Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 75 of 206
Found at i:21265386 original size:18 final size:16
Alignment explanation
Indices: 21265357--21265390 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
21265347 TATTTTTAAC
21265357 ATAATTTTATTATTTT
1 ATAATTTTATTATTTT
21265373 ATAATATTTAATTATTTT
1 ATAAT-TTT-ATTATTTT
21265391 TCGACAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 3 0.19
18 8 0.50
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
ATAATTTTATTATTTT
Found at i:21267373 original size:44 final size:44
Alignment explanation
Indices: 21267307--21267394 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
21267297 CATTTATTCA
*
21267307 AAAAGAAAAATGAAAAATTAAGTATCCGATAAAATGAACGGGAT
1 AAAAGAAAAATGAAAAAATAAGTATCCGATAAAATGAACGGGAT
21267351 AAAAGAAAAATGAAAAAATAAGTATCCGATAAAATGAACGGGAT
1 AAAAGAAAAATGAAAAAATAAGTATCCGATAAAATGAACGGGAT
21267395 TTTATCTCGT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.58, C:0.07, G:0.18, T:0.17
Consensus pattern (44 bp):
AAAAGAAAAATGAAAAAATAAGTATCCGATAAAATGAACGGGAT
Found at i:21268328 original size:17 final size:17
Alignment explanation
Indices: 21268306--21268339 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
21268296 TTTTTGTTGG
21268306 TGACATTTCCAACCCTT
1 TGACATTTCCAACCCTT
21268323 TGACATTTCCAACCCTT
1 TGACATTTCCAACCCTT
21268340 GAATAATGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.35, G:0.06, T:0.35
Consensus pattern (17 bp):
TGACATTTCCAACCCTT
Found at i:21274562 original size:18 final size:17
Alignment explanation
Indices: 21274531--21274565 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
21274521 TATTTTTAAC
*
21274531 ATAATTTTATTTATTTT
1 ATAATTTTAATTATTTT
21274548 ATAATATTTAATTATTTT
1 ATAAT-TTTAATTATTTT
21274566 TCGACAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
ATAATTTTAATTATTTT
Found at i:21280044 original size:33 final size:34
Alignment explanation
Indices: 21280002--21280145 Score: 100
Period size: 33 Copynumber: 4.3 Consensus size: 34
21279992 TGTATATATG
21280002 TAAGACCATAGTC-GGGCTATGACATTCTGATGA
1 TAAGACCATAGTCTGGGCTATGACATTCTGATGA
* * * * * * * **
21280035 TAAGACCATA-ACTAGGTTATGGCACTATAAACA
1 TAAGACCATAGTCTGGGCTATGACATTCTGATGA
* * * * *
21280068 TAAGACCATGGT-TGGACTAAGACATTGTTTAT-A
1 TAAGACCATAGTCTGGGCTATGACATT-CTGATGA
21280101 TGTAAGACCATAG-CTGGGCTATGACATTCTGATGA
1 --TAAGACCATAGTCTGGGCTATGACATTCTGATGA
21280136 TAAGACCATA
1 TAAGACCATA
21280146 AGTGGGTTAT
Statistics
Matches: 79, Mismatches: 25, Indels: 14
0.67 0.21 0.12
Matches are distributed among these distances:
32 1 0.01
33 50 0.63
34 5 0.06
35 23 0.29
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.28
Consensus pattern (34 bp):
TAAGACCATAGTCTGGGCTATGACATTCTGATGA
Found at i:21280102 original size:101 final size:101
Alignment explanation
Indices: 21279962--21280179 Score: 323
Period size: 101 Copynumber: 2.2 Consensus size: 101
21279952 TCAATTATTC
* *
21279962 AAACGTAAGACCATGGTTGGAGCATGGCAGTGTATATATGTAAGACCATAG-TCGGGCTATGACA
1 AAACGTAAGACCATGGTTGGAGCAAGACAGTGTATATATGTAAGACCATAGCT-GGGCTATGACA
21280026 TTCTGATGATAAGACCATAACTAGGTTATGGCACTAT
65 TTCTGATGATAAGACCATAACTAGGTTATGGCACTAT
* * *
21280063 AAACATAAGACCATGGTTGGA-CTAAGACATTGTTTATATGTAAGACCATAGCTGGGCTATGACA
1 AAACGTAAGACCATGGTTGGAGC-AAGACAGTGTATATATGTAAGACCATAGCTGGGCTATGACA
* * *
21280127 TTCTGATGATAAGACCATAAGTGGGTTATGGTACTAT
65 TTCTGATGATAAGACCATAACTAGGTTATGGCACTAT
*
21280164 GAACGTAAGACCATGG
1 AAACGTAAGACCATGG
21280180 CAGGGCCATG
Statistics
Matches: 105, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
100 1 0.01
101 103 0.98
102 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.27
Consensus pattern (101 bp):
AAACGTAAGACCATGGTTGGAGCAAGACAGTGTATATATGTAAGACCATAGCTGGGCTATGACAT
TCTGATGATAAGACCATAACTAGGTTATGGCACTAT
Found at i:21282719 original size:55 final size:55
Alignment explanation
Indices: 21282653--21282762 Score: 202
Period size: 55 Copynumber: 2.0 Consensus size: 55
21282643 CTAAAGTCTG
*
21282653 ATTTTGGAAAATGAGGTATTAGTACCTCATTTCTGTAAATTGAGCCTGTAATATT
1 ATTTTGGAAAATGAGGTATTAGTACCTCATTTCTGTAAACTGAGCCTGTAATATT
*
21282708 ATTTTGGAAAATGAGGTATTAGTACGTCATTTCTGTAAACTGAGCCTGTAATATT
1 ATTTTGGAAAATGAGGTATTAGTACCTCATTTCTGTAAACTGAGCCTGTAATATT
21282763 TACGGAGCTG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (55 bp):
ATTTTGGAAAATGAGGTATTAGTACCTCATTTCTGTAAACTGAGCCTGTAATATT
Found at i:21285591 original size:30 final size:30
Alignment explanation
Indices: 21285555--21285721 Score: 156
Period size: 30 Copynumber: 5.5 Consensus size: 30
21285545 GGTTGATACC
*
21285555 ATCCCTTTCCATAATTCAATAGCTGAAGCT
1 ATCCCTTTCCATAATTCAATAGCCGAAGCT
*
21285585 ATCCCTTTCCATTATTCAATAGCCGAAGCT
1 ATCCCTTTCCATAATTCAATAGCCGAAGCT
* * *** * * * *
21285615 ATCCTTTTTCATAATTTTGGTGGTCGTCA-CC
1 ATCCCTTTCCATAA-TTCAATAGCCG-AAGCT
**
21285646 ATCCCTTTCCATAATTTGATAGCCGAAGCT
1 ATCCCTTTCCATAATTCAATAGCCGAAGCT
* * *
21285676 ATCCCTTTTCATGACTCAATAGCCGAAGCT
1 ATCCCTTTCCATAATTCAATAGCCGAAGCT
*
21285706 ATCCCTTTTCATAATT
1 ATCCCTTTCCATAATT
21285722 TTGATAGTCG
Statistics
Matches: 108, Mismatches: 26, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
29 1 0.01
30 87 0.81
31 19 0.18
32 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.11, T:0.37
Consensus pattern (30 bp):
ATCCCTTTCCATAATTCAATAGCCGAAGCT
Found at i:21285707 original size:91 final size:91
Alignment explanation
Indices: 21285552--21285778 Score: 319
Period size: 91 Copynumber: 2.5 Consensus size: 91
21285542 GAGGGTTGAT
** * * * *
21285552 ACCATCCCTTTCCATAATTCAATAGCTGAAGCTATCCCTTTCCATTATTCAATAGCCGAAGCTAT
1 ACCATCCCTTTCCATAATTTGATAGCCGAAGCTATCCCTTTTCATGACTCAATAGCCGAAGCTAT
* * *
21285617 CCTTTTTCATAATTTTGGTGGTCGTC
66 CCCTTTTCATAATTTTGATAGTCGTC
21285643 ACCATCCCTTTCCATAATTTGATAGCCGAAGCTATCCCTTTTCATGACTCAATAGCCGAAGCTAT
1 ACCATCCCTTTCCATAATTTGATAGCCGAAGCTATCCCTTTTCATGACTCAATAGCCGAAGCTAT
21285708 CCCTTTTCATAATTTTGATAGTCGTC
66 CCCTTTTCATAATTTTGATAGTCGTC
* * * ** *
21285734 ACAATCCCTTTTCATAGTTTGATAATCGAAACTATCCCTTTTCAT
1 ACCATCCCTTTCCATAATTTGATAGCCGAAGCTATCCCTTTTCAT
21285779 TGGTCAATGA
Statistics
Matches: 121, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
91 121 1.00
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.37
Consensus pattern (91 bp):
ACCATCCCTTTCCATAATTTGATAGCCGAAGCTATCCCTTTTCATGACTCAATAGCCGAAGCTAT
CCCTTTTCATAATTTTGATAGTCGTC
Found at i:21285757 original size:30 final size:31
Alignment explanation
Indices: 21285706--21285778 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 31
21285696 AGCCGAAGCT
* * **
21285706 ATCCCTTTTCATAATTTTGATAGTCGTCACA
1 ATCCCTTTTCATAAGTTTGATAATCGAAACA
*
21285737 ATCCCTTTTCAT-AGTTTGATAATCGAAACT
1 ATCCCTTTTCATAAGTTTGATAATCGAAACA
21285767 ATCCCTTTTCAT
1 ATCCCTTTTCAT
21285779 TGGTCAATGA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 25 0.68
31 12 0.32
ACGTcount: A:0.26, C:0.23, G:0.08, T:0.42
Consensus pattern (31 bp):
ATCCCTTTTCATAAGTTTGATAATCGAAACA
Found at i:21289022 original size:21 final size:21
Alignment explanation
Indices: 21288998--21289050 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
21288988 CATTGTTTCT
* *
21288998 AATCTCACTGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
*
21289019 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
21289040 AATCTCACCGC
1 AATCTCACCGC
21289051 CACCACTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.30, C:0.36, G:0.09, T:0.25
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:21292057 original size:22 final size:19
Alignment explanation
Indices: 21292007--21292058 Score: 50
Period size: 22 Copynumber: 2.5 Consensus size: 19
21291997 TTTAAGATTT
*
21292007 ATGTTTAATTTGAGTATTA
1 ATGTTTATTTTGAGTATTA
*
21292026 ATTGTGTATTTATGAAGTATTA
1 A-TGTTTATTT-TG-AGTATTA
21292048 CATGTTTATTT
1 -ATGTTTATTT
21292059 GAAGTAATCG
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 1 0.04
20 7 0.27
21 2 0.08
22 15 0.58
23 1 0.04
ACGTcount: A:0.29, C:0.02, G:0.15, T:0.54
Consensus pattern (19 bp):
ATGTTTATTTTGAGTATTA
Found at i:21298555 original size:17 final size:16
Alignment explanation
Indices: 21298530--21298565 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
21298520 TCAAAACCAC
21298530 AAAATTTAAAAAATTT
1 AAAATTTAAAAAATTT
*
21298546 AAAATATTAATAAATTT
1 AAAAT-TTAAAAAATTT
21298563 AAA
1 AAA
21298566 TACGCTTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AAAATTTAAAAAATTT
Found at i:21300699 original size:19 final size:18
Alignment explanation
Indices: 21300664--21300701 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
21300654 TTCTTAATGG
21300664 GGTTTTGTTCGTTTTTTT
1 GGTTTTGTTCGTTTTTTT
21300682 GGTTTATGTTC-TTGTTTTT
1 GGTTT-TGTTCGTT-TTTTT
21300701 G
1 G
21300702 ATAAACTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.03, C:0.05, G:0.24, T:0.68
Consensus pattern (18 bp):
GGTTTTGTTCGTTTTTTT
Found at i:21306185 original size:50 final size:50
Alignment explanation
Indices: 21306060--21306356 Score: 274
Period size: 50 Copynumber: 5.8 Consensus size: 50
21306050 ATTTGGGTAA
* * *
21306060 AGAGATCCCATGTAAGACCATGTTTGGGACATGGCATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATG
* *
21306116 AGAGGTCCTATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* *
21306166 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * * *
21306216 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGACATGGGCACCTATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * * * * *
21306266 AGAACTCTCATGTAAGACCATATCTAGGATATGGCATTGGCA--GTACAAG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
* ** * * *
21306315 AAACATCCCATGTAAGACTATGTCTGGGACATAGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
21306357 TGTTATATTC
Statistics
Matches: 203, Mismatches: 37, Indels: 9
0.82 0.15 0.04
Matches are distributed among these distances:
49 35 0.17
50 126 0.62
53 3 0.01
55 1 0.00
56 38 0.19
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.24
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:21311797 original size:56 final size:50
Alignment explanation
Indices: 21311725--21311965 Score: 347
Period size: 50 Copynumber: 4.7 Consensus size: 50
21311715 ATATGGTTAA
* * **
21311725 AGAGATCCCATGTAAGACCATGTCTGGGATATGGTATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCATC---GAG---ATG
*
21311781 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCATCGAAATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCATCGAGATG
21311831 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCATCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCATCGAGATG
* *
21311881 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCATCGAGATG
* *
21311931 AGAGGTCCCCTGTAAGACCATGTTTGGGACATGGC
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGC
21311966 ATGGACACCT
Statistics
Matches: 175, Mismatches: 10, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
50 133 0.76
53 2 0.01
56 40 0.23
ACGTcount: A:0.26, C:0.20, G:0.31, T:0.24
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCATCGAGATG
Found at i:21311836 original size:50 final size:51
Alignment explanation
Indices: 21311725--21312022 Score: 336
Period size: 50 Copynumber: 5.8 Consensus size: 51
21311715 ATATGGTTAA
* * **
21311725 AGAGATCCCATGTAAGACCATGTCTGGGATATGGTATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCATC---GA-A-TATG
21311781 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCATCGAA-ATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCATCGAATATG
*
21311831 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCATCG-AGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCATCGAATATG
* *
21311881 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCATCGAATATG
* * * **
21311931 AGAGGTCCCCTGTAAGACCATGTTTGGGACATGGC-ATGGACA-CCTATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGG-CATCGAATATG
* ** * * * *
21311981 AAAACTCTCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
21312023 GTACAAGAAA
Statistics
Matches: 219, Mismatches: 19, Indels: 14
0.87 0.08 0.06
Matches are distributed among these distances:
49 5 0.02
50 168 0.77
51 3 0.01
52 1 0.00
53 2 0.01
56 40 0.18
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.24
Consensus pattern (51 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCATCGAATATG
Found at i:21312007 original size:150 final size:152
Alignment explanation
Indices: 21311725--21312071 Score: 373
Period size: 150 Copynumber: 2.3 Consensus size: 152
21311715 ATATGGTTAA
* * *
21311725 AGAGATCCCATGTAAGACCATGTCTGGGATATGGTATTGGCATCATTGAGATTATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCA-T-AG--TATGAGAGGTCCC
* * * ** *
21311790 ATGTAAGACCATGTCTGGGACATGGCGTTGGCATCGAAATGAGAGGTCCCATGTAAGACCATGTC
62 ATGTAAGACCATGTCTGGGACATGGCGATGGCACCGAAATGAAAACTCCCATGTAAGACCATATC
*
21311855 TGGGACATGGCGTTGGCATCGAGATG
127 TGGGACATGGCATTGGCATCGAGATG
* * *
21311881 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCA-AG-ATGAGAGGTCCCCTGT
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCATAGTATGAGAGGTCCCATGT
* * * *
21311944 AAGACCATGTTTGGGACATGGC-ATGGACACCTATATGAAAACTCTCATGTAAGACCATATCTGG
66 AAGACCATGTCTGGGACATGGCGATGG-CACCGAAATGAAAACTCCCATGTAAGACCATATCTGG
*
21312008 GATATGGCATTGGCAGTAC-A-A-G
130 GACATGGCATTGGCA-T-CGAGATG
* * * * * *
21312030 AAACATCCCATGTAAGACTATGTCTAGGACATAGCTTTGGCA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
21312072 TGTTATATTT
Statistics
Matches: 163, Mismatches: 25, Indels: 13
0.81 0.12 0.06
Matches are distributed among these distances:
149 39 0.24
150 79 0.48
151 2 0.01
152 1 0.01
153 2 0.01
156 40 0.25
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (152 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCATAGTATGAGAGGTCCCATGT
AAGACCATGTCTGGGACATGGCGATGGCACCGAAATGAAAACTCCCATGTAAGACCATATCTGGG
ACATGGCATTGGCATCGAGATG
Found at i:21316048 original size:21 final size:21
Alignment explanation
Indices: 21316005--21316058 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
21315995 AAGTTGCTAG
*
21316005 CACGACCATGTGACCTATCCA
1 CACGACCATGTGACCTAGCCA
*
21316026 CACGGCCATGTGACC-AGCTCA
1 CACGACCATGTGACCTAGC-CA
*
21316047 CACGACTATGTG
1 CACGACCATGTG
21316059 GTCTATCTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 2 0.07
21 26 0.93
ACGTcount: A:0.26, C:0.35, G:0.20, T:0.19
Consensus pattern (21 bp):
CACGACCATGTGACCTAGCCA
Found at i:21316957 original size:21 final size:20
Alignment explanation
Indices: 21316920--21316963 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
21316910 ATAGAAATCG
*
21316920 ATAGAATTCTTATTTAGACAA
1 ATAGAATTCTTAGTTAGA-AA
21316941 ATAGAATT-TGTAGTTAGAAA
1 ATAGAATTCT-TAGTTAGAAA
21316961 ATA
1 ATA
21316964 ATTCTCACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.45, C:0.05, G:0.14, T:0.36
Consensus pattern (20 bp):
ATAGAATTCTTAGTTAGAAA
Found at i:21321390 original size:43 final size:44
Alignment explanation
Indices: 21321338--21321473 Score: 145
Period size: 43 Copynumber: 3.2 Consensus size: 44
21321328 TTTTAGAAAT
*
21321338 AAACACCGCTAAAAG-TCATAACATTTAGCGGCG-TGTCTACCAC
1 AAACGCCGCTAAAAGATCATAACATTTAGCGGCGCT-TCTACCAC
* *
21321381 AAACGCCGCT-AAAGATCATGACCTTTAGCGGCGCTTCTACCAC
1 AAACGCCGCTAAAAGATCATAACATTTAGCGGCGCTTCTACCAC
* * * * * * *
21321424 AAACGCCACT-AAACATCTTAACCTTTAGCAGCGCTTATACCAT
1 AAACGCCGCTAAAAGATCATAACATTTAGCGGCGCTTCTACCAC
21321467 AAACGCC
1 AAACGCC
21321474 ACTATAAATA
Statistics
Matches: 81, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
42 4 0.05
43 76 0.94
44 1 0.01
ACGTcount: A:0.33, C:0.31, G:0.15, T:0.21
Consensus pattern (44 bp):
AAACGCCGCTAAAAGATCATAACATTTAGCGGCGCTTCTACCAC
Found at i:21321851 original size:16 final size:16
Alignment explanation
Indices: 21321830--21321860 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
21321820 TTAAAGAAAC
*
21321830 CAAATTATATTAAAAT
1 CAAATTATACTAAAAT
21321846 CAAATTATACTAAAA
1 CAAATTATACTAAAA
21321861 CCATAATCAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.10, G:0.00, T:0.32
Consensus pattern (16 bp):
CAAATTATACTAAAAT
Found at i:21325200 original size:2 final size:2
Alignment explanation
Indices: 21325193--21325220 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
21325183 TCTTGCAAGG
21325193 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
21325221 TAGTTCAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21326156 original size:26 final size:26
Alignment explanation
Indices: 21326111--21326160 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
21326101 ATTAAAAACT
*
21326111 AGAAAAGAAGCTAACTAACATCCAAA
1 AGAAAAGAAGCTAACAAACATCCAAA
21326137 AGAAAAGAAGCTAGA-AAACATCCA
1 AGAAAAGAAGCTA-ACAAACATCCA
21326161 TTGGGAAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 21 0.95
27 1 0.05
ACGTcount: A:0.58, C:0.18, G:0.14, T:0.10
Consensus pattern (26 bp):
AGAAAAGAAGCTAACAAACATCCAAA
Found at i:21327382 original size:14 final size:14
Alignment explanation
Indices: 21327365--21327402 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
21327355 CACTAACTCT
*
21327365 TAACCTCTAAGCT-C
1 TAACCCCTAA-CTAC
21327379 TAACCCCTAACTAC
1 TAACCCCTAACTAC
21327393 TAACCCCTAA
1 TAACCCCTAA
21327403 ACCTTATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 2 0.09
14 20 0.91
ACGTcount: A:0.34, C:0.39, G:0.03, T:0.24
Consensus pattern (14 bp):
TAACCCCTAACTAC
Found at i:21327563 original size:80 final size:82
Alignment explanation
Indices: 21327397--21327565 Score: 202
Period size: 80 Copynumber: 2.1 Consensus size: 82
21327387 AACTACTAAC
*
21327397 CCCTAAACCTTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAAACCCTAACTC
1 CCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAAACCCTAACTC
* * *
21327462 AAATCACTACCCCTAAC
66 AAATCACAACCCATAAA
** * *
21327479 CCCTAAACATTATTT-A-ATATAAATTAAAGCACACTAATTAATCTAAACCTTAAATCCTAAC-C
1 CCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAAACCCTAACTC
* *
21327541 TAA-CACCGAATCCATAAA
66 AAATCA-C-AACCCATAAA
21327559 CCCTAAA
1 CCCTAAA
21327566 TCCCTAACTC
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
78 2 0.03
79 4 0.05
80 54 0.72
81 1 0.01
82 14 0.19
ACGTcount: A:0.46, C:0.27, G:0.01, T:0.27
Consensus pattern (82 bp):
CCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAAACCCTAACTC
AAATCACAACCCATAAA
Found at i:21327623 original size:34 final size:35
Alignment explanation
Indices: 21327559--21327624 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 35
21327549 AATCCATAAA
* * *
21327559 CCCTAAATCCCTAACTCTTAATCTCTAACCCTAAC
1 CCCTAAATCACTAACCCTTAATCACTAACCCTAAC
21327594 CCCTAAATCAC-AACCCTTAAATCAC-AACCCT
1 CCCTAAATCACTAACCCTT-AATCACTAACCCT
21327625 TAAACCAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
34 12 0.44
35 15 0.56
ACGTcount: A:0.35, C:0.41, G:0.00, T:0.24
Consensus pattern (35 bp):
CCCTAAATCACTAACCCTTAATCACTAACCCTAAC
Found at i:21327637 original size:14 final size:14
Alignment explanation
Indices: 21327591--21327628 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
21327581 CTCTAACCCT
*
21327591 AACCCCTAAATCAC
1 AACCCTTAAATCAC
21327605 AACCCTTAAATCAC
1 AACCCTTAAATCAC
21327619 AACCCTTAAA
1 AACCCTTAAA
21327629 CCAAAACCCC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.45, C:0.37, G:0.00, T:0.18
Consensus pattern (14 bp):
AACCCTTAAATCAC
Found at i:21327653 original size:14 final size:15
Alignment explanation
Indices: 21327636--21327665 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
21327626 AAACCAAAAC
21327636 CCCTAA-TCCATAAT
1 CCCTAATTCCATAAT
21327650 CCCTAATTCCATAAT
1 CCCTAATTCCATAAT
21327665 C
1 C
21327666 TATAAACCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.33, C:0.37, G:0.00, T:0.30
Consensus pattern (15 bp):
CCCTAATTCCATAAT
Found at i:21328122 original size:41 final size:41
Alignment explanation
Indices: 21328065--21328260 Score: 304
Period size: 41 Copynumber: 4.8 Consensus size: 41
21328055 AAATGTTTTC
*
21328065 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCTA-AGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGCCC-AGAGCATTA
* *
21328106 GCGGCGCTTTTCCAAAAATGCCGCTAACGCCCAGAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGCCCAGAGCATTA
* *
21328147 GCGGCGCTTTTCAAAAAACGCCACTAAAGCCCAGAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGCCCAGAGCATTA
*
21328188 GCGGCGCTTCTCCAAAAACGCCGCTAAAGCCCAGAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGCCCAGAGCATTA
* *
21328229 GCGACGCTTTTCCAAAAACACCGCTAAAGCCC
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGCCC
21328261 CGAAAGGTCA
Statistics
Matches: 141, Mismatches: 13, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
40 1 0.01
41 140 0.99
ACGTcount: A:0.30, C:0.32, G:0.20, T:0.18
Consensus pattern (41 bp):
GCGGCGCTTTTCCAAAAACGCCGCTAAAGCCCAGAGCATTA
Found at i:21328544 original size:29 final size:29
Alignment explanation
Indices: 21328511--21328569 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
21328501 CATTAGACTC
21328511 TAAATCAAGCATTTGGAGAATTAAAATTT
1 TAAATCAAGCATTTGGAGAATTAAAATTT
21328540 TAAATCAAGCATTTGGAGAATTAAAATTT
1 TAAATCAAGCATTTGGAGAATTAAAATTT
21328569 T
1 T
21328570 TTCTCCCAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.44, C:0.07, G:0.14, T:0.36
Consensus pattern (29 bp):
TAAATCAAGCATTTGGAGAATTAAAATTT
Found at i:21334477 original size:3 final size:3
Alignment explanation
Indices: 21334471--21334500 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
21334461 TAGAGATGAT
*
21334471 GAG GAG GAG GAG GAG GAG GAG AAG GAG GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
21334501 ACCCCCATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.37, C:0.00, G:0.63, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:21339852 original size:117 final size:117
Alignment explanation
Indices: 21339640--21339874 Score: 452
Period size: 117 Copynumber: 2.0 Consensus size: 117
21339630 AAGTTTAATT
21339640 TATACTCATCATCAAAACATGAGGCCCAACCAATTTCATACTTAAATGAATTATCAAAGAATCAC
1 TATACTCATCATCAAAACATGAGGCCCAACCAATTTCATACTTAAATGAATTATCAAAGAATCAC
21339705 AAAAAGAGGTAAGGGTTAAGAATTACTTAGTAAATCTTGAAGAGGTCAATGA
66 AAAAAGAGGTAAGGGTTAAGAATTACTTAGTAAATCTTGAAGAGGTCAATGA
21339757 TATACTCATCATCAAAACATGAGGCCCAACCAATTTCATACTTAAATGAATTATCAAAGAATCAC
1 TATACTCATCATCAAAACATGAGGCCCAACCAATTTCATACTTAAATGAATTATCAAAGAATCAC
**
21339822 AAAAAGAGGTAAGGGTTAAGAATTGGTTAGTAAATCTTGAAGAGGTCAATGA
66 AAAAAGAGGTAAGGGTTAAGAATTACTTAGTAAATCTTGAAGAGGTCAATGA
21339874 T
1 T
21339875 GGAATTGATG
Statistics
Matches: 116, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
117 116 1.00
ACGTcount: A:0.43, C:0.15, G:0.16, T:0.26
Consensus pattern (117 bp):
TATACTCATCATCAAAACATGAGGCCCAACCAATTTCATACTTAAATGAATTATCAAAGAATCAC
AAAAAGAGGTAAGGGTTAAGAATTACTTAGTAAATCTTGAAGAGGTCAATGA
Found at i:21341771 original size:17 final size:17
Alignment explanation
Indices: 21341722--21341773 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 17
21341712 AGTATAGGAA
*
21341722 GTAATCTTAGAAGATAT
1 GTAATCTTAGAAGATTT
* *
21341739 GCAATCTTGGAAGATTT
1 GTAATCTTAGAAGATTT
*
21341756 GTAATATTAGAAGATTT
1 GTAATCTTAGAAGATTT
21341773 G
1 G
21341774 ATTCTATAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.37, C:0.06, G:0.21, T:0.37
Consensus pattern (17 bp):
GTAATCTTAGAAGATTT
Found at i:21350729 original size:9 final size:9
Alignment explanation
Indices: 21350715--21350758 Score: 56
Period size: 9 Copynumber: 5.1 Consensus size: 9
21350705 GGGTATTTAA
21350715 TAATATAAT
1 TAATATAAT
21350724 TAATATAAT
1 TAATATAAT
*
21350733 T-A-ATCAT
1 TAATATAAT
*
21350740 CAATATAAT
1 TAATATAAT
21350749 TAATATAAT
1 TAATATAAT
21350758 T
1 T
21350759 TATTATTTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 4 0.14
8 2 0.07
9 23 0.79
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (9 bp):
TAATATAAT
Found at i:21350798 original size:19 final size:18
Alignment explanation
Indices: 21350776--21350811 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
21350766 TCAATAATTA
*
21350776 TTTAATATTAAAATTTTAT
1 TTTAATAAT-AAATTTTAT
21350795 TTTAATAATAAATTTTA
1 TTTAATAATAAATTTTA
21350812 GAAATTATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTAATAATAAATTTTAT
Found at i:21351513 original size:22 final size:22
Alignment explanation
Indices: 21351462--21351513 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 22
21351452 ATGTTTGGTG
* * *
21351462 TCTCGAAACATTGATTTTCATG
1 TCTCGAGACATTGATTATCATA
*
21351484 TCTTGAGACATTGAGTTAT-ATA
1 TCTCGAGACATTGA-TTATCATA
21351506 TCTCGAGA
1 TCTCGAGA
21351514 TTGATCTTCG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
22 21 0.88
23 3 0.12
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.38
Consensus pattern (22 bp):
TCTCGAGACATTGATTATCATA
Found at i:21358893 original size:32 final size:32
Alignment explanation
Indices: 21358857--21358953 Score: 94
Period size: 32 Copynumber: 3.1 Consensus size: 32
21358847 TGAGAGGGAA
*
21358857 TATTACAAAAATATGCAGTTACCATGCTTAGG
1 TATTACGAAAATATGCAGTTACCATGCTTAGG
* *** * *
21358889 TATTAGGTTGATAT---GTT-CCATGTTTAGAA
1 TATTACGAAAATATGCAGTTACCATGCTTAG-G
21358918 TATTACGAAAATATGCAGTTACCATGCTTAGG
1 TATTACGAAAATATGCAGTTACCATGCTTAGG
21358950 TATT
1 TATT
21358954 GGGTTGATAT
Statistics
Matches: 47, Mismatches: 13, Indels: 10
0.67 0.19 0.14
Matches are distributed among these distances:
28 9 0.19
29 13 0.28
32 16 0.34
33 9 0.19
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (32 bp):
TATTACGAAAATATGCAGTTACCATGCTTAGG
Found at i:21362262 original size:19 final size:19
Alignment explanation
Indices: 21362217--21362263 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
21362207 TTAATGATGA
21362217 TTAT-ATATT-TATATATG
1 TTATAATATTATATATATG
*
21362234 TTA-ACTTATTATATATATG
1 TTATA-ATATTATATATATG
21362253 TTATAATATTA
1 TTATAATATTA
21362264 ATAAAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
17 3 0.12
18 4 0.17
19 16 0.67
20 1 0.04
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.55
Consensus pattern (19 bp):
TTATAATATTATATATATG
Found at i:21362370 original size:14 final size:14
Alignment explanation
Indices: 21362329--21362371 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
21362319 AAAATTTATC
*
21362329 AAAGAAAAGAAAGAA
1 AAAG-AAAGAGAGAA
21362344 AAAGAAAGAGAGAA
1 AAAGAAAGAGAGAA
21362358 AAAGCAAAG-GAGAA
1 AAAG-AAAGAGAGAA
21362372 CGCACGGCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 18 0.69
15 8 0.31
ACGTcount: A:0.72, C:0.02, G:0.26, T:0.00
Consensus pattern (14 bp):
AAAGAAAGAGAGAA
Found at i:21370352 original size:13 final size:13
Alignment explanation
Indices: 21370326--21370359 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
21370316 TTTATTATCA
*
21370326 TTTTTCTTTGTCT
1 TTTTTCTTTCTCT
*
21370339 TTTTTTTTTCTCT
1 TTTTTCTTTCTCT
21370352 TTTTTCTT
1 TTTTTCTT
21370360 GCAAATTGGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (13 bp):
TTTTTCTTTCTCT
Found at i:21372762 original size:14 final size:14
Alignment explanation
Indices: 21372743--21372782 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
21372733 TTGATTGCCA
21372743 GTAAAATGTTTTCT
1 GTAAAATGTTTTCT
**
21372757 GTAAAATCATTTCT
1 GTAAAATGTTTTCT
*
21372771 GGAAAATGTTTT
1 GTAAAATGTTTT
21372783 ACTTTTCTGT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.45
Consensus pattern (14 bp):
GTAAAATGTTTTCT
Found at i:21372791 original size:20 final size:20
Alignment explanation
Indices: 21372766--21372805 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
21372756 TGTAAAATCA
*
21372766 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
21372786 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
21372806 GAAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:21372794 original size:34 final size:35
Alignment explanation
Indices: 21372751--21372817 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
21372741 CAGTAAAATG
* *
21372751 TTTTCTGTAAAATCATTT-CTGGAAAATGTTTTAC
1 TTTTCTGTAAAATCATTTACTGAAAAATATTTTAC
*
21372785 TTTTCTGTAAAATGATTTACTGAAAAATATTTT
1 TTTTCTGTAAAATCATTTACTGAAAAATATTTT
21372818 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.33, C:0.09, G:0.10, T:0.48
Consensus pattern (35 bp):
TTTTCTGTAAAATCATTTACTGAAAAATATTTTAC
Found at i:21375539 original size:23 final size:23
Alignment explanation
Indices: 21375509--21375563 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
21375499 CCAATCAAAC
21375509 GCCGGAAAAGTTGGAAATGATTT
1 GCCGGAAAAGTTGGAAATGATTT
21375532 GCCGGAAAAGTTGGAAATGATTT
1 GCCGGAAAAGTTGGAAATGATTT
*
21375555 TCCGGAAAA
1 GCCGGAAAA
21375564 TCAATTCTGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.36, C:0.11, G:0.29, T:0.24
Consensus pattern (23 bp):
GCCGGAAAAGTTGGAAATGATTT
Found at i:21377028 original size:103 final size:102
Alignment explanation
Indices: 21376780--21377147 Score: 619
Period size: 102 Copynumber: 3.6 Consensus size: 102
21376770 TAACCGTTAT
* *
21376780 CGGTGGATTCCGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGGG
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGGG
21376845 GAATCAGCACTTAGCAACCCCCTTCACATTTCAGATG
66 GAATCAGCACTTAGCAACCCCCTTCACATTTCAGATG
* * ** *
21376882 CGGTGGAATCAGCACTTAGTAACCACCAATGAATAGGGGAATCAGCACTTAGCAACCCCTCGGGG
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGGG
* * *
21376947 GAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
66 GAATCAGCACTTAGCAACCCCC-TTCACATTTCAGATG
21376985 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGGG
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGGG
21377050 GAATCAGCACTTAGCAACCCCCTTCACATTTCAGATG
66 GAATCAGCACTTAGCAACCCCCTTCACATTTCAGATG
* *
21377087 CGGTGGATTCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACATCAACCCCTT
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTT
21377148 TATATGCAAT
Statistics
Matches: 245, Mismatches: 20, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
102 151 0.62
103 94 0.38
ACGTcount: A:0.31, C:0.30, G:0.21, T:0.19
Consensus pattern (102 bp):
CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGGG
GAATCAGCACTTAGCAACCCCCTTCACATTTCAGATG
Found at i:21377031 original size:33 final size:33
Alignment explanation
Indices: 21376989--21377134 Score: 115
Period size: 33 Copynumber: 4.3 Consensus size: 33
21376979 AAAATACGGT
21376989 GGAATCAGCACTTAGCAACCACCAATGAATCGG
1 GGAATCAGCACTTAGCAACCACCAATGAATCGG
** *
21377022 GGAATCAGCACACAGCAACC-CC--T---TGGG
1 GGAATCAGCACTTAGCAACCACCAATGAATCGG
* *
21377049 GGAATCAGCACTTAGCAACCCCCTTCACATTTCAGATGCGG
1 GGAATCAGCACTTAGCAA-CCAC--CA-A--TGA-AT-CGG
*
21377090 TGGATTCAGCACTTAGCAACCACCAATGAATCGG
1 -GGAATCAGCACTTAGCAACCACCAATGAATCGG
21377124 GGAATCAGCAC
1 GGAATCAGCAC
21377135 ACATCAACCC
Statistics
Matches: 88, Mismatches: 10, Indels: 30
0.69 0.08 0.23
Matches are distributed among these distances:
27 19 0.22
28 2 0.02
29 1 0.01
30 1 0.01
31 1 0.01
32 2 0.02
33 28 0.32
34 3 0.03
35 2 0.02
36 3 0.03
38 1 0.01
39 2 0.02
40 1 0.01
41 5 0.06
42 17 0.19
ACGTcount: A:0.32, C:0.29, G:0.22, T:0.17
Consensus pattern (33 bp):
GGAATCAGCACTTAGCAACCACCAATGAATCGG
Found at i:21378801 original size:21 final size:22
Alignment explanation
Indices: 21378775--21378824 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
21378765 CAACCGAGAC
*
21378775 TATAAATTTT-TTAAAAAAAAT
1 TATAAATTTTATCAAAAAAAAT
*
21378796 TATAAATTTTATCAAAAAAATT
1 TATAAATTTTATCAAAAAAAAT
21378818 TATAAAT
1 TATAAAT
21378825 AGAAAGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 10 0.38
22 16 0.62
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
TATAAATTTTATCAAAAAAAAT
Found at i:21380934 original size:25 final size:28
Alignment explanation
Indices: 21380903--21380954 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
21380893 TTATGTTATT
*
21380903 TAAAT-AA-ATTTTAAATATA-ATAATA
1 TAAATAAATATTTTAAAAATACATAATA
21380928 TAAATAAATATTTTAAAAATACATAAT
1 TAAATAAATATTTTAAAAATACATAAT
21380955 TTCACTCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 5 0.22
26 2 0.09
27 11 0.48
28 5 0.22
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (28 bp):
TAAATAAATATTTTAAAAATACATAATA
Found at i:21392849 original size:34 final size:34
Alignment explanation
Indices: 21392806--21392875 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
21392796 TCTTGAAATT
21392806 TTCTGAAGATTTTTCTTGTGTAAGCCTCTAAAGC
1 TTCTGAAGATTTTTCTTGTGTAAGCCTCTAAAGC
21392840 TTCTGAAGATTTTTCTTGTGTAAGCCTCTAAAGC
1 TTCTGAAGATTTTTCTTGTGTAAGCCTCTAAAGC
21392874 TT
1 TT
21392876 TTTCTCCATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.43
Consensus pattern (34 bp):
TTCTGAAGATTTTTCTTGTGTAAGCCTCTAAAGC
Found at i:21399395 original size:9 final size:9
Alignment explanation
Indices: 21399381--21399412 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
21399371 TTCGCATCAT
21399381 TTTCTCTTA
1 TTTCTCTTA
21399390 TTTCTCTTA
1 TTTCTCTTA
*
21399399 TTTATCTTA
1 TTTCTCTTA
21399408 TTTCT
1 TTTCT
21399413 TAATAGCAAG
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:0.12, C:0.19, G:0.00, T:0.69
Consensus pattern (9 bp):
TTTCTCTTA
Found at i:21404564 original size:183 final size:183
Alignment explanation
Indices: 21404250--21404951 Score: 1127
Period size: 183 Copynumber: 3.8 Consensus size: 183
21404240 TTAGCAATGA
* * * * * * *
21404250 ATATCGATATACCCAACAATTCGGCAATGTATAACCATTAATGAATCAAGTTCGACAATATATAA
1 ATATCCATATACCAAACAATTCGACAAGGTATAACCATTCACGAATCAAGTTCGGCAATATATAA
21404315 TCATATACAAATCCAATTCGGCATCCTATATTCATAAACAA-TCTAATATCGACAATATATAACC
66 TCATATACAAATCCAATTCGGCATCCTATATTCATAAACAATTC-AATATCGACAATATATAACC
* *
21404379 ATGTACAAATTAATTTCAACAAGGTACAACATTTACGAATCAATTCGACAACTT
130 ATGTACAAATTAATTTCAGCAAGGTACAACATATACGAATCAATTCGACAACTT
* ** * *
21404433 ATATCCATATACCAAACAATTTGGTAAGGTATAACCATTCACAAATCAAGTTTGGCAATATATAA
1 ATATCCATATACCAAACAATTCGACAAGGTATAACCATTCACGAATCAAGTTCGGCAATATATAA
* *
21404498 TCATATACAAATCCAATTCGGCATCCTATATTCGTAAACAATTCAATATCGATAATATATAACCA
66 TCATATACAAATCCAATTCGGCATCCTATATTCATAAACAATTCAATATCGACAATATATAACCA
21404563 TGTACAAATTAATTTCAGCAAGGTACAACATATACGAATCAATTCGACAACTT
131 TGTACAAATTAATTTCAGCAAGGTACAACATATACGAATCAATTCGACAACTT
21404616 ATATCCATATACCAAACAATTCGACAAGGTATAACCATTCACGAATCAAGTTCGGCAATATATAA
1 ATATCCATATACCAAACAATTCGACAAGGTATAACCATTCACGAATCAAGTTCGGCAATATATAA
* * *
21404681 TCATATACAAATCCAATTCAGCATCTTATATTCATAAACAATTCAATATCAACAATATATAACCA
66 TCATATACAAATCCAATTCGGCATCCTATATTCATAAACAATTCAATATCGACAATATATAACCA
* * *
21404746 TGTACAAATTAATTTCAGCAATGTATATAACATATATGAATCAATTCGACAACTT
131 TGTACAAATTAATTTCAGCAA-G-GTACAACATATACGAATCAATTCGACAACTT
*
21404801 ATATCCATATACCAAACAATTCGACAAGGTATAACCATTCACGAATCAAGTTTGGCAATATATAA
1 ATATCCATATACCAAACAATTCGACAAGGTATAACCATTCACGAATCAAGTTCGGCAATATATAA
* * *
21404866 TCATATCCAAATCCAATTCGGCATCCTATATTCATAAACAATTCAATATTGACAATAAATAACCA
66 TCATATACAAATCCAATTCGGCATCCTATATTCATAAACAATTCAATATCGACAATATATAACCA
*
21404931 TGTACAAATTAATTTTAGCAA
131 TGTACAAATTAATTTCAGCAA
21404952 TGTATATAAC
Statistics
Matches: 481, Mismatches: 35, Indels: 4
0.93 0.07 0.01
Matches are distributed among these distances:
183 307 0.64
184 3 0.01
185 171 0.36
ACGTcount: A:0.43, C:0.20, G:0.08, T:0.29
Consensus pattern (183 bp):
ATATCCATATACCAAACAATTCGACAAGGTATAACCATTCACGAATCAAGTTCGGCAATATATAA
TCATATACAAATCCAATTCGGCATCCTATATTCATAAACAATTCAATATCGACAATATATAACCA
TGTACAAATTAATTTCAGCAAGGTACAACATATACGAATCAATTCGACAACTT
Found at i:21404627 original size:30 final size:29
Alignment explanation
Indices: 21404591--21404849 Score: 125
Period size: 30 Copynumber: 8.5 Consensus size: 29
21404581 CAAGGTACAA
21404591 CATATACGAATCAATTCGACAACTTATATC
1 CATATACGAATCAATTCGACAA-TTATATC
* * * *
21404621 CATATACCAAACAATTCGACAAGGTATAAC
1 CATATACGAATCAATTCGACAA-TTATATC
*
21404651 CAT-TCACGAATCAAGTTCGGCAATATATAAT-
1 CATAT-ACGAATCAA-TTCGACAAT-TAT-ATC
* * *
21404682 CATATACAAATCCAATTC-AGCATCTTATATT
1 CATATACGAAT-CAATTCGA-CA-ATTATATC
* * *
21404713 CATAAAC-AATTCAATATCAACAATATATAAC
1 CATATACGAA-TCAAT-TCGACAAT-TATATC
* * * *
21404744 CATGTACAAATTAATTTC-AGCAATGTATATAA
1 CATATACGAATCAA-TTCGA-CAAT-TATAT-C
*
21404776 CATATATGAATCAATTCGACAACTTATATC
1 CATATACGAATCAATTCGACAA-TTATATC
* * * *
21404806 CATATACCAAACAATTCGACAAGGTATAAC
1 CATATACGAATCAATTCGACAA-TTATATC
21404836 CAT-TCACGAATCAA
1 CATAT-ACGAATCAA
21404850 GTTTGGCAAT
Statistics
Matches: 173, Mismatches: 36, Indels: 40
0.69 0.14 0.16
Matches are distributed among these distances:
29 2 0.01
30 79 0.46
31 70 0.40
32 22 0.13
ACGTcount: A:0.44, C:0.21, G:0.07, T:0.28
Consensus pattern (29 bp):
CATATACGAATCAATTCGACAATTATATC
Found at i:21404931 original size:368 final size:366
Alignment explanation
Indices: 21404250--21404951 Score: 1145
Period size: 368 Copynumber: 1.9 Consensus size: 366
21404240 TTAGCAATGA
* * * * *
21404250 ATATCGATATACCCAACAATTCGGCAATGTATAACCATTAATGAATCAAGTTCGACAATATATAA
1 ATATCCATATACCAAACAATTCGACAAGGTATAACCATTAACGAATCAAGTTCGACAATATATAA
* *
21404315 TCATATACAAATCCAATTCGGCATCCTATATTCATAAACAATCTAATATCGACAATATATAACCA
66 TCATATACAAATCCAATTCAGCATCCTATATTCATAAACAATCTAATATCAACAATATATAACCA
* *
21404380 TGTACAAATTAATTTCAACAAGGTACAACATTTACGAATCAATTCGACAACTTATATCCATATAC
131 TGTACAAATTAATTTCAACAAGATACAACATATACGAATCAATTCGACAACTTATATCCATATAC
* **
21404445 CAAACAATTTGGTAAGGTATAACCATTCACAAATCAAGTTTGGCAATATATAATCATATACAAAT
196 CAAACAATTCGACAAGGTATAACCATTCACAAATCAAGTTTGGCAATATATAATCATATACAAAT
* * *
21404510 CCAATTCGGCATCCTATATTCGTAAACAATTCAATATCGATAATATATAACCATGTACAAATTAA
261 CCAATTCGGCATCCTATATTCATAAACAATTCAATATCGACAATAAATAACCATGTACAAATTAA
21404575 TTTCAGCAAGGTACAACATATACGAATCAATTCGACAACTT
326 TTTCAGCAAGGTACAACATATACGAATCAATTCGACAACTT
* *
21404616 ATATCCATATACCAAACAATTCGACAAGGTATAACCATTCACGAATCAAGTTCGGCAATATATAA
1 ATATCCATATACCAAACAATTCGACAAGGTATAACCATTAACGAATCAAGTTCGACAATATATAA
*
21404681 TCATATACAAATCCAATTCAGCATCTTATATTCATAAACAAT-TCAATATCAACAATATATAACC
66 TCATATACAAATCCAATTCAGCATCCTATATTCATAAACAATCT-AATATCAACAATATATAACC
* * *
21404745 ATGTACAAATTAATTTCAGCAATGTATATAACATATATGAATCAATTCGACAACTTATATCCATA
130 ATGTACAAATTAATTTCAACAA-G-ATACAACATATACGAATCAATTCGACAACTTATATCCATA
* *
21404810 TACCAAACAATTCGACAAGGTATAACCATTCACGAATCAAGTTTGGCAATATATAATCATATCCA
193 TACCAAACAATTCGACAAGGTATAACCATTCACAAATCAAGTTTGGCAATATATAATCATATACA
*
21404875 AATCCAATTCGGCATCCTATATTCATAAACAATTCAATATTGACAATAAATAACCATGTACAAAT
258 AATCCAATTCGGCATCCTATATTCATAAACAATTCAATATCGACAATAAATAACCATGTACAAAT
*
21404940 TAATTTTAGCAA
323 TAATTTCAGCAA
21404952 TGTATATAAC
Statistics
Matches: 308, Mismatches: 25, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
365 1 0.00
366 138 0.45
367 1 0.00
368 168 0.55
ACGTcount: A:0.43, C:0.20, G:0.08, T:0.29
Consensus pattern (366 bp):
ATATCCATATACCAAACAATTCGACAAGGTATAACCATTAACGAATCAAGTTCGACAATATATAA
TCATATACAAATCCAATTCAGCATCCTATATTCATAAACAATCTAATATCAACAATATATAACCA
TGTACAAATTAATTTCAACAAGATACAACATATACGAATCAATTCGACAACTTATATCCATATAC
CAAACAATTCGACAAGGTATAACCATTCACAAATCAAGTTTGGCAATATATAATCATATACAAAT
CCAATTCGGCATCCTATATTCATAAACAATTCAATATCGACAATAAATAACCATGTACAAATTAA
TTTCAGCAAGGTACAACATATACGAATCAATTCGACAACTT
Found at i:21407952 original size:26 final size:26
Alignment explanation
Indices: 21407916--21407976 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
21407906 ACCTACAGTA
21407916 GTTTCAGAATATCATAATATATATCT
1 GTTTCAGAATATCATAATATATATCT
* * *
21407942 GTTTTAGAATATCATAATATGTATCA
1 GTTTCAGAATATCATAATATATATCT
*
21407968 ATTTCAGAA
1 GTTTCAGAA
21407977 CACTTACAGG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (26 bp):
GTTTCAGAATATCATAATATATATCT
Found at i:21412401 original size:41 final size:41
Alignment explanation
Indices: 21412344--21412533 Score: 220
Period size: 41 Copynumber: 4.6 Consensus size: 41
21412334 TGAGTCCAAC
*
21412344 AGGCTTCGTGACGGTGTATTATACCAGGCTTTGTGCCTAGA
1 AGGCTTCGTGACGGTGTATTATATCAGGCTTTGTGCCTAGA
* **
21412385 AGGCTTCGTGACGGTGTATTATATCAGGCTTTGTGCTTATC
1 AGGCTTCGTGACGGTGTATTATATCAGGCTTTGTGCCTAGA
* * * * *
21412426 AGGCTTCGTGCCGGTATATTATATCAAGCGTTGTGCCTAGT
1 AGGCTTCGTGACGGTGTATTATATCAGGCTTTGTGCCTAGA
* * * * *
21412467 AGGCTTCATGTCGATGTGTTATATCAGGCTTTGAGCCTAGCA
1 AGGCTTCGTGACGGTGTATTATATCAGGCTTTGTGCCTAG-A
* *
21412509 A-GCTTCGTGACAGTGTATTGTATCA
1 AGGCTTCGTGACGGTGTATTATATCA
21412534 TGTAGGTTGT
Statistics
Matches: 122, Mismatches: 26, Indels: 2
0.81 0.17 0.01
Matches are distributed among these distances:
41 121 0.99
42 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.35
Consensus pattern (41 bp):
AGGCTTCGTGACGGTGTATTATATCAGGCTTTGTGCCTAGA
Found at i:21412427 original size:16 final size:16
Alignment explanation
Indices: 21412406--21412436 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
21412396 CGGTGTATTA
*
21412406 TATCAGGCTTTGTGCT
1 TATCAGGCTTCGTGCT
21412422 TATCAGGCTTCGTGC
1 TATCAGGCTTCGTGC
21412437 CGGTATATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.23, G:0.26, T:0.39
Consensus pattern (16 bp):
TATCAGGCTTCGTGCT
Found at i:21419123 original size:27 final size:27
Alignment explanation
Indices: 21419077--21419149 Score: 73
Period size: 28 Copynumber: 2.7 Consensus size: 27
21419067 AATGTAGGAA
21419077 AAAAATGATAAAAATA--AAA-TTCAAT
1 AAAAAT-ATAAAAATATTAAATTTCAAT
* *
21419102 AAAAGT-TATAAAATGATTAAATTTTAAT
1 AAAAATATA-AAAAT-ATTAAATTTCAAT
21419130 AAAAATATAAAAATATTAAA
1 AAAAATATAAAAATATTAAA
21419150 AAATTAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
23 2 0.05
24 5 0.13
25 6 0.15
27 9 0.23
28 15 0.38
29 2 0.05
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.30
Consensus pattern (27 bp):
AAAAATATAAAAATATTAAATTTCAAT
Found at i:21419177 original size:19 final size:20
Alignment explanation
Indices: 21419155--21419197 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
21419145 TTAAAAAATT
21419155 AAAAAAA-TATAAAATTGTA
1 AAAAAAATTATAAAATTGTA
* *
21419174 AAAAAAATTATAAGATTTTA
1 AAAAAAATTATAAAATTGTA
21419194 AAAA
1 AAAA
21419198 GTCGTAAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (20 bp):
AAAAAAATTATAAAATTGTA
Found at i:21419256 original size:10 final size:10
Alignment explanation
Indices: 21419120--21419262 Score: 52
Period size: 10 Copynumber: 14.7 Consensus size: 10
21419110 TAAAATGATT
*
21419120 AAATTTTAATA
1 AAATTATAA-A
*
21419131 AAAATAT-AA
1 AAATTATAAA
21419140 AAA-TATTAAA
1 AAATTA-TAAA
21419150 AAATTA-AAA
1 AAATTATAAA
21419159 AAA-TAT-AA
1 AAATTATAAA
* *
21419167 AATTGTAAAAA
1 AAAT-TATAAA
21419178 AAATTAT--A
1 AAATTATAAA
* *
21419186 AGATTTTAAA
1 AAATTATAAA
* **
21419196 AAGTCGTAAGA
1 AAATTATAA-A
21419207 AAATTATAAA
1 AAATTATAAA
*
21419217 AAAATATAAA
1 AAATTATAAA
* **
21419227 AAA-AATGTA
1 AAATTATAAA
*
21419236 AAATTCTTAAA
1 AAATT-ATAAA
21419247 AAATTAT-AA
1 AAATTATAAA
21419256 AAATTAT
1 AAATTAT
21419263 TGTAATAAAA
Statistics
Matches: 96, Mismatches: 24, Indels: 26
0.66 0.16 0.18
Matches are distributed among these distances:
8 14 0.15
9 26 0.27
10 30 0.31
11 26 0.27
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.30
Consensus pattern (10 bp):
AAATTATAAA
Found at i:21419476 original size:11 final size:12
Alignment explanation
Indices: 21419476--21419512 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
21419466 TTATAAAATT
*
21419476 TATAATTTTTTA
1 TATAAATTTTTA
21419488 -ATAAATTTTTA
1 TATAAATTTTTA
21419499 -ATAAATTTTTA
1 TATAAATTTTTA
21419510 TAT
1 TAT
21419513 TTTTATTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 21 0.91
12 2 0.09
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TATAAATTTTTA
Found at i:21419487 original size:19 final size:21
Alignment explanation
Indices: 21419462--21419511 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
21419452 TTTTTTTATG
21419462 ATTTTTATAAA-ATTT-ATAA
1 ATTTTTATAAATATTTAATAA
* *
21419481 TTTTTTAATAAATTTTTAATAA
1 ATTTTT-ATAAATATTTAATAA
21419503 ATTTTTATA
1 ATTTTTATA
21419512 TTTTTATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
19 5 0.20
20 5 0.20
21 6 0.24
22 9 0.36
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
ATTTTTATAAATATTTAATAA
Found at i:21419496 original size:12 final size:12
Alignment explanation
Indices: 21419479--21419508 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
21419469 TAAAATTTAT
21419479 AATTTTTTAATA
1 AATTTTTTAATA
21419491 AA-TTTTTAATA
1 AATTTTTTAATA
21419502 AATTTTT
1 AATTTTT
21419509 ATATTTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
AATTTTTTAATA
Found at i:21419556 original size:29 final size:29
Alignment explanation
Indices: 21419483--21419556 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 29
21419473 ATTTATAATT
* * *
21419483 TTTTAATAAATTTTTAATAAATTTTTATAT
1 TTTTATTAAA-TTTTAATAAATTTGTATAC
*
21419513 TTTTATTAAAATTTAAT-AATTTGTATAAC
1 TTTTATTAAATTTTAATAAATTTGTAT-AC
*
21419542 TTTTATTAACTTTTA
1 TTTTATTAAATTTTA
21419557 TTTTTTATAA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
28 8 0.22
29 20 0.54
30 9 0.24
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (29 bp):
TTTTATTAAATTTTAATAAATTTGTATAC
Found at i:21419570 original size:15 final size:17
Alignment explanation
Indices: 21419542--21419574 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
21419532 TTTGTATAAC
21419542 TTTTATTAACTTTTATT
1 TTTTATTAACTTTTATT
21419559 TTTTA-TAA-TTTTATT
1 TTTTATTAACTTTTATT
21419574 T
1 T
21419575 GCCACATGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 3 0.19
17 5 0.31
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTATTAACTTTTATT
Found at i:21423065 original size:20 final size:20
Alignment explanation
Indices: 21423036--21423080 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
21423026 AGAACTTGAC
21423036 AGAATAGAACAGCA-CAGAGT
1 AGAATAGAACAG-AGCAGAGT
* *
21423056 AGAATGGAACAGAGTAGAGT
1 AGAATAGAACAGAGCAGAGT
21423076 AGAAT
1 AGAAT
21423081 TGAATAGAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 21 0.95
ACGTcount: A:0.49, C:0.09, G:0.29, T:0.13
Consensus pattern (20 bp):
AGAATAGAACAGAGCAGAGT
Found at i:21427248 original size:98 final size:98
Alignment explanation
Indices: 21427072--21427266 Score: 338
Period size: 98 Copynumber: 2.0 Consensus size: 98
21427062 ACAATAAAAT
*
21427072 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATTCT
1 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCT
*
21427137 TCTAGAATCCCAAACTCGGAATATTTCCTTTAC
66 TCTAAAATCCCAAACTCGGAATATTTCCTTTAC
*
21427170 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACTCAATACGTTAGGGCACAATTCC
1 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT-C
*
21427235 TT-TAAAATTCCAAACTCGGAATATTTCCTTTA
65 TTCTAAAATCCCAAACTCGGAATATTTCCTTTA
21427267 TTGCTTTTAG
Statistics
Matches: 92, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
98 89 0.97
99 3 0.03
ACGTcount: A:0.37, C:0.23, G:0.10, T:0.30
Consensus pattern (98 bp):
TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCT
TCTAAAATCCCAAACTCGGAATATTTCCTTTAC
Found at i:21428588 original size:19 final size:19
Alignment explanation
Indices: 21428564--21428695 Score: 192
Period size: 19 Copynumber: 6.8 Consensus size: 19
21428554 AATCATATAT
21428564 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
**
21428583 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
21428602 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
21428621 TCTAAAATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
21428642 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
* *
21428661 TCTAGGATTGCATATTATA
1 TCTAAGATTGCATATCATA
*
21428680 TCTAGGATTGCATATC
1 TCTAAGATTGCATATC
21428696 CTCAAAAATT
Statistics
Matches: 102, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
19 84 0.82
21 18 0.18
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:21428647 original size:59 final size:59
Alignment explanation
Indices: 21428575--21428694 Score: 186
Period size: 59 Copynumber: 2.0 Consensus size: 59
21428565 CTAAGATTGC
*
21428575 ATATCATATCTAAGATTATATATCATATCTAAGATTGCATATCATATCTAAAATTGCAT
1 ATATCATATCTAAGATTACATATCATATCTAAGATTGCATATCATATCTAAAATTGCAT
* * * **
21428634 ATATCATATCTAAGATTGCATATCATATCTAGGATTGCATATTATATCTAGGATTGCAT
1 ATATCATATCTAAGATTACATATCATATCTAAGATTGCATATCATATCTAAAATTGCAT
21428693 AT
1 AT
21428695 CCTCAAAAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39
Consensus pattern (59 bp):
ATATCATATCTAAGATTACATATCATATCTAAGATTGCATATCATATCTAAAATTGCAT
Found at i:21429070 original size:43 final size:43
Alignment explanation
Indices: 21428999--21429101 Score: 143
Period size: 43 Copynumber: 2.4 Consensus size: 43
21428989 GTTAGGATAT
* * *
21428999 TATTATGGGATATTATCTCTTAGCAATTTGATTCCTAATGGGA
1 TATTATAGGATATTATTTCTTAGCAATTTGACTCCTAATGGGA
* * *
21429042 TGTTATAGGTTATTATTTCTTAGCAATTTGACTCCTAATTGGA
1 TATTATAGGATATTATTTCTTAGCAATTTGACTCCTAATGGGA
*
21429085 TATTATGGGATATTATT
1 TATTATAGGATATTATT
21429102 ATGGGATATT
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 51 1.00
ACGTcount: A:0.27, C:0.10, G:0.17, T:0.46
Consensus pattern (43 bp):
TATTATAGGATATTATTTCTTAGCAATTTGACTCCTAATGGGA
Found at i:21429103 original size:13 final size:13
Alignment explanation
Indices: 21429085--21429113 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
21429075 CCTAATTGGA
21429085 TATTATGGGATAT
1 TATTATGGGATAT
21429098 TATTATGGGATAT
1 TATTATGGGATAT
21429111 TAT
1 TAT
21429114 CTGTTAGCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.48
Consensus pattern (13 bp):
TATTATGGGATAT
Found at i:21444806 original size:16 final size:16
Alignment explanation
Indices: 21444794--21444824 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
21444784 TTCTTTTGTG
21444794 TATTTACTCTTTTATA
1 TATTTACTCTTTTATA
21444810 TATTTACTCTTTTAT
1 TATTTACTCTTTTAT
21444825 GTTGATGACA
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:0.23, C:0.13, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTTACTCTTTTATA
Found at i:21446857 original size:29 final size:29
Alignment explanation
Indices: 21446825--21446882 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
21446815 TTTTCATTCC
21446825 ATCCATCTTCTTTCTTTCTTTTTTTTCTT
1 ATCCATCTTCTTTCTTTCTTTTTTTTCTT
21446854 ATCCATCTTCTTTCTTTCTTTTTTTTCTT
1 ATCCATCTTCTTTCTTTCTTTTTTTTCTT
21446883 CCTTTCGTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.07, C:0.24, G:0.00, T:0.69
Consensus pattern (29 bp):
ATCCATCTTCTTTCTTTCTTTTTTTTCTT
Found at i:21451024 original size:7 final size:7
Alignment explanation
Indices: 21451008--21451038 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
21450998 GGATCTGCCG
21451008 TAAACCC
1 TAAACCC
*
21451015 TAATCCC
1 TAAACCC
21451022 TAAACCC
1 TAAACCC
21451029 TAAACCC
1 TAAACCC
21451036 TAA
1 TAA
21451039 TCCATTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.42, C:0.39, G:0.00, T:0.19
Consensus pattern (7 bp):
TAAACCC
Found at i:21451542 original size:18 final size:18
Alignment explanation
Indices: 21451507--21451546 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
21451497 AAATTTTGAT
21451507 TTTTTATATATTTTTTAA
1 TTTTTATATATTTTTTAA
21451525 TTTTTAT-TATTTTCTTAA
1 TTTTTATATATTTT-TTAA
21451543 TTTT
1 TTTT
21451547 GTAGAACTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTTATATATTTTTTAA
Found at i:21453078 original size:33 final size:32
Alignment explanation
Indices: 21452957--21453074 Score: 98
Period size: 33 Copynumber: 3.7 Consensus size: 32
21452947 CTTAGAAAAT
* *
21452957 ATAAAAATAA-AATATTTGAAATATAATTTAAT
1 ATAAAAATAATAATA-TTAAAATATAATTTAAA
*
21452989 AT-AAAATAATTAAT-TTCAAAATACAATTTAAA
1 ATAAAAATAA-TAATATT-AAAATATAATTTAAA
* * * **
21453021 GTAAAACTAAAAAATATTTTAATATAATTTAAA
1 ATAAAAAT-AATAATATTAAAATATAATTTAAA
*
21453054 ATAAAAATAATTATATTAAAA
1 ATAAAAATAATAATATTAAAA
21453075 ATATTATTAA
Statistics
Matches: 65, Mismatches: 15, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
31 9 0.14
32 24 0.37
33 28 0.43
34 4 0.06
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.36
Consensus pattern (32 bp):
ATAAAAATAATAATATTAAAATATAATTTAAA
Found at i:21453119 original size:56 final size:58
Alignment explanation
Indices: 21453059--21453180 Score: 178
Period size: 59 Copynumber: 2.1 Consensus size: 58
21453049 TTAAAATAAA
* *
21453059 AATAATTATATTAAAAATATTATTAAATTA-TA-TA-TTTTTATTAAATTATATTTAAT
1 AATAATCATATT-AAAATATGATTAAATTATTATTATTTTTTATTAAATTATATTTAAT
*
21453115 AATAATCATATTAAAATATGATTAAATTATTTATTATTTTTTATTAAATTATTTTTAAT
1 AATAATCATATTAAAATATGATTAAATTA-TTATTATTTTTTATTAAATTATATTTAAT
21453174 AATAATC
1 AATAATC
21453181 CGTTTAAAAT
Statistics
Matches: 59, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
55 16 0.27
56 11 0.19
57 2 0.03
58 2 0.03
59 28 0.47
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.52
Consensus pattern (58 bp):
AATAATCATATTAAAATATGATTAAATTATTATTATTTTTTATTAAATTATATTTAAT
Found at i:21453997 original size:34 final size:35
Alignment explanation
Indices: 21453953--21454019 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
21453943 CAGTAAAATA
*
21453953 TTTTCCGTAAAATGATTT-CGGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
* *
21453987 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTT
21454020 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:21455618 original size:19 final size:19
Alignment explanation
Indices: 21455571--21455620 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
21455561 AAATTGATAA
*
21455571 AATCATGTTAAATGGTTTC
1 AATCATGTTAAATAGTTTC
* *
21455590 AATTGA-GTTAAATATTTTC
1 AA-TCATGTTAAATAGTTTC
21455609 AATCATGTTAAA
1 AATCATGTTAAA
21455621 AATGTATTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 2 0.08
19 21 0.84
20 2 0.08
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (19 bp):
AATCATGTTAAATAGTTTC
Found at i:21455783 original size:21 final size:21
Alignment explanation
Indices: 21455757--21455837 Score: 135
Period size: 21 Copynumber: 3.9 Consensus size: 21
21455747 AATTTTCACA
*
21455757 AAAAAGTATTGATACATTTAC
1 AAAAAGTATTGATACCTTTAC
*
21455778 AAAAAGTATTGATACCTTTAT
1 AAAAAGTATTGATACCTTTAC
21455799 AAAAAGTATTGATACCTTTAC
1 AAAAAGTATTGATACCTTTAC
*
21455820 AAAAAGTATCGATACCTT
1 AAAAAGTATTGATACCTT
21455838 CTACCAAATA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.33
Consensus pattern (21 bp):
AAAAAGTATTGATACCTTTAC
Found at i:21456846 original size:52 final size:52
Alignment explanation
Indices: 21456769--21456897 Score: 163
Period size: 52 Copynumber: 2.4 Consensus size: 52
21456759 GAGTTGGGAC
*
21456769 ACACGGCTGTGTCCTAGCCCGTGTCTCTACCCT-TGTAACTCACTGACTTGAG
1 ACACGGCTGTGTCCCAGCCCGTGTCTCTA-CCTGTGTAACTCACTGACTTGAG
*
21456821 ACACGG-TCGTGTCCCAGCCCGTGTCTCTACCTGTGTAACTCACTGACTTGGG
1 ACACGGCT-GTGTCCCAGCCCGTGTCTCTACCTGTGTAACTCACTGACTTGAG
* * *
21456873 TCACACGGCTATGTCACAGGCCGTG
1 --ACACGGCTGTGTCCCAGCCCGTG
21456898 CATACCTAAA
Statistics
Matches: 67, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
51 4 0.06
52 44 0.66
54 18 0.27
55 1 0.01
ACGTcount: A:0.17, C:0.33, G:0.24, T:0.26
Consensus pattern (52 bp):
ACACGGCTGTGTCCCAGCCCGTGTCTCTACCTGTGTAACTCACTGACTTGAG
Found at i:21457189 original size:23 final size:23
Alignment explanation
Indices: 21457163--21457241 Score: 113
Period size: 23 Copynumber: 3.3 Consensus size: 23
21457153 CTACTTAGGT
**
21457163 TACCAAACTTTAAGCTAAATGCA
1 TACCAAACTTTAAGCTAAACACA
21457186 TACCAAACTTTAAGCTAAACACA
1 TACCAAACTTTAAGCTAAACACA
*
21457209 TACCAAACTTTAAGCTAAGCTATCA
1 TACCAAACTTTAAGCTAAAC-A-CA
21457234 TACCAAAC
1 TACCAAAC
21457242 ATAACCTCAA
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
23 40 0.78
24 1 0.02
25 10 0.20
ACGTcount: A:0.44, C:0.25, G:0.06, T:0.24
Consensus pattern (23 bp):
TACCAAACTTTAAGCTAAACACA
Found at i:21476396 original size:22 final size:24
Alignment explanation
Indices: 21476353--21476396 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
21476343 TGATAATATG
21476353 TTTTGATATAACAAATTAAAGTAT
1 TTTTGATATAACAAATTAAAGTAT
*
21476377 TTTTGA-ATAA-AAGTTAAAGT
1 TTTTGATATAACAAATTAAAGT
21476397 TGAACATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.45, C:0.02, G:0.11, T:0.41
Consensus pattern (24 bp):
TTTTGATATAACAAATTAAAGTAT
Found at i:21485171 original size:38 final size:37
Alignment explanation
Indices: 21485120--21485191 Score: 99
Period size: 38 Copynumber: 1.9 Consensus size: 37
21485110 GAGGGTTGAG
* *
21485120 TATTAAGGTTTGGGTAGAAACCTTAAGGTAGTTGCAA
1 TATTAAGGTTTGGGTAGAAACATTAAGGGAGTTGCAA
* *
21485157 TATTAAGAGTTTGGGTATAAATATTAAGGGAGTTG
1 TATTAAG-GTTTGGGTAGAAACATTAAGGGAGTTG
21485192 TAAGGTTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 7 0.23
38 23 0.77
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.35
Consensus pattern (37 bp):
TATTAAGGTTTGGGTAGAAACATTAAGGGAGTTGCAA
Found at i:21487031 original size:20 final size:21
Alignment explanation
Indices: 21486994--21487054 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
21486984 ATAATAAATC
* *
21486994 AAAATAAAATTTAGAAAT-TA
1 AAAATAAAATTAAAAAATATA
*
21487014 AAAATAAAATTAAAAAATATT
1 AAAATAAAATTAAAAAATATA
* *
21487035 GAAATAAAAATAAAAAATAT
1 AAAATAAAATTAAAAAATAT
21487055 TAAATTAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
20 16 0.46
21 19 0.54
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.26
Consensus pattern (21 bp):
AAAATAAAATTAAAAAATATA
Found at i:21487041 original size:21 final size:20
Alignment explanation
Indices: 21487015--21487059 Score: 72
Period size: 21 Copynumber: 2.2 Consensus size: 20
21487005 TAGAAATTAA
*
21487015 AAATAAAATTAAAAAATATT
1 AAATAAAAATAAAAAATATT
21487035 GAAATAAAAATAAAAAATATT
1 -AAATAAAAATAAAAAATATT
21487056 AAAT
1 AAAT
21487060 TAATAGAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (20 bp):
AAATAAAAATAAAAAATATT
Found at i:21489723 original size:49 final size:45
Alignment explanation
Indices: 21489670--21489765 Score: 111
Period size: 45 Copynumber: 2.0 Consensus size: 45
21489660 AAATTTGAAG
*
21489670 AAGAGAAGAAGAAGAAGAAGAGACCGGGAAGGGGAAAAAGAAAGAAAAA
1 AAGAGAAGAAG-AGAAG-AGAGA--GGGAAGGAGAAAAAGAAAGAAAAA
* * * *
21489719 AAGAGAAGTAGAGTAGAGAGAGGGAAGGAGAAAGAGAAGGAAAAA
1 AAGAGAAGAAGAGAAGAGAGAGGGAAGGAGAAAAAGAAAGAAAAA
21489764 AA
1 AA
21489766 ATAAATAGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
45 23 0.55
47 5 0.12
48 4 0.10
49 10 0.24
ACGTcount: A:0.59, C:0.02, G:0.36, T:0.02
Consensus pattern (45 bp):
AAGAGAAGAAGAGAAGAGAGAGGGAAGGAGAAAAAGAAAGAAAAA
Found at i:21489788 original size:13 final size:13
Alignment explanation
Indices: 21489772--21489801 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
21489762 AAAAATAAAT
21489772 AGAAAAGGGAAGG
1 AGAAAAGGGAAGG
21489785 AG-AAAGGGAAGG
1 AGAAAAGGGAAGG
21489797 AGAAA
1 AGAAA
21489802 TTTGTGTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (13 bp):
AGAAAAGGGAAGG
Found at i:21490467 original size:15 final size:17
Alignment explanation
Indices: 21490441--21490484 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 17
21490431 TTATTATATA
21490441 TATTAT-ATTTTAAACT
1 TATTATCATTTTAAACT
21490457 TA-TA-CATTTT--ACT
1 TATTATCATTTTAAACT
21490470 TATTATCATTTTAAA
1 TATTATCATTTTAAA
21490485 ATAATAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 9
0.72 0.00 0.28
Matches are distributed among these distances:
13 5 0.22
14 2 0.09
15 13 0.57
16 2 0.09
17 1 0.04
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (17 bp):
TATTATCATTTTAAACT
Found at i:21492847 original size:40 final size:41
Alignment explanation
Indices: 21492735--21492959 Score: 393
Period size: 41 Copynumber: 5.5 Consensus size: 41
21492725 TTTAACATAT
*
21492735 TCACCGGCACTTAGCCTGCTAGGCTTATAGA-CTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATA-ACCTGATTCAGA
21492776 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
*
21492817 TCACCGGCAC-TAGCTTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
21492857 TCACCGGCAC-TAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
21492897 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
*
21492938 TCACCGGCACTTAGCCTACTAG
1 TCACCGGCACTTAGCCTGCTAG
21492960 ACATAAAGTC
Statistics
Matches: 178, Mismatches: 4, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
40 79 0.44
41 99 0.56
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
Found at i:21496100 original size:49 final size:48
Alignment explanation
Indices: 21496047--21496294 Score: 304
Period size: 48 Copynumber: 5.1 Consensus size: 48
21496037 GTATTTATTT
* **
21496047 AATTAGATTAATTGTAACATTAAAACTTGGAACAAACTTTGTGGTCATA
1 AATTAGATTAATTGCAACATTAAAACTTGGAACAAACTTTGTAAT-ATA
* * *
21496096 AATTAGATTAATTGCAACATTAAAACTTGGAACAAATTTTATGATCATA
1 AATTAGATTAATTGCAACATTAAAACTTGGAACAAACTTTGTAAT-ATA
*
21496145 AATTAGATTAATTGCAACATTAAAACTTGGAGCAAACTTTGTAATATA
1 AATTAGATTAATTGCAACATTAAAACTTGGAACAAACTTTGTAATATA
* * * *
21496193 AATTA-AATACAGTACAACATTAAAACTTGGAACAAAATTTGTAATATA
1 AATTAGATTA-ATTGCAACATTAAAACTTGGAACAAACTTTGTAATATA
* * *
21496241 AATTA-AATATATTACAACATTAAAACTT-GATACAAACTTAGTAATATA
1 AATTAGATTA-ATTGCAACATTAAAACTTGGA-ACAAACTTTGTAATATA
21496289 AATTAG
1 AATTAG
21496295 GTACATTGGA
Statistics
Matches: 179, Mismatches: 17, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
47 5 0.03
48 88 0.49
49 86 0.48
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.33
Consensus pattern (48 bp):
AATTAGATTAATTGCAACATTAAAACTTGGAACAAACTTTGTAATATA
Found at i:21499717 original size:4 final size:4
Alignment explanation
Indices: 21499708--21499747 Score: 62
Period size: 4 Copynumber: 9.5 Consensus size: 4
21499698 AAAAATACAT
21499708 TTTC TTTC TTTC TTTC TTCTC TTTTC TTTC TTTC TTTC TT
1 TTTC TTTC TTTC TTTC TT-TC -TTTC TTTC TTTC TTTC TT
21499748 CACTCCCTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 28 0.82
5 4 0.12
6 2 0.06
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTC
Found at i:21499735 original size:18 final size:17
Alignment explanation
Indices: 21499708--21499747 Score: 64
Period size: 18 Copynumber: 2.4 Consensus size: 17
21499698 AAAAATACAT
21499708 TTTC-TTTCTTTCTTTC
1 TTTCTTTTCTTTCTTTC
21499724 TTCTCTTTTCTTTCTTTC
1 TT-TCTTTTCTTTCTTTC
21499742 TTTCTT
1 TTTCTT
21499748 CACTCCCTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.09
17 6 0.27
18 14 0.64
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTCTTTTCTTTCTTTC
Found at i:21499735 original size:22 final size:22
Alignment explanation
Indices: 21499707--21499748 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
21499697 TAAAAATACA
21499707 TTTTCTTTCTTTCTTTCTTCTC
1 TTTTCTTTCTTTCTTTCTTCTC
21499729 TTTTCTTTCTTTCTTTCTTC
1 TTTTCTTTCTTTCTTTCTTC
21499749 ACTCCCTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (22 bp):
TTTTCTTTCTTTCTTTCTTCTC
Found at i:21499761 original size:22 final size:22
Alignment explanation
Indices: 21499710--21499758 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
21499700 AAATACATTT
* **
21499710 TCTTTCTTTCTTTCTTCTCTTT
1 TCTTTCTTTCTTTCTTCACTCC
21499732 TCTTTCTTTCTTTCTTCACTCCC
1 TCTTTCTTTCTTTCTTCACT-CC
21499755 TCTT
1 TCTT
21499759 CTTCCTCATG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.65
Consensus pattern (22 bp):
TCTTTCTTTCTTTCTTCACTCC
Found at i:21519202 original size:14 final size:14
Alignment explanation
Indices: 21519183--21519218 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
21519173 CTGTTTGTGG
21519183 GAAATTTCAGGGAC
1 GAAATTTCAGGGAC
21519197 GAAATTTCAGGGAC
1 GAAATTTCAGGGAC
21519211 GAAATTTC
1 GAAATTTC
21519219 TTTCAGGAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25
Consensus pattern (14 bp):
GAAATTTCAGGGAC
Found at i:21529163 original size:18 final size:19
Alignment explanation
Indices: 21529137--21529173 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
21529127 AATATTTGAA
21529137 TGGAAAGAAGAGA-GAAAG
1 TGGAAAGAAGAGAGGAAAG
*
21529155 TGGAGAGAAGAGAGGAAAG
1 TGGAAAGAAGAGAGGAAAG
21529174 ATGTGAATGC
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:0.51, C:0.00, G:0.43, T:0.05
Consensus pattern (19 bp):
TGGAAAGAAGAGAGGAAAG
Found at i:21529596 original size:22 final size:22
Alignment explanation
Indices: 21529554--21529598 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
21529544 TTATTAACCC
*
21529554 AAATTAAATTGTATATAAATTA
1 AAATTAAATTATATATAAATTA
*
21529576 AAATT-AATTATATTATGAATTA
1 AAATTAAATTATA-TATAAATTA
21529598 A
1 A
21529599 CACATAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.42
Consensus pattern (22 bp):
AAATTAAATTATATATAAATTA
Found at i:21530931 original size:51 final size:51
Alignment explanation
Indices: 21530833--21530931 Score: 126
Period size: 51 Copynumber: 1.9 Consensus size: 51
21530823 CATTTTTCAT
* *
21530833 TTTCATTTTGGAGAAAACCACATTCATTTCCAAATGATTCCATTTCTCCAA
1 TTTCATTTTGGAGAAAACCACAATCATTTCCAAATGATTCCAATTCTCCAA
** * * * *
21530884 TTTCATTTTGGAGAAAATTATAATCATTTCCCAATGTTTTCAATTCTC
1 TTTCATTTTGGAGAAAACCACAATCATTTCCAAATGATTCCAATTCTC
21530932 TGTTTTCACT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 40 1.00
ACGTcount: A:0.30, C:0.20, G:0.08, T:0.41
Consensus pattern (51 bp):
TTTCATTTTGGAGAAAACCACAATCATTTCCAAATGATTCCAATTCTCCAA
Found at i:21534516 original size:18 final size:18
Alignment explanation
Indices: 21534493--21534528 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
21534483 ATTTTCTGTA
21534493 AAATTATATTAGAATGAG
1 AAATTATATTAGAATGAG
21534511 AAATTATATTAGAATGAG
1 AAATTATATTAGAATGAG
21534529 CCTGCTAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (18 bp):
AAATTATATTAGAATGAG
Found at i:21535372 original size:32 final size:32
Alignment explanation
Indices: 21535336--21535402 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
21535326 GGCCGTGTAA
* * * **
21535336 GCCACACGGGCTAGGCTAATTTGGGCGTGTGG
1 GCCACACAGGCAAGGCCAATTTCAGCGTGTGG
21535368 GCCACACAGGCAAGGCCAATTTCAGCGTGTGG
1 GCCACACAGGCAAGGCCAATTTCAGCGTGTGG
21535400 GCC
1 GCC
21535403 CATACGAGTA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.19, C:0.27, G:0.36, T:0.18
Consensus pattern (32 bp):
GCCACACAGGCAAGGCCAATTTCAGCGTGTGG
Found at i:21546774 original size:24 final size:24
Alignment explanation
Indices: 21546745--21546813 Score: 74
Period size: 24 Copynumber: 2.9 Consensus size: 24
21546735 AATGGGTTAC
21546745 AAGAAGATGAAA-GATG-AAGAGTT-
1 AAGAAGATGAAATG-TGAAAG-GTTG
21546768 AAGGAAGATGAAATGTGAAAGGTTG
1 AA-GAAGATGAAATGTGAAAGGTTG
21546793 AAGAAGATGAAAAT-TGAAAGG
1 AAGAAGATG-AAATGTGAAAGG
21546814 CTGATTATAA
Statistics
Matches: 41, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
23 2 0.05
24 29 0.71
25 10 0.24
ACGTcount: A:0.51, C:0.00, G:0.32, T:0.17
Consensus pattern (24 bp):
AAGAAGATGAAATGTGAAAGGTTG
Found at i:21551448 original size:18 final size:18
Alignment explanation
Indices: 21551422--21551456 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
21551412 CTTGTTGGAT
*
21551422 TTTCTTTTTGGATTTTTC
1 TTTCATTTTGGATTTTTC
*
21551440 TTTCATTTTGTATTTTT
1 TTTCATTTTGGATTTTT
21551457 AAGCTAGCCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.09, C:0.09, G:0.09, T:0.74
Consensus pattern (18 bp):
TTTCATTTTGGATTTTTC
Found at i:21553751 original size:23 final size:23
Alignment explanation
Indices: 21553699--21553829 Score: 79
Period size: 23 Copynumber: 5.7 Consensus size: 23
21553689 CTTGCAACGA
* * *
21553699 CTTTGTGGCGTCTTTTGTAATGT
1 CTTTGTGGCATATTCTGTAATGT
* *
21553722 ATGTGTGGCATATTCTGTAATGT
1 CTTTGTGGCATATTCTGTAATGT
* * ** * *
21553745 CTTTGTGTCCTACACTGCAATGC
1 CTTTGTGGCATATTCTGTAATGT
* *
21553768 CTTTATGGCATATTCTGTAAT-A
1 CTTTGTGGCATATTCTGTAATGT
**
21553790 CGTTTGTGG-AGTATTCTACAATG-
1 C-TTTGTGGCA-TATTCTGTAATGT
21553813 CTTTTGTGGCATATTCT
1 C-TTTGTGGCATATTCT
21553830 ACAATGCATT
Statistics
Matches: 80, Mismatches: 24, Indels: 8
0.71 0.21 0.07
Matches are distributed among these distances:
22 2 0.03
23 77 0.96
24 1 0.01
ACGTcount: A:0.18, C:0.16, G:0.21, T:0.44
Consensus pattern (23 bp):
CTTTGTGGCATATTCTGTAATGT
Found at i:21553830 original size:23 final size:23
Alignment explanation
Indices: 21553762--21553844 Score: 87
Period size: 23 Copynumber: 3.6 Consensus size: 23
21553752 TCCTACACTG
* * *
21553762 CAATGCCTTTATGGCATATTCTG
1 CAATGCATTTGTGGCATATTCTA
* * *
21553785 TAATACGTTTGTGG-AGTATTCTA
1 CAATGCATTTGTGGCA-TATTCTA
*
21553808 CAATGCTTTTGTGGCATATTCTA
1 CAATGCATTTGTGGCATATTCTA
21553831 CAATGCATTTGTGG
1 CAATGCATTTGTGG
21553845 TAAGTTCCGT
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
22 1 0.02
23 47 0.96
24 1 0.02
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.41
Consensus pattern (23 bp):
CAATGCATTTGTGGCATATTCTA
Found at i:21560619 original size:24 final size:24
Alignment explanation
Indices: 21560581--21560832 Score: 145
Period size: 24 Copynumber: 10.8 Consensus size: 24
21560571 TGAATTGGAT
* *
21560581 AATTTACAATAAATAATATATAATA
1 AATTTAAAAT-AATAATATATGATA
* *
21560606 AATTTGAAATAATAATACAT-ATAA
1 AATTTAAAATAATAATATATGAT-A
*
21560630 AATTT-AAA-AAT--TTTGATGAT-
1 AATTTAAAATAATAATAT-ATGATA
* * **
21560650 AATTCTAGAATAATCATACGTGATA
1 AATT-TAAAATAATAATATATGATA
** * *
21560675 AATCCAAAATAATAGTATATAATA
1 AATTTAAAATAATAATATATGATA
*
21560699 AATTT-AAA-AATATTA-ATGATA
1 AATTTAAAATAATAATATATGATA
* *
21560720 AATTTGAAATAA-ATATACATGATA
1 AATTTAAAATAATA-ATATATGATA
** *
21560744 AATTTAAAATAATGTTA-ACGA-A
1 AATTTAAAATAATAATATATGATA
21560766 GAATTTAAAATAATAATAT-TGATA
1 -AATTTAAAATAATAATATATGATA
* *
21560790 AA-TTACAAATAATAAAACATGATA
1 AATTTA-AAATAATAATATATGATA
*
21560814 AATCTAAAATAATAATATA
1 AATTTAAAATAATAATATA
21560833 CAATAAACTT
Statistics
Matches: 173, Mismatches: 34, Indels: 41
0.70 0.14 0.17
Matches are distributed among these distances:
20 5 0.03
21 13 0.08
22 21 0.12
23 47 0.27
24 73 0.42
25 14 0.08
ACGTcount: A:0.56, C:0.05, G:0.06, T:0.34
Consensus pattern (24 bp):
AATTTAAAATAATAATATATGATA
Found at i:21560653 original size:69 final size:67
Alignment explanation
Indices: 21560578--21560866 Score: 183
Period size: 69 Copynumber: 4.1 Consensus size: 67
21560568 AAATGAATTG
* * * *
21560578 GATAATTTACAATAAATAATATATAATAAATTTGAAATAATAATACAT-ATAAAATTTAAAAATT
1 GATAATTTA-AATAAAT-ATACATGATAAATTTAAAATAATAATACATAAT-AAATTTAAAAATA
*
21560642 TTGAT
63 TTAAT
* ** * *
21560647 GATAATTCTAGAAT-AATCATACGTGATAAATCCAAAATAATAGTATATAATAAATTTAAAAATA
1 GATAATT-TA-AATAAAT-ATACATGATAAATTTAAAATAATAATACATAATAAATTTAAAAATA
21560711 TTAAT
63 TTAAT
** * *
21560716 GATAAATTTGAAATAAATATACATGATAAATTTAAAATAATGTTA-ACGAA-GAATTTAAAATAA
1 GAT-AATTT-AAATAAATATACATGATAAATTTAAAATAATAATACA-TAATAAATTT-AAA-AA
* *
21560779 TAATATT
61 TATTAAT
* * * * * * *
21560786 GATAAATTACAA-ATAATAAAACATGATAAATCTAAAATAATAATATACAATAAACTTAGATAAT
1 GATAATTTA-AATA-AAT-ATACATGATAAATTTAAAATAATAATACATAATAAATTTA-AAAAT
*
21560850 ATTAAC
62 ATTAAT
21560856 GATTAATTTAA
1 GA-TAATTTAA
21560867 TGATAATAAG
Statistics
Matches: 171, Mismatches: 34, Indels: 29
0.73 0.15 0.12
Matches are distributed among these distances:
68 8 0.05
69 91 0.53
70 60 0.35
71 12 0.07
ACGTcount: A:0.55, C:0.05, G:0.06, T:0.34
Consensus pattern (67 bp):
GATAATTTAAATAAATATACATGATAAATTTAAAATAATAATACATAATAAATTTAAAAATATTA
AT
Found at i:21560849 original size:70 final size:69
Alignment explanation
Indices: 21560670--21560850 Score: 170
Period size: 70 Copynumber: 2.6 Consensus size: 69
21560660 TAATCATACG
* * * * * **
21560670 TGATAAATCCAAAATAATAGTATATAATAAATTTAAAAATATTAATGATAAATTTGAAATAAATA
1 TGATAAATCTAAAATAATAATATACAATAAATTTAATAATAATAATGATAAATTACAAATAAATA
*
21560735 TACA
66 AACA
* ** * *
21560739 TGATAAATTTAAAATAATGTTA-ACGAA-GAATTTAAAATAATAATATTGATAAATTACAAAT-A
1 TGATAAATCTAAAATAATAATATAC-AATAAATTT--AATAATAATAATGATAAATTACAAATAA
21560801 ATAAAACA
63 AT-AAACA
*
21560809 TGATAAATCTAAAATAATAATATACAATAAACTTAGATAATA
1 TGATAAATCTAAAATAATAATATACAATAAATTTA-ATAATA
21560851 TTAACGATTA
Statistics
Matches: 88, Mismatches: 17, Indels: 13
0.75 0.14 0.11
Matches are distributed among these distances:
68 6 0.07
69 24 0.27
70 52 0.59
71 6 0.07
ACGTcount: A:0.57, C:0.05, G:0.06, T:0.32
Consensus pattern (69 bp):
TGATAAATCTAAAATAATAATATACAATAAATTTAATAATAATAATGATAAATTACAAATAAATA
AACA
Found at i:21561663 original size:19 final size:19
Alignment explanation
Indices: 21561636--21561680 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
21561626 TCTTTTTTCC
*
21561636 TCCCTTTACATTGATTTTT
1 TCCCTTTACACTGATTTTT
*
21561655 TCTCTTTACACTGATTTTT
1 TCCCTTTACACTGATTTTT
21561674 TCCCTTT
1 TCCCTTT
21561681 TTTATGAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.13, C:0.24, G:0.04, T:0.58
Consensus pattern (19 bp):
TCCCTTTACACTGATTTTT
Found at i:21564839 original size:21 final size:21
Alignment explanation
Indices: 21564815--21564855 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
21564805 GTTCCAATCC
*
21564815 TTTTCTTACCCGTTTCATTTA
1 TTTTCTTACCCGTCTCATTTA
21564836 TTTTCTTACCCGTCTCATTT
1 TTTTCTTACCCGTCTCATTT
21564856 GGATAGTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.12, C:0.27, G:0.05, T:0.56
Consensus pattern (21 bp):
TTTTCTTACCCGTCTCATTTA
Found at i:21568367 original size:31 final size:30
Alignment explanation
Indices: 21568323--21568381 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
21568313 ATAAGAATAT
*
21568323 GAAAGATAAAGAATTAAGAAAAATGAAAGA
1 GAAAGATAAAGAATGAAGAAAAATGAAAGA
* *
21568353 GAAAGAATTAAGAATGATGAAAAATGAAA
1 GAAAG-ATAAAGAATGAAGAAAAATGAAA
21568382 AGTTGATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 5 0.20
31 20 0.80
ACGTcount: A:0.64, C:0.00, G:0.20, T:0.15
Consensus pattern (30 bp):
GAAAGATAAAGAATGAAGAAAAATGAAAGA
Found at i:21568372 original size:24 final size:23
Alignment explanation
Indices: 21568314--21568374 Score: 86
Period size: 24 Copynumber: 2.6 Consensus size: 23
21568304 AAAAGAGTTA
*
21568314 TAAGAATATGAAAGATAAAGAAT
1 TAAGAATATGAAAGAGAAAGAAT
*
21568337 TAAGAAAAATGAAAGAGAAAGAAT
1 TAAG-AATATGAAAGAGAAAGAAT
21568361 TAAGAATGATGAAA
1 TAAGAAT-ATGAAA
21568375 AATGAAAAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
23 6 0.18
24 27 0.82
ACGTcount: A:0.62, C:0.00, G:0.20, T:0.18
Consensus pattern (23 bp):
TAAGAATATGAAAGAGAAAGAAT
Found at i:21569882 original size:35 final size:35
Alignment explanation
Indices: 21569843--21569963 Score: 115
Period size: 35 Copynumber: 3.4 Consensus size: 35
21569833 TTTAATTAAA
21569843 TTTATTAAATGAATTTAGATTTTGTCAATAAAAAC
1 TTTATTAAATGAATTTAGATTTTGTCAATAAAAAC
* * ** *
21569878 TTTATTGAATGAA-TTA-ATATCATAATACGTAAAAAC
1 TTTATTAAATGAATTTAGATTTTGTCA-A--TAAAAAC
*
21569914 -TTA-TAAATTAGAATTTAGATTTTGTCAAAAAAAAC
1 TTTATTAAA-T-GAATTTAGATTTTGTCAATAAAAAC
21569949 TTTATTAAATGAATT
1 TTTATTAAATGAATT
21569964 AATATCATAA
Statistics
Matches: 66, Mismatches: 11, Indels: 18
0.69 0.12 0.19
Matches are distributed among these distances:
33 5 0.08
34 7 0.11
35 27 0.41
36 14 0.21
37 8 0.12
38 5 0.08
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.40
Consensus pattern (35 bp):
TTTATTAAATGAATTTAGATTTTGTCAATAAAAAC
Found at i:21580395 original size:35 final size:35
Alignment explanation
Indices: 21580356--21580427 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 35
21580346 ATTGTGAAAA
*
21580356 TATTGGCGTTGTGGC-GAGACGTTAAATGAATGAAG
1 TATTGGCGTTGTGGCAG-GACGTTAAATGAATAAAG
* *
21580391 TATTGGTGTTGTGGCAGGACGTTACATGAATAAAG
1 TATTGGCGTTGTGGCAGGACGTTAAATGAATAAAG
21580426 TA
1 TA
21580428 ACGATGTTGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 32 0.97
36 1 0.03
ACGTcount: A:0.29, C:0.08, G:0.32, T:0.31
Consensus pattern (35 bp):
TATTGGCGTTGTGGCAGGACGTTAAATGAATAAAG
Found at i:21580436 original size:35 final size:35
Alignment explanation
Indices: 21580363--21580438 Score: 91
Period size: 35 Copynumber: 2.2 Consensus size: 35
21580353 AAATATTGGC
* ** *
21580363 GTTGTGGCGAGACGTTAAATGAATGAAGTATTGGT
1 GTTGTGGCGAGACGTTAAATGAATAAAGTAACGAT
*
21580398 GTTGTGGC-AGGACGTTACATGAATAAAGTAACGAT
1 GTTGTGGCGA-GACGTTAAATGAATAAAGTAACGAT
21580433 GTTGTG
1 GTTGTG
21580439 AGGGAATGTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
34 1 0.03
35 34 0.97
ACGTcount: A:0.29, C:0.08, G:0.33, T:0.30
Consensus pattern (35 bp):
GTTGTGGCGAGACGTTAAATGAATAAAGTAACGAT
Found at i:21580469 original size:69 final size:69
Alignment explanation
Indices: 21580387--21580523 Score: 170
Period size: 69 Copynumber: 2.0 Consensus size: 69
21580377 TTAAATGAAT
** *
21580387 GAAGTATTGGTGTTGTGGCAGGACGTTACATGAATA-AAGTAACGATGTTGTGAG-GGAATGTTA
1 GAAGTATCAGTGTTGTGGCAGGACGTTA-ATGAAGAGAAGTAACGATGTTGTG-GTGGAATGTTA
21580450 ATTAAC
64 ATTAAC
* * * * *
21580456 GAAGTATCAGTGTTGTGGTAGGATGTTAATTAAGAGAAGTATCGGTGTTGTGGTGGAATGTTAAT
1 GAAGTATCAGTGTTGTGGCAGGACGTTAATGAAGAGAAGTAACGATGTTGTGGTGGAATGTTAAT
21580521 TAA
66 TAA
21580524 AATTGGACTG
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
68 6 0.10
69 52 0.90
ACGTcount: A:0.31, C:0.05, G:0.31, T:0.33
Consensus pattern (69 bp):
GAAGTATCAGTGTTGTGGCAGGACGTTAATGAAGAGAAGTAACGATGTTGTGGTGGAATGTTAAT
TAAC
Found at i:21580504 original size:35 final size:35
Alignment explanation
Indices: 21580441--21580524 Score: 127
Period size: 35 Copynumber: 2.4 Consensus size: 35
21580431 ATGTTGTGAG
* *
21580441 GGAATGTTAATTAACGAAGTATCAGTGTTGTGGTA
1 GGAATGTTAATTAAAGAAGTATCGGTGTTGTGGTA
21580476 GG-ATGTTAATTAAGAGAