCC
1 TATGTGGTACTTCGGTGTAA-AC
2703396 TATGTGGTACTTCGGTGTAAAC
1 TATGTGGTACTTCGGTGTAAAC
2703418 TATGTGGT
1 TATGTGGT
2703426 CATTCGGGAT
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
21 14 0.33
22 11 0.26
23 18 0.42
ACGTcount: A:0.22, C:0.15, G:0.27, T:0.36
Consensus pattern (22 bp):
TATGTGGTACTTCGGTGTAAAC
Found at i:2709135 original size:54 final size:55
Alignment explanation
Indices: 2708994--2709155 Score: 211
Period size: 55 Copynumber: 3.0 Consensus size: 55
2708984 TCTTAAAGGT
* ** * * *
2708994 AAAACATTGAATACCATTTGTGTATCGGTATACTGAGGAGTGTATCGACACACTC
1 AAAACATCGAATGTCATTTGTGTATCGGTACACTGAGGAGTGTATCGATACCCTC
*
2709049 AAAACATCGAATGTCATTTGTGTATCGATACACTGAGGAGTGTATCGATACCCTC
1 AAAACATCGAATGTCATTTGTGTATCGGTACACTGAGGAGTGTATCGATACCCTC
* * *
2709104 -AAACATCGAGTG-CTATTTGTGTATCGGTACACTGAAGAGTGTATCAATACCC
1 AAAACATCGAATGTC-ATTTGTGTATCGGTACACTGAGGAGTGTATCGATACCC
2709156 CTAATTATGA
Statistics
Matches: 95, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
53 1 0.01
54 46 0.48
55 48 0.51
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.29
Consensus pattern (55 bp):
AAAACATCGAATGTCATTTGTGTATCGGTACACTGAGGAGTGTATCGATACCCTC
Found at i:2709677 original size:21 final size:21
Alignment explanation
Indices: 2709650--2709698 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
2709640 AGTCGAGGGT
* *
2709650 ATATGTGGTCATTCATGATAA
1 ATATGTGGTCATCCAGGATAA
*
2709671 TTATGTGGTCATCCAGGATAA
1 ATATGTGGTCATCCAGGATAA
2709692 ATATGTG
1 ATATGTG
2709699 ACACTTGATG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.31, C:0.10, G:0.22, T:0.37
Consensus pattern (21 bp):
ATATGTGGTCATCCAGGATAA
Found at i:2714153 original size:9 final size:8
Alignment explanation
Indices: 2714097--2714195 Score: 55
Period size: 8 Copynumber: 12.5 Consensus size: 8
2714087 ACACATAATA
2714097 TAATATTT
1 TAATATTT
2714105 TAATATATATT
1 T-A-ATAT-TT
*
2714116 TAATTTTT
1 TAATATTT
* *
2714124 TAAAAATT
1 TAATATTT
2714132 TAAT-TTT
1 TAATATTT
2714139 T-AT-TTT
1 TAATATTT
*
2714145 CAATATTT
1 TAATATTT
2714153 TAATA-TT
1 TAATATTT
*
2714160 TAAAATTT
1 TAATATTT
*
2714168 AAAATATTT
1 -TAATATTT
*
2714177 TTATA-TT
1 TAATATTT
*
2714184 TAAAATTT
1 TAATATTT
2714192 TAAT
1 TAAT
2714196 TTTAAGATTT
Statistics
Matches: 67, Mismatches: 16, Indels: 16
0.68 0.16 0.16
Matches are distributed among these distances:
6 5 0.07
7 16 0.24
8 28 0.42
9 10 0.15
10 5 0.07
11 3 0.04
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (8 bp):
TAATATTT
Found at i:2714173 original size:24 final size:24
Alignment explanation
Indices: 2714146--2714191 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
2714136 TTTTATTTTC
2714146 AATATTTTAATATTTAAAATTTAA
1 AATATTTTAATATTTAAAATTTAA
*
2714170 AATATTTTTATATTTAAAATTT
1 AATATTTTAATATTTAAAATTT
2714192 TAATTTTAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
AATATTTTAATATTTAAAATTTAA
Found at i:2714200 original size:31 final size:30
Alignment explanation
Indices: 2714151--2714210 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
2714141 TTTTCAATAT
*
2714151 TTTAATATTTAAAATTTAAAATATTTTTATA
1 TTTAAAATTTAAAATTTAAAAT-TTTTTATA
* * *
2714182 TTTAAAATTTTAATTTTAAGATTTTTTAT
1 TTTAAAATTTAAAATTTAAAATTTTTTAT
2714211 TTATTTTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 7 0.28
31 18 0.72
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (30 bp):
TTTAAAATTTAAAATTTAAAATTTTTTATA
Found at i:2716105 original size:10 final size:11
Alignment explanation
Indices: 2716081--2716105 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2716071 TTAATGTGTG
2716081 TTTTTATTTAT
1 TTTTTATTTAT
2716092 TTTTTATTTAT
1 TTTTTATTTAT
2716103 TTT
1 TTT
2716106 GCTTTGACTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTATTTAT
Found at i:2716740 original size:28 final size:29
Alignment explanation
Indices: 2716686--2716741 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
2716676 GGCACTAGAG
**
2716686 GTGCAAAAAAAATCCGAATATTTGATTTT
1 GTGCAAAAAAAATCCGAATATCAGATTTT
*
2716715 GTGCAAAAAATATCCGAA-ATCAGATTT
1 GTGCAAAAAAAATCCGAATATCAGATTT
2716742 GGGAAAAACC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.30
Consensus pattern (29 bp):
GTGCAAAAAAAATCCGAATATCAGATTTT
Found at i:2717597 original size:19 final size:19
Alignment explanation
Indices: 2717573--2717609 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
2717563 CTTTGTGTTC
2717573 CTCTGTTTTCATTTTATCT
1 CTCTGTTTTCATTTTATCT
2717592 CTCTGTTTTCATTTTATC
1 CTCTGTTTTCATTTTATC
2717610 GATCGTTTTA
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:0.11, C:0.22, G:0.05, T:0.62
Consensus pattern (19 bp):
CTCTGTTTTCATTTTATCT
Found at i:2721367 original size:18 final size:18
Alignment explanation
Indices: 2721340--2721410 Score: 70
Period size: 18 Copynumber: 3.8 Consensus size: 18
2721330 ACTGAATATT
2721340 TGTCCCGAAGGACCATTA
1 TGTCCCGAAGGACCATTA
* * *
2721358 TGTCCTGAAGGTCCACTGA
1 TGTCCCGAAGGACCA-TTA
** *
2721377 TTGTTTCGAAGAACCATTA
1 -TGTCCCGAAGGACCATTA
2721396 TGTCCCGAAGGACCA
1 TGTCCCGAAGGACCA
2721411 CTGATAATCC
Statistics
Matches: 39, Mismatches: 12, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
18 25 0.64
19 4 0.10
20 10 0.26
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (18 bp):
TGTCCCGAAGGACCATTA
Found at i:2722081 original size:19 final size:19
Alignment explanation
Indices: 2722057--2722146 Score: 171
Period size: 19 Copynumber: 4.7 Consensus size: 19
2722047 TTTAAACAGG
2722057 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
2722076 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
2722095 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
*
2722114 TGCATCGATGCACTCCCTA
1 TGCATCGATGCACTCCTTA
2722133 TGCATCGATGCACT
1 TGCATCGATGCACT
2722147 AATTGCATTC
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
19 70 1.00
ACGTcount: A:0.21, C:0.32, G:0.17, T:0.30
Consensus pattern (19 bp):
TGCATCGATGCACTCCTTA
Found at i:2728354 original size:18 final size:18
Alignment explanation
Indices: 2728284--2728356 Score: 56
Period size: 18 Copynumber: 3.9 Consensus size: 18
2728274 ACTGAATATT
* *
2728284 TGTCCCGAATGACCATTA
1 TGTCCCGAAGGACCACTA
* *
2728302 TGTCCTGAAGGTCCACTGA
1 TGTCCCGAAGGACCACT-A
* ** *
2728321 TTATTTCGAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
2728340 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
2728357 GATAATCCCT
Statistics
Matches: 39, Mismatches: 14, Indels: 4
0.68 0.25 0.07
Matches are distributed among these distances:
18 26 0.67
19 2 0.05
20 11 0.28
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.26
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:2728608 original size:2 final size:2
Alignment explanation
Indices: 2728601--2728659 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
2728591 TATAACATTA
2728601 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
2728643 AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC A
2728660 TGTATATATA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2729070 original size:19 final size:19
Alignment explanation
Indices: 2729046--2729094 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
2729036 AAACAAGTGT
*
2729046 ATCGATGCACTCCTTATGC
1 ATCGATGCACTCCCTATGC
2729065 ATCGATGCACTCCCTATGC
1 ATCGATGCACTCCCTATGC
2729084 ATCGATGCACT
1 ATCGATGCACT
2729095 AATTGCATTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.22, C:0.33, G:0.16, T:0.29
Consensus pattern (19 bp):
ATCGATGCACTCCCTATGC
Found at i:2730203 original size:43 final size:43
Alignment explanation
Indices: 2730095--2730427 Score: 391
Period size: 43 Copynumber: 7.7 Consensus size: 43
2730085 ACCGTTACAG
2730095 CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCTC
1 CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTT-CTC
* * *
2730139 TAGGTTCCTTTTCTGTGTGCAAGGGTAAGCCTTATAGTTTCTC
1 CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCTC
* * *
2730182 CAAGTTCCTTTGCTGTGTGCAAGGGTAAGCCGTACAGTTTCCC
1 CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCTC
* * * *
2730225 CAGGCTCCTTTGCAGTGTGCAAGGGTAAGTCTTACAGTTTCCCC
1 CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTT-CTC
* * *
2730269 CAGGTTCTTTTGCTGTGTGCAAGGGTAAACCTTATAGTTTCTC
1 CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCTC
* * * *
2730312 TAGGTTCCTTTGTTGTATGCAAGGGTAAGCCTTATAGTTTC-C
1 CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCTC
* * *
2730354 CAAGGTTCCTTTGTTGTGTGCAAGGGTAAGACCTTACCA-TTTTTG
1 C-AGGTTCCTTTGCTGTGTGCAAGGGTAAG-CCTTA-CAGTTTCTC
* * *
2730399 CAGGCTCCTCTGCTTTGTGCACAGGGTAA
1 CAGGTTCCTTTGCTGTGTGCA-AGGGTAA
2730428 ATATGTTTTA
Statistics
Matches: 248, Mismatches: 35, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
42 1 0.00
43 140 0.56
44 98 0.40
45 9 0.04
ACGTcount: A:0.18, C:0.22, G:0.25, T:0.35
Consensus pattern (43 bp):
CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCTC
Found at i:2730281 original size:87 final size:86
Alignment explanation
Indices: 2730095--2730390 Score: 412
Period size: 87 Copynumber: 3.4 Consensus size: 86
2730085 ACCGTTACAG
*
2730095 CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCTCTAGGTTCCTTTTCTGTGTGCA
1 CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCC-CTAGGTTCCTTTGCTGTGTGCA
*
2730160 AGGGTAAGCCTTATAGTTTCTC
65 AGGGTAAGCCTTATAGTTTCCC
* * * * *
2730182 CAAGTTCCTTTGCTGTGTGCAAGGGTAAGCCGTACAGTTTCCCCAGGCTCCTTTGCAGTGTGCAA
1 CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCTAGGTTCCTTTGCTGTGTGCAA
* *
2730247 GGGTAAGTCTTACAGTTTCCCC
66 GGGTAAGCCTTATAGTTT-CCC
* * * * * *
2730269 CAGGTTCTTTTGCTGTGTGCAAGGGTAAACCTTATAGTTTCTCTAGGTTCCTTTGTTGTATGCAA
1 CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCTAGGTTCCTTTGCTGTGTGCAA
2730334 GGGTAAGCCTTATAGTTTCCC
66 GGGTAAGCCTTATAGTTTCCC
* *
2730355 AAGGTTCCTTTGTTGTGTGCAAGGGTAAGACCTTAC
1 CAGGTTCCTTTGCTGTGTGCAAGGGTAAG-CCTTAC
2730391 CATTTTTGCA
Statistics
Matches: 180, Mismatches: 27, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
86 63 0.35
87 117 0.65
ACGTcount: A:0.18, C:0.22, G:0.25, T:0.35
Consensus pattern (86 bp):
CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCTAGGTTCCTTTGCTGTGTGCAA
GGGTAAGCCTTATAGTTTCCC
Found at i:2730333 original size:130 final size:130
Alignment explanation
Indices: 2730095--2730390 Score: 441
Period size: 130 Copynumber: 2.3 Consensus size: 130
2730085 ACCGTTACAG
* *
2730095 CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCTCTAGGTTCCTTTTCTGTGTGCA
1 CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCCAGGTTCCTTTTCTGTGTGCA
* *
2730160 AGGGTAAGCCTTATAGTTTCTCCAAGTTCCTTTGCTGTGTGCAAGGGTAAGCCGTACAGTTTCCC
66 AGGGTAAACCTTATAGTTTCTCCAAGTTCCTTTGCTGTATGCAAGGGTAAGCCGTACAGTTTCCC
* * *
2730225 CAGGCTCCTTTGCAGTGTGCAAGGGTAAGTCTTACAGTTTCCCCCAGGTT-CTTTTGCTGTGTGC
1 CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCCAGGTTCCTTTT-CTGTGTGC
* * * * *
2730289 AAGGGTAAACCTTATAGTTTCTCTAGGTTCCTTTGTTGTATGCAAGGGTAAGCCTTATAGTTTCC
65 AAGGGTAAACCTTATAGTTTCTCCAAGTTCCTTTGCTGTATGCAAGGGTAAGCCGTACAGTTTCC
2730354 C
130 C
* *
2730355 AAGGTTCCTTTGTTGTGTGCAAGGGTAAGACCTTAC
1 CAGGTTCCTTTGCTGTGTGCAAGGGTAAG-CCTTAC
2730391 CATTTTTGCA
Statistics
Matches: 147, Mismatches: 17, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
129 5 0.03
130 137 0.93
131 5 0.03
ACGTcount: A:0.18, C:0.22, G:0.25, T:0.35
Consensus pattern (130 bp):
CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCCAGGTTCCTTTTCTGTGTGCA
AGGGTAAACCTTATAGTTTCTCCAAGTTCCTTTGCTGTATGCAAGGGTAAGCCGTACAGTTTCCC
Found at i:2731789 original size:18 final size:17
Alignment explanation
Indices: 2731753--2731809 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 17
2731743 AGAACATAAA
2731753 TAAAATTTAAAAAATAT
1 TAAAATTTAAAAAATAT
2731770 TAAAATTATAAATAAA-AT
1 TAAAATT-TAAA-AAATAT
* *
2731788 TAAAATATTTAAAAATAG
1 TAAAAT-TTAAAAAATAT
2731806 TAAA
1 TAAA
2731810 TAAATATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
17 10 0.29
18 20 0.59
19 4 0.12
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (17 bp):
TAAAATTTAAAAAATAT
Found at i:2731802 original size:28 final size:28
Alignment explanation
Indices: 2731748--2731828 Score: 85
Period size: 28 Copynumber: 2.8 Consensus size: 28
2731738 TTAAAAGAAC
2731748 ATAAATAAAATTTAAAAAATATTAAAATT
1 ATAAATAAAATTTAAAAAATATTAAAA-T
*
2731777 ATAAATAAAA-TTAAAATAT-TTAAAAAT
1 ATAAATAAAATTTAAAAAATATT-AAAAT
2731804 AGTAAATAAATATTTTTAAAAAATA
1 A-TAAATAAA-A--TTTAAAAAATA
2731829 ATAATTAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
27 4 0.09
28 20 0.47
29 11 0.26
32 8 0.19
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (28 bp):
ATAAATAAAATTTAAAAAATATTAAAAT
Found at i:2731825 original size:24 final size:23
Alignment explanation
Indices: 2731779--2731842 Score: 69
Period size: 24 Copynumber: 2.8 Consensus size: 23
2731769 TTAAAATTAT
* *
2731779 AAATAA-AATTAAAATATTT-AA
1 AAATAATAAATAAAATTTTTAAA
*
2731800 AAATAGTAAATAAATATTTTTAAA
1 AAATAATAAATAAA-ATTTTTAAA
*
2731824 AAATAATAATTAAAATTTT
1 AAATAATAAATAAAATTTT
2731843 GTGGAAAGTA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 5 0.14
22 6 0.17
23 10 0.29
24 14 0.40
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (23 bp):
AAATAATAAATAAAATTTTTAAA
Found at i:2738406 original size:31 final size:30
Alignment explanation
Indices: 2738370--2738444 Score: 104
Period size: 26 Copynumber: 2.6 Consensus size: 30
2738360 TATTATTTCG
2738370 GGTCGGGTCGGGTCGGGTGAAACTTTATTT
1 GGTCGGGTCGGGTCGGGTGAAACTTTATTT
2738400 --T--GGTCGGGTCGGGTGAAACTTTATTTT
1 GGTCGGGTCGGGTCGGGTGAAACTTTA-TTT
*
2738427 GGTCGGGTCGGATCGGGT
1 GGTCGGGTCGGGTCGGGT
2738445 TTTTTAAGTT
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
26 22 0.56
27 3 0.08
28 1 0.03
29 1 0.03
31 12 0.31
ACGTcount: A:0.12, C:0.13, G:0.41, T:0.33
Consensus pattern (30 bp):
GGTCGGGTCGGGTCGGGTGAAACTTTATTT
Found at i:2738411 original size:26 final size:26
Alignment explanation
Indices: 2738375--2738437 Score: 126
Period size: 26 Copynumber: 2.4 Consensus size: 26
2738365 TTTCGGGTCG
2738375 GGTCGGGTCGGGTGAAACTTTATTTT
1 GGTCGGGTCGGGTGAAACTTTATTTT
2738401 GGTCGGGTCGGGTGAAACTTTATTTT
1 GGTCGGGTCGGGTGAAACTTTATTTT
2738427 GGTCGGGTCGG
1 GGTCGGGTCGG
2738438 ATCGGGTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.13, C:0.13, G:0.40, T:0.35
Consensus pattern (26 bp):
GGTCGGGTCGGGTGAAACTTTATTTT
Found at i:2738689 original size:27 final size:28
Alignment explanation
Indices: 2738649--2738707 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
2738639 CTTTATTTTG
*
2738649 TTCGGGTCG-GGTTTTTTAAGTGTGATA
1 TTCGGGTCGAGTTTTTTTAAGTGTGATA
*
2738676 TTCGGGTCGAGTTTTTTTAAGTGTGCTA
1 TTCGGGTCGAGTTTTTTTAAGTGTGATA
2738704 TTCG
1 TTCG
2738708 AATCGGGTCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 9 0.31
28 20 0.69
ACGTcount: A:0.14, C:0.10, G:0.31, T:0.46
Consensus pattern (28 bp):
TTCGGGTCGAGTTTTTTTAAGTGTGATA
Found at i:2738858 original size:239 final size:243
Alignment explanation
Indices: 2738444--2738931 Score: 750
Period size: 244 Copynumber: 2.0 Consensus size: 243
2738434 TCGGATCGGG
* ** *
2738444 TTTTTTAAGTTTGATATTCGGGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCAACC
1 TTTTTTAAGTGTGATATTCGAATCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCAGACCAACC
* *
2738509 CGAAAATATATATAATTCAGGTCAGGTCAGATTAAGTCATTGTTTTTATTAAATAAAAACAATTT
66 CAAAAATATATATAATTCA-G--AGGTCAGATTAAGTCACTGTTTTTATTAAATAAAAACAATTT
* * *
2738574 TTTATTATTTCGGGTCGGGTTGAGTTGGATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAA
128 TTTATTATTTCAGGTCGGGTCGAGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAA
2738639 CTTTATTTTG-T-TCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGAGT
193 CTTTATTTTGTTGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGAGT
* **
2738688 TTTTTTAAGTGTGCTATTCGAATCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCAGACTGACC
1 TTTTTTAAGTGTGATATTCGAATCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCAGACCAACC
* * *
2738753 CAAAAATATATATAATTC-G-GGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATATTTTTTT
66 CAAAAATATATATAATTCAGAGGTCAGATTAAGTCACTGTTTTTATTAAATAAAAACAATTTTTT
*
2738816 ATTATTTCAGGTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTT
131 ATTATTTCAGGTCGGGTCGAGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTT
2738881 TATTTTGTTCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGAGT
196 TATTTTGTT---GTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGAGT
2738932 CGGGTCGGGT
Statistics
Matches: 223, Mismatches: 16, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
239 108 0.48
240 1 0.00
242 1 0.00
244 113 0.51
ACGTcount: A:0.25, C:0.12, G:0.26, T:0.38
Consensus pattern (243 bp):
TTTTTTAAGTGTGATATTCGAATCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCAGACCAACC
CAAAAATATATATAATTCAGAGGTCAGATTAAGTCACTGTTTTTATTAAATAAAAACAATTTTTT
ATTATTTCAGGTCGGGTCGAGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTT
TATTTTGTTGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGAGT
Found at i:2738955 original size:38 final size:38
Alignment explanation
Indices: 2738892--2738980 Score: 137
Period size: 38 Copynumber: 2.4 Consensus size: 38
2738882 ATTTTGTTCG
* *
2738892 GGTCGGGTCGGG-TTTTTTAAGTGTGATATTCGGGTC-
1 GGTCGGGTCGGGTTTTTTTAACTGTGATATTCGGGACA
2738928 GAGTCGGGTCGGGTTTTTTTAACTGTGATATTCGGGACA
1 G-GTCGGGTCGGGTTTTTTTAACTGTGATATTCGGGACA
2738967 GGTCGGGTCGGGTT
1 GGTCGGGTCGGGTT
2738981 CAGGTTTTGG
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
36 1 0.02
37 11 0.23
38 35 0.73
39 1 0.02
ACGTcount: A:0.12, C:0.12, G:0.39, T:0.36
Consensus pattern (38 bp):
GGTCGGGTCGGGTTTTTTTAACTGTGATATTCGGGACA
Found at i:2747341 original size:29 final size:29
Alignment explanation
Indices: 2747308--2747382 Score: 114
Period size: 29 Copynumber: 2.6 Consensus size: 29
2747298 GCCAACCCAT
**
2747308 AGGTCGCCATGCTTTCCGGGCGACCTAAG
1 AGGTCGCCATGCACTCCGGGCGACCTAAG
* *
2747337 AGGTCGCCATGCACTCCGGGCGACCTTAT
1 AGGTCGCCATGCACTCCGGGCGACCTAAG
2747366 AGGTCGCCATGCACTCC
1 AGGTCGCCATGCACTCC
2747383 CAGTGACCTT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.17, C:0.35, G:0.28, T:0.20
Consensus pattern (29 bp):
AGGTCGCCATGCACTCCGGGCGACCTAAG
Found at i:2747390 original size:29 final size:29
Alignment explanation
Indices: 2747306--2747392 Score: 93
Period size: 29 Copynumber: 3.0 Consensus size: 29
2747296 AAGCCAACCC
** ** *
2747306 ATAGGTCGCCATGCTTTCCGGGCGACCTA
1 ATAGGTCGCCATGCACTCCCAGCGACCTT
* **
2747335 AGAGGTCGCCATGCACTCCGGGCGACCTT
1 ATAGGTCGCCATGCACTCCCAGCGACCTT
*
2747364 ATAGGTCGCCATGCACTCCCAGTGACCTT
1 ATAGGTCGCCATGCACTCCCAGCGACCTT
2747393 GTTTTTCTTG
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.18, C:0.33, G:0.26, T:0.22
Consensus pattern (29 bp):
ATAGGTCGCCATGCACTCCCAGCGACCTT
Found at i:2747452 original size:27 final size:27
Alignment explanation
Indices: 2747420--2747472 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
2747410 TATTTCTGCA
* *
2747420 CGTCCCCTCTTGCTCTCCGCTGCATGC
1 CGTCCCCTCCTGCTCCCCGCTGCATGC
2747447 CGTCCCCTCCTGCTCCCCGCTGCATG
1 CGTCCCCTCCTGCTCCCCGCTGCATG
2747473 TCGCTGCAGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.04, C:0.51, G:0.19, T:0.26
Consensus pattern (27 bp):
CGTCCCCTCCTGCTCCCCGCTGCATGC
Found at i:2747699 original size:26 final size:25
Alignment explanation
Indices: 2747669--2747725 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 25
2747659 CATAAAAGAA
*
2747669 AGAAAGGGAGAAGAGATTGCAGCCG
1 AGAAAGGGAGAAGAGAGTGCAGCCG
*
2747694 AGGAAAGGGAGAAGATAGTGCAGCCG
1 A-GAAAGGGAGAAGAGAGTGCAGCCG
2747720 AGAAAG
1 AGAAAG
2747726 AAAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 6 0.21
26 23 0.79
ACGTcount: A:0.42, C:0.11, G:0.40, T:0.07
Consensus pattern (25 bp):
AGAAAGGGAGAAGAGAGTGCAGCCG
Found at i:2748251 original size:15 final size:16
Alignment explanation
Indices: 2748224--2748253 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2748214 AAGTTTACTT
2748224 TATAAGTTTATTATAC
1 TATAAGTTTATTATAC
2748240 TATAAG-TTATTATA
1 TATAAGTTTATTATA
2748254 TTAAATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (16 bp):
TATAAGTTTATTATAC
Found at i:2750500 original size:11 final size:11
Alignment explanation
Indices: 2750480--2750564 Score: 50
Period size: 11 Copynumber: 7.5 Consensus size: 11
2750470 ATTTCATTAC
2750480 TAGT-AATCAT
1 TAGTAAATCAT
2750490 TAGTAAATCAT
1 TAGTAAATCAT
*
2750501 TAGTATCAAATAAT
1 TAG--T-AAATCAT
* *
2750515 TA--AATATTAA
1 TAGTAA-ATCAT
*
2750525 TAATAAATCAT
1 TAGTAAATCAT
*
2750536 TAGTAATAATAAT
1 TAGT-A-AATCAT
2750549 TAGTAAATCAT
1 TAGTAAATCAT
2750560 TAGTA
1 TAGTA
2750565 TCAAATCATT
Statistics
Matches: 58, Mismatches: 8, Indels: 17
0.70 0.10 0.20
Matches are distributed among these distances:
9 2 0.03
10 9 0.16
11 25 0.43
12 4 0.07
13 10 0.17
14 8 0.14
ACGTcount: A:0.49, C:0.06, G:0.07, T:0.38
Consensus pattern (11 bp):
TAGTAAATCAT
Found at i:2750543 original size:14 final size:13
Alignment explanation
Indices: 2750527--2750575 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
2750517 AATATTAATA
2750527 ATAAATCATTAGT
1 ATAAATCATTAGT
*
2750540 A-ATAATAATTAG-
1 ATA-AATCATTAGT
2750552 -TAAATCATTAGT
1 ATAAATCATTAGT
2750564 ATCAAATCATTA
1 AT-AAATCATTA
2750576 AATATTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
11 8 0.28
12 2 0.07
13 10 0.34
14 9 0.31
ACGTcount: A:0.49, C:0.08, G:0.06, T:0.37
Consensus pattern (13 bp):
ATAAATCATTAGT
Found at i:2750615 original size:59 final size:58
Alignment explanation
Indices: 2750457--2750597 Score: 187
Period size: 59 Copynumber: 2.4 Consensus size: 58
2750447 TTTTAGTATC
* * * * *
2750457 AAATATTATTATAATTTCATTACTAGTAATCATTAGTAAATCATTAGTATCAAATAATT
1 AAATATTATAATAA-ATCATTAATAATAATAATTAGTAAATCATTAGTATCAAATAATT
* *
2750516 AAATATTAATAATAAATCATTAGTAATAATAATTAGTAAATCATTAGTATCAAATCATT
1 AAATATT-ATAATAAATCATTAATAATAATAATTAGTAAATCATTAGTATCAAATAATT
2750575 AAATATT-TAA-AAATCATTAATAA
1 AAATATTATAATAAATCATTAATAA
2750598 ATTCGACTAT
Statistics
Matches: 74, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
56 12 0.16
57 3 0.04
59 53 0.72
60 6 0.08
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.39
Consensus pattern (58 bp):
AAATATTATAATAAATCATTAATAATAATAATTAGTAAATCATTAGTATCAAATAATT
Found at i:2750699 original size:14 final size:14
Alignment explanation
Indices: 2750678--2750996 Score: 200
Period size: 14 Copynumber: 24.1 Consensus size: 14
2750668 ATTATTAATA
2750678 ATTATTAAATCATT
1 ATTATTAAATCATT
*
2750692 AGTATTAAATCATT
1 ATTATTAAATCATT
*
2750706 ATTA-TAAA--ATC
1 ATTATTAAATCATT
* *
2750717 ATTACTAAATCACT
1 ATTATTAAATCATT
* *
2750731 ACTATTAAATGATT
1 ATTATTAAATCATT
*
2750745 ATTA-T-AATGATT
1 ATTATTAAATCATT
2750757 ATTATTAAATC---
1 ATTATTAAATCATT
2750768 ATTATT--ATCATT
1 ATTATTAAATCATT
2750780 ATTATTAAATCATT
1 ATTATTAAATCATT
*
2750794 ATTA-T-AATGATT
1 ATTATTAAATCATT
*
2750806 ATTACTAAATCATT
1 ATTATTAAATCATT
*
2750820 ATTA-T-AATGATT
1 ATTATTAAATCATT
*
2750832 ATTATCAAATCATT
1 ATTATTAAATCATT
2750846 ATTAAATCATCAAATCATT
1 ATT--AT--T-AAATCATT
* *
2750865 AAATATTAAA--ATC
1 -ATTATTAAATCATT
2750878 ATTATTAAATCATT
1 ATTATTAAATCATT
*
2750892 ATTA-T-AATGATT
1 ATTATTAAATCATT
*
2750904 ATTATCAAATCATT
1 ATTATTAAATCATT
* *
2750918 ACTA-T-AATGATT
1 ATTATTAAATCATT
*
2750930 ATTATCAAATCATT
1 ATTATTAAATCATT
* *
2750944 ACTA-T-AATGATT
1 ATTATTAAATCATT
*
2750956 ATTATCAAATCATT
1 ATTATTAAATCATT
* *
2750970 AATA-T-AATGATT
1 ATTATTAAATCATT
*
2750982 ATTATCAAATCATT
1 ATTATTAAATCATT
2750996 A
1 A
2750997 CTAAATCATC
Statistics
Matches: 233, Mismatches: 42, Indels: 60
0.70 0.13 0.18
Matches are distributed among these distances:
9 3 0.01
11 12 0.05
12 86 0.37
13 12 0.05
14 102 0.44
15 3 0.01
16 3 0.01
18 2 0.01
19 8 0.03
20 2 0.01
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (14 bp):
ATTATTAAATCATT
Found at i:2750762 original size:26 final size:26
Alignment explanation
Indices: 2750678--2750996 Score: 320
Period size: 26 Copynumber: 12.6 Consensus size: 26
2750668 ATTATTAATA
* *
2750678 ATTATTAAATCATTAGTATTAAATCATT
1 ATTATTAAATCATTATTA-T-AATGATT
* * * *
2750706 ATTATAAAATCATTACTA-AATCACT
1 ATTATTAAATCATTATTATAATGATT
* *
2750731 ACTATTAAATGATTATTATAATGATT
1 ATTATTAAATCATTATTATAATGATT
*
2750757 ATTATTAAATCATTA-T-T-ATCATT
1 ATTATTAAATCATTATTATAATGATT
2750780 ATTATTAAATCATTATTATAATGATT
1 ATTATTAAATCATTATTATAATGATT
*
2750806 ATTACTAAATCATTATTATAATGATT
1 ATTATTAAATCATTATTATAATGATT
* * *
2750832 ATTATCAAATCATTATTA-AATCATCAA
1 ATTATTAAATCATTATTATAATGAT--T
* *
2750859 ATCATT-AA--A-TATTA-AA--ATC
1 ATTATTAAATCATTATTATAATGATT
2750878 ATTATTAAATCATTATTATAATGATT
1 ATTATTAAATCATTATTATAATGATT
* *
2750904 ATTATCAAATCATTACTATAATGATT
1 ATTATTAAATCATTATTATAATGATT
* *
2750930 ATTATCAAATCATTACTATAATGATT
1 ATTATTAAATCATTATTATAATGATT
* *
2750956 ATTATCAAATCATTAATATAATGATT
1 ATTATTAAATCATTATTATAATGATT
*
2750982 ATTATCAAATCATTA
1 ATTATTAAATCATTA
2750997 CTAAATCATC
Statistics
Matches: 252, Mismatches: 26, Indels: 28
0.82 0.08 0.09
Matches are distributed among these distances:
19 5 0.02
20 2 0.01
21 2 0.01
22 1 0.00
23 32 0.13
24 5 0.02
25 27 0.11
26 158 0.63
27 4 0.02
28 16 0.06
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (26 bp):
ATTATTAAATCATTATTATAATGATT
Found at i:2750859 original size:19 final size:19
Alignment explanation
Indices: 2750835--2750890 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
2750825 AATGATTATT
2750835 ATCAAATCATTATTAAATC
1 ATCAAATCATTATTAAATC
2750854 ATCAAATC---ATTAAAT-
1 ATCAAATCATTATTAAATC
*
2750869 ATTAAAATCATTATTAAATC
1 A-TCAAATCATTATTAAATC
2750889 AT
1 AT
2750891 TATTATAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
15 1 0.03
16 13 0.42
19 16 0.52
20 1 0.03
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (19 bp):
ATCAAATCATTATTAAATC
Found at i:2750956 original size:150 final size:147
Alignment explanation
Indices: 2750733--2751046 Score: 504
Period size: 150 Copynumber: 2.1 Consensus size: 147
2750723 AAATCACTAC
* * * *
2750733 TATTAAATGATTATTATAATGATTATTATTAAATCATTATTATCATTATTATTAAATCATTATTA
1 TATTAAATCATTATTATAATGATTATTATCAAATCATTATTATCATTATTATCAAATCATTACTA
* *
2750798 TAATGATTATTA-CTAAATCATTATTATAATGATTATTATCAAATCATTATTAAATCATCAAATC
66 TAATGATTATTATC-AAATCATTAATATAATGATTATTATCAAATCATTACTAAATCATCAAATC
2750862 ATTAAATATTAAAATCAT
130 ATTAAATATTAAAATCAT
*
2750880 TATTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTA
1 TATTAAATCATTATTATAATGATTATTATCAAATCATTA-T-T-ATCATTATTATCAAATCATTA
2750945 CTATAATGATTATTATCAAATCATTAATATAATGATTATTATCAAATCATTACTAAATCATCAAA
63 CTATAATGATTATTATCAAATCATTAATATAATGATTATTATCAAATCATTACTAAATCATCAAA
*
2751010 TCATTAAATATTAAATTCAT
128 TCATTAAATATTAAAATCAT
*
2751030 TATTAAATCATTTTTAT
1 TATTAAATCATTATTAT
2751047 GGTTAATTGA
Statistics
Matches: 154, Mismatches: 9, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
147 37 0.24
148 1 0.01
149 1 0.01
150 114 0.74
151 1 0.01
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.45
Consensus pattern (147 bp):
TATTAAATCATTATTATAATGATTATTATCAAATCATTATTATCATTATTATCAAATCATTACTA
TAATGATTATTATCAAATCATTAATATAATGATTATTATCAAATCATTACTAAATCATCAAATCA
TTAAATATTAAAATCAT
Found at i:2751023 original size:52 final size:52
Alignment explanation
Indices: 2750850--2751023 Score: 165
Period size: 52 Copynumber: 3.3 Consensus size: 52
2750840 ATCATTATTA
* * * * * *
2750850 AATCATCAAATCATTAAATATTAA-AATCATTATTAAATCATTATTATAATGAT
1 AATCATTAAATCATT-AATA-TAATGATTATTATCAAATCATTACTATAATCAT
* * * * *
2750903 TATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTATAATGAT
1 AATCATTAAATCATTAATATAATGATTATTATCAAATCATTACTATAATCAT
* * *
2750955 TATTATCAAATCATTAATATAATGATTATTATCAAATCATTACTA-AATCAT
1 AATCATTAAATCATTAATATAATGATTATTATCAAATCATTACTATAATCAT
2751006 CAAATCATTAAAT-ATTAA
1 --AATCATTAAATCATTAA
2751024 ATTCATTATT
Statistics
Matches: 106, Mismatches: 12, Indels: 7
0.85 0.10 0.06
Matches are distributed among these distances:
51 8 0.08
52 77 0.73
53 21 0.20
ACGTcount: A:0.47, C:0.11, G:0.02, T:0.40
Consensus pattern (52 bp):
AATCATTAAATCATTAATATAATGATTATTATCAAATCATTACTATAATCAT
Found at i:2751272 original size:14 final size:14
Alignment explanation
Indices: 2751253--2751325 Score: 56
Period size: 14 Copynumber: 4.7 Consensus size: 14
2751243 TAATAATTAC
2751253 TAAATCATTACTAT
1 TAAATCATTACTAT
2751267 TAAATCATTAACTAT
1 TAAATCATT-ACTAT
* *
2751282 TAATAATAATTTCATTAT
1 T-A-AATCA-TT-ACTAT
2751300 TACTAATCATTACTAT
1 TA--AATCATTACTAT
*
2751316 CAAATCATTA
1 TAAATCATTA
2751326 AATATTAATA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
14 17 0.35
15 6 0.12
16 6 0.12
17 7 0.15
18 12 0.25
ACGTcount: A:0.44, C:0.14, G:0.00, T:0.42
Consensus pattern (14 bp):
TAAATCATTACTAT
Found at i:2751312 original size:49 final size:49
Alignment explanation
Indices: 2751248--2751485 Score: 431
Period size: 49 Copynumber: 4.8 Consensus size: 49
2751238 ATTACTAATA
* *
2751248 ATTACTAAATCATTACTATTAAATCATTAACTATTAATAATAATTTCATT
1 ATTACT-AATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
*
2751298 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAAATTCATT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
2751347 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
*
2751396 ATTACTAATCATTACTATCAAATCATTATATATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
2751445 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATA
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATA
2751486 GATGGGTGCC
Statistics
Matches: 182, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
49 176 0.97
50 6 0.03
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.42
Consensus pattern (49 bp):
ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
Found at i:2751332 original size:21 final size:21
Alignment explanation
Indices: 2751308--2751381 Score: 60
Period size: 21 Copynumber: 3.2 Consensus size: 21
2751298 ATTACTAATC
2751308 ATTACTATCAAATCATTAAAT
1 ATTACTATCAAATCATTAAAT
*
2751329 ATTAATAAT-AAATTCATTATTACTAAT
1 ATTACT-ATCAAA-TC---ATTA--AAT
2751356 CATTACTATCAAATCATTAAAT
1 -ATTACTATCAAATCATTAAAT
2751378 ATTA
1 ATTA
2751382 ATAATAATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 18
0.68 0.03 0.29
Matches are distributed among these distances:
21 12 0.29
22 7 0.17
24 4 0.10
25 4 0.10
27 7 0.17
28 8 0.19
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (21 bp):
ATTACTATCAAATCATTAAAT
Found at i:2751443 original size:22 final size:22
Alignment explanation
Indices: 2751369--2751446 Score: 59
Period size: 22 Copynumber: 3.3 Consensus size: 22
2751359 TACTATCAAA
*
2751369 TCATTAAATATTAATAATAATT
1 TCATTATATATTAATAATAATT
* **
2751391 TCATTAT-TACTAATCATTACTATCAAA
1 TCATTATATATTAAT-A--A-TA--ATT
2751418 TCATTATATATTAATAATAATT
1 TCATTATATATTAATAATAATT
2751440 TCATTAT
1 TCATTAT
2751447 TACTAATCAT
Statistics
Matches: 42, Mismatches: 7, Indels: 14
0.67 0.11 0.22
Matches are distributed among these distances:
21 6 0.14
22 15 0.36
24 3 0.07
25 3 0.07
27 9 0.21
28 6 0.14
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (22 bp):
TCATTATATATTAATAATAATT
Found at i:2755143 original size:53 final size:50
Alignment explanation
Indices: 2755083--2755220 Score: 124
Period size: 53 Copynumber: 2.7 Consensus size: 50
2755073 AACAACAATA
2755083 AATTAAACAAATTAATTTTTATATAATATAA-TATA-TTATAATATAACTTAAACT
1 AATTAAAC-AATTAATTTTTATATAATATAACT-TAGTTA-AA-ATAAC--AAACT
* *
2755137 AA-TAAACTATT--TCTTTATTATAATATAACTTAGTTAAAATAACAAACT
1 AATTAAACAATTAATTTTTA-TATAATATAACTTAGTTAAAATAACAAACT
*
2755185 AATTAAGAACTAATTAATTTTTTTATAATATAACTT
1 AATT-A-AAC-AATTAATTTTTATATAATATAACTT
2755221 CAACTTCAAC
Statistics
Matches: 70, Mismatches: 5, Indels: 19
0.74 0.05 0.20
Matches are distributed among these distances:
48 7 0.10
49 1 0.01
50 11 0.16
51 17 0.24
52 10 0.14
53 18 0.26
54 6 0.09
ACGTcount: A:0.49, C:0.07, G:0.01, T:0.43
Consensus pattern (50 bp):
AATTAAACAATTAATTTTTATATAATATAACTTAGTTAAAATAACAAACT
Found at i:2755315 original size:44 final size:50
Alignment explanation
Indices: 2755257--2755374 Score: 140
Period size: 51 Copynumber: 2.4 Consensus size: 50
2755247 GTTTAAAGAC
*
2755257 ACTAACAAATTAATTAAAT-ATTTTTTT-TAT-AT-T-TA-ATAACTTAA
1 ACTAACAAACTAATTAAATAATTTTTTTATATAATATATATATAACTTAA
* *
2755301 ACTAAGAAACTAATTAACTAATTTTTTTATATAATATAATATATAACTTAA
1 ACTAACAAACTAATTAAATAATTTTTTTATATAATAT-ATATATAACTTAA
2755352 ACTAACAAACTAATATAATATAA
1 ACTAACAAACTAAT-TAA-ATAA
2755375 CTTAAACTAA
Statistics
Matches: 60, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
44 16 0.27
45 8 0.13
46 3 0.05
47 2 0.03
48 1 0.02
50 2 0.03
51 22 0.37
52 3 0.05
53 3 0.05
ACGTcount: A:0.50, C:0.08, G:0.01, T:0.41
Consensus pattern (50 bp):
ACTAACAAACTAATTAAATAATTTTTTTATATAATATATATATAACTTAA
Found at i:2755380 original size:28 final size:30
Alignment explanation
Indices: 2755332--2755394 Score: 112
Period size: 28 Copynumber: 2.2 Consensus size: 30
2755322 TTTTTTTATA
2755332 TAATATAATATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
2755362 TAATAT-A-ATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
2755390 TAATA
1 TAATA
2755395 ATTTATACTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 26 0.79
29 1 0.03
30 6 0.18
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Found at i:2755401 original size:28 final size:28
Alignment explanation
Indices: 2755336--2755401 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
2755326 TTTATATAAT
2755336 ATAATATATAACTTAAACTAACAAACTA
1 ATAATATATAACTTAAACTAACAAACTA
2755364 AT-ATAATATAACTTAAACTAACAAACTA
1 ATAAT-ATATAACTTAAACTAACAAACTA
*
2755392 ATAATTTATA
1 ATAATATATA
2755402 CTAACAAACT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
27 2 0.06
28 31 0.89
29 2 0.06
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (28 bp):
ATAATATATAACTTAAACTAACAAACTA
Found at i:2755404 original size:21 final size:21
Alignment explanation
Indices: 2755371--2755419 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
2755361 CTAATATAAT
2755371 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
2755392 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
2755413 ATTAACT
1 A-TAACT
2755420 AAATTTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:2755796 original size:21 final size:21
Alignment explanation
Indices: 2755771--2755840 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
2755761 TGCTGCAATA
2755771 ATGCAGCTATGGATGCAACGC
1 ATGCAGCTATGGATGCAACGC
* * * *
2755792 ATGCAGCTACGGATAC-ATGA
1 ATGCAGCTATGGATGCAACGC
*
2755812 ATCTCCCAGCTATGGATGCAACGC
1 A--T-GCAGCTATGGATGCAACGC
2755836 ATGCA
1 ATGCA
2755841 TGAGGGAGCA
Statistics
Matches: 35, Mismatches: 10, Indels: 8
0.66 0.19 0.15
Matches are distributed among these distances:
20 3 0.09
21 16 0.46
22 2 0.06
23 11 0.31
24 3 0.09
ACGTcount: A:0.30, C:0.26, G:0.24, T:0.20
Consensus pattern (21 bp):
ATGCAGCTATGGATGCAACGC
Found at i:2755902 original size:29 final size:29
Alignment explanation
Indices: 2755860--2755928 Score: 111
Period size: 29 Copynumber: 2.4 Consensus size: 29
2755850 AGAGGATTAA
* *
2755860 AGCTTGGTCGCGGGGTAGAATCTCCTAGG
1 AGCTTGGTCGCGGGGCAGAATCTCCCAGG
2755889 AGCTTGGTCGCGGGGCAGAATCTCCCAGG
1 AGCTTGGTCGCGGGGCAGAATCTCCCAGG
*
2755918 AGTTTGGTCGC
1 AGCTTGGTCGC
2755929 CGGGACTCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.16, C:0.23, G:0.38, T:0.23
Consensus pattern (29 bp):
AGCTTGGTCGCGGGGCAGAATCTCCCAGG
Found at i:2764093 original size:27 final size:27
Alignment explanation
Indices: 2764041--2764094 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
2764031 ACCAAAACCT
**
2764041 GTGAAAATAACCATGTCAAGTTAATGC
1 GTGAAAATAACCATGTCAAGACAATGC
2764068 GTGAAAATAACCATGTCAAGACAATGC
1 GTGAAAATAACCATGTCAAGACAATGC
2764095 TCAACTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.43, C:0.17, G:0.19, T:0.22
Consensus pattern (27 bp):
GTGAAAATAACCATGTCAAGACAATGC
Found at i:2765309 original size:16 final size:16
Alignment explanation
Indices: 2765288--2765318 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2765278 TCGCAGACTG
2765288 CATAAAATATCGAGTA
1 CATAAAATATCGAGTA
2765304 CATAAAATATCGAGT
1 CATAAAATATCGAGT
2765319 GGCGGACTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.26
Consensus pattern (16 bp):
CATAAAATATCGAGTA
Found at i:2770660 original size:536 final size:536
Alignment explanation
Indices: 2769648--2770715 Score: 1590
Period size: 536 Copynumber: 2.0 Consensus size: 536
2769638 GCCAACACAC
* *
2769648 TTCAATCATGTAATTTTATATTCACACCCAGAGAGGGCAACCTTTTAGCAACTGATAAAAACAAC
1 TTCAATCATGTAATTATAGATTCACACCCAGAGAGGGCAACCTTTTAGCAACTGATAAAAACAAC
*
2769713 TCAAATGATCTATAAGTCATACCTAGTCTCCAAGTGTGCTTAAGTGTATCATGAAATGCCCATAA
66 TCAAATGATCTATAAGTCATACCTAGTCTCCAAGTATGCTTAAGTGTATCATGAAATGCCCATAA
* * *
2769778 CTCAGCAATCCAAATCGAATAGTTATCAATGCTCTTTGGAAAACCAAAAATATAAGTCCCTTGGT
131 CTCAGCAATCAAAATCGAATAGTTATCAATGCTCTTTGAAAAACCAAAAATATAAGTCCCTTAGT
* * * *
2769843 TGCATTGAAGAACACCACATGCAGTTGCCGTCAAGTCATTAATTCTAAAAAAAGTATTCGTGTTA
196 TGCATCGAAGAACACCACATGCAGTTGCCGCCAAGCCATTAATTCTAAAAAAAGTATTCATGTTA
*
2769908 GTCTTGATCCATCCCTCAGGTGATCTCATCCATTTAGTAGGTATCAGTTCTGCAAGCATTGCCAC
261 GTCTTGATCCATCCCTCAGGTGATCTCATCCATTTAGTAGGTATCAGTTCTGCAAGCATTGCAAC
* * *
2769973 TTTCCTTGAAGTACGGCTAGTCAACAGCTCTCATACAAACTTCTTGTTGTTCAATTTCCTCCAAA
326 TTTCCTCGAACTACGACTAGTCAACAGCTCTCATACAAACTTCTTGTTGTTCAATTTCCTCCAAA
* * * * *
2770038 GTGATTAGCGAATGATAGGCGAGCTTGGAAGAAATTTATTTTCGATCCTCCCATTGCCAACCAAG
391 GTGATTAGCGAATGATAAGAGAGCTTGGAAGAAAATTATGTTCGATCCTCCCACTGCCAACCAAG
2770103 AGTATCTATTTCAAGCGAGATTTGTGGGGGATTAAAAACAACTTTTTCCCTTAGGA-ACGGATCC
456 AGTATCTATTTCAAGCGAGATTTGTGGGGGATTAAAAACAACTTTTTCCCTTAGGATA-GGATCC
*
2770167 AGTAGAGCATCTTCTAT
520 AATAGAGCATCTTCTAT
* *
2770184 TTCAATCATGTACTTATAGATTCACACCCAGAGAGGGCAACCTTTTAGCAACTGATAAAAATAAC
1 TTCAATCATGTAATTATAGATTCACACCCAGAGAGGGCAACCTTTTAGCAACTGATAAAAACAAC
* * *
2770249 TCAAATGATCTATAAGTCCTAGCTAGTCTCCCAGTATG-TATAAGTGTATCATGAAATGCCCATA
66 TCAAATGATCTATAAGTCATACCTAGTCTCCAAGTATGCT-TAAGTGTATCATGAAATGCCCATA
* * * ** *
2770313 ACTCATCAATCAAAATCGGATAGTTATCGATGCTCTTTGAAAAACCAAATGTCTAAGTCCCTTAG
130 ACTCAGCAATCAAAATCGAATAGTTATCAATGCTCTTTGAAAAACCAAAAATATAAGTCCCTTAG
* ** * * *
2770378 TTGCATCGAAGGACACCACATGCAGTTGTTGCCATGCCATTAATTCTCATAAAAGTATTCATGTT
195 TTGCATCGAAGAACACCACATGCAGTTGCCGCCAAGCCATTAATTCTAAAAAAAGTATTCATGTT
* ** *
2770443 AG-CTTTGATCCATCCCTCAGGTGATCTCTTCCATTTAGTAGGTATTGGTTCTGCATGCATTGCA
260 AGTC-TTGATCCATCCCTCAGGTGATCTCATCCATTTAGTAGGTATCAGTTCTGCAAGCATTGCA
* *
2770507 ACTTTCCTCGAACTACGACTAGTCAACAGGTCTCATACAAACTTCTTGTTGTTCATTTTCCTCCA
324 ACTTTCCTCGAACTACGACTAGTCAACAGCTCTCATACAAACTTCTTGTTGTTCAATTTCCTCCA
*
2770572 AAGTGATTAGCGAATGATAATAGAGCTTGGAAGTGAAAATT-TGTT-GATCCTCCCAACT-CCAA
389 AAGTGATTAGCGAATGATAAGAGAGCTTGGAA--GAAAATTATGTTCGATCCTCCC-ACTGCCAA
** * * * *
2770634 CCCGGAGTATTTATTTCACGCGAGATTTGTGGGGGATTAAACACAACTTTTTTCCTTAGGATAGG
451 CCAAGAGTATCTATTTCAAGCGAGATTTGTGGGGGATTAAAAACAACTTTTTCCCTTAGGATAGG
2770699 ATCCAATAGAGCATCTT
516 ATCCAATAGAGCATCTT
2770716 GAATTTTATT
Statistics
Matches: 476, Mismatches: 50, Indels: 12
0.88 0.09 0.02
Matches are distributed among these distances:
535 2 0.00
536 462 0.97
537 6 0.01
538 6 0.01
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (536 bp):
TTCAATCATGTAATTATAGATTCACACCCAGAGAGGGCAACCTTTTAGCAACTGATAAAAACAAC
TCAAATGATCTATAAGTCATACCTAGTCTCCAAGTATGCTTAAGTGTATCATGAAATGCCCATAA
CTCAGCAATCAAAATCGAATAGTTATCAATGCTCTTTGAAAAACCAAAAATATAAGTCCCTTAGT
TGCATCGAAGAACACCACATGCAGTTGCCGCCAAGCCATTAATTCTAAAAAAAGTATTCATGTTA
GTCTTGATCCATCCCTCAGGTGATCTCATCCATTTAGTAGGTATCAGTTCTGCAAGCATTGCAAC
TTTCCTCGAACTACGACTAGTCAACAGCTCTCATACAAACTTCTTGTTGTTCAATTTCCTCCAAA
GTGATTAGCGAATGATAAGAGAGCTTGGAAGAAAATTATGTTCGATCCTCCCACTGCCAACCAAG
AGTATCTATTTCAAGCGAGATTTGTGGGGGATTAAAAACAACTTTTTCCCTTAGGATAGGATCCA
ATAGAGCATCTTCTAT
Found at i:2779643 original size:23 final size:23
Alignment explanation
Indices: 2779616--2779664 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
2779606 TGGTGGTTGG
2779616 TTTAATGG-ATATTTAGACTTTAT
1 TTTAATGGTATATTTA-ACTTTAT
*
2779639 TTTAATGGTATATTTAAGTTTAT
1 TTTAATGGTATATTTAACTTTAT
2779662 TTT
1 TTT
2779665 GGTTCTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.57
Consensus pattern (23 bp):
TTTAATGGTATATTTAACTTTAT
Found at i:2789863 original size:11 final size:11
Alignment explanation
Indices: 2789847--2789877 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
2789837 TTCTTTTCAT
*
2789847 TTTATTTGCTG
1 TTTATTTACTG
2789858 TTTATTTACTG
1 TTTATTTACTG
2789869 TTTATTTAC
1 TTTATTTAC
2789878 CATCTTCCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.16, C:0.10, G:0.10, T:0.65
Consensus pattern (11 bp):
TTTATTTACTG
Found at i:2803278 original size:37 final size:35
Alignment explanation
Indices: 2803218--2803322 Score: 122
Period size: 37 Copynumber: 2.9 Consensus size: 35
2803208 TCCTGCATGT
** *
2803218 ATTCTTGTATGTACATTGCTATATCTGTCATTACC
1 ATTCTTGTATACATATTGCTATATCTGTCATTACC
*
2803253 ATTCTTGTATACATTAATTGCTATATCT-ACTATTACC
1 ATTCTTGTATACA-T-ATTGCTATATCTGTC-ATTACC
* *
2803290 ATTCTTGTATATATATTGCTATACCTGTCATTA
1 ATTCTTGTATACATATTGCTATATCTGTCATTA
2803323 TCAAATATGT
Statistics
Matches: 59, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
35 26 0.44
36 3 0.05
37 30 0.51
ACGTcount: A:0.27, C:0.18, G:0.09, T:0.47
Consensus pattern (35 bp):
ATTCTTGTATACATATTGCTATATCTGTCATTACC
Found at i:2807226 original size:18 final size:18
Alignment explanation
Indices: 2807205--2807241 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2807195 TAAAATTATC
*
2807205 GGTGAAAATAGGATTACT
1 GGTGAAAATAAGATTACT
*
2807223 GGTGGAAATAAGATTACT
1 GGTGAAAATAAGATTACT
2807241 G
1 G
2807242 AAAATGTTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.38, C:0.05, G:0.30, T:0.27
Consensus pattern (18 bp):
GGTGAAAATAAGATTACT
Found at i:2808355 original size:18 final size:19
Alignment explanation
Indices: 2808332--2808373 Score: 68
Period size: 20 Copynumber: 2.2 Consensus size: 19
2808322 CAATAATCCT
2808332 ATTCT-CTGGTAATCTTAC
1 ATTCTACTGGTAATCTTAC
2808350 ATTCTCACTGGTAATCTTAC
1 ATTCT-ACTGGTAATCTTAC
2808370 ATTC
1 ATTC
2808374 CCTGAACCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 5 0.23
20 17 0.77
ACGTcount: A:0.24, C:0.24, G:0.10, T:0.43
Consensus pattern (19 bp):
ATTCTACTGGTAATCTTAC
Found at i:2815478 original size:13 final size:13
Alignment explanation
Indices: 2815460--2815485 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2815450 GCTATTGTCT
2815460 GGCTAAAAAAACC
1 GGCTAAAAAAACC
2815473 GGCTAAAAAAACC
1 GGCTAAAAAAACC
2815486 TATCATTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.23, G:0.15, T:0.08
Consensus pattern (13 bp):
GGCTAAAAAAACC
Found at i:2817699 original size:3 final size:3
Alignment explanation
Indices: 2817691--2817719 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2817681 CAGAACGAGT
2817691 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2817720 GGAATGTTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2821903 original size:17 final size:17
Alignment explanation
Indices: 2821881--2821916 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
2821871 GATCCTGAAC
2821881 TGTAAACAAAGAATAGG
1 TGTAAACAAAGAATAGG
2821898 TGTAAACAAAGAATAGG
1 TGTAAACAAAGAATAGG
2821915 TG
1 TG
2821917 ATATTTTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.50, C:0.06, G:0.25, T:0.19
Consensus pattern (17 bp):
TGTAAACAAAGAATAGG
Found at i:2822158 original size:23 final size:23
Alignment explanation
Indices: 2822128--2822174 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
2822118 ATCATTTAAC
2822128 TGTTTAAATATTATAAATTAAAT
1 TGTTTAAATATTATAAATTAAAT
2822151 TGTTTAAATATTATAAATTAAAT
1 TGTTTAAATATTATAAATTAAAT
2822174 T
1 T
2822175 ACTTTCCGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (23 bp):
TGTTTAAATATTATAAATTAAAT
Found at i:2823062 original size:16 final size:13
Alignment explanation
Indices: 2823032--2823057 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2823022 TTTTAAGGTA
2823032 ATTTTTTTATAAT
1 ATTTTTTTATAAT
2823045 ATTTTTTTATAAT
1 ATTTTTTTATAAT
2823058 TATATATGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
ATTTTTTTATAAT
Found at i:2839265 original size:20 final size:20
Alignment explanation
Indices: 2839221--2839259 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
2839211 ATTACCGTGC
2839221 GCCATTCCTAAAATCACATT
1 GCCATTCCTAAAATCACATT
2839241 GCCATTCCTAAAATCACAT
1 GCCATTCCTAAAATCACAT
2839260 CTCCATCCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.31, G:0.05, T:0.28
Consensus pattern (20 bp):
GCCATTCCTAAAATCACATT
Found at i:2839722 original size:12 final size:12
Alignment explanation
Indices: 2839705--2839761 Score: 59
Period size: 11 Copynumber: 5.1 Consensus size: 12
2839695 AAAAAAATTA
2839705 ATTAAATAAAAT
1 ATTAAATAAAAT
*
2839717 ATT-AA-AATA-
1 ATTAAATAAAAT
2839726 ATTAAATAAAAT
1 ATTAAATAAAAT
*
2839738 ACT-AATAAAAT
1 ATTAAATAAAAT
*
2839749 ATTAAATATAAT
1 ATTAAATAAAAT
2839761 A
1 A
2839762 AAATATACCT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
9 3 0.08
10 5 0.14
11 15 0.42
12 13 0.36
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (12 bp):
ATTAAATAAAAT
Found at i:2839729 original size:21 final size:23
Alignment explanation
Indices: 2839698--2839761 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 23
2839688 TAACTGCAAA
2839698 AAAATTAATTAAATAAAATA-T-T
1 AAAA-TAATTAAATAAAATACTAT
2839720 AAAATAATTAAATAAAATACTAAT
1 AAAATAATTAAATAAAATACT-AT
*
2839744 AAAAT-ATTAAATATAATA
1 AAAATAATTAAATAAAATA
2839762 AAATATACCT
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
21 15 0.39
22 5 0.13
23 12 0.32
24 6 0.16
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (23 bp):
AAAATAATTAAATAAAATACTAT
Found at i:2840252 original size:31 final size:31
Alignment explanation
Indices: 2840214--2840309 Score: 138
Period size: 31 Copynumber: 3.1 Consensus size: 31
2840204 GGGGAAATAA
2840214 TCTCTAACGTTATCGATCCGTTCGATTTTAG
1 TCTCTAACGTTATCGATCCGTTCGATTTTAG
* *
2840245 TCTCTAACTTTATCGATCCGTTCGATTTTAT
1 TCTCTAACGTTATCGATCCGTTCGATTTTAG
* * * *
2840276 TCCCTAATGTTATCAATTCGTTCGATTTTAG
1 TCTCTAACGTTATCGATCCGTTCGATTTTAG
2840307 TCT
1 TCT
2840310 ATCAGTCATC
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 56 1.00
ACGTcount: A:0.20, C:0.22, G:0.12, T:0.46
Consensus pattern (31 bp):
TCTCTAACGTTATCGATCCGTTCGATTTTAG
Done.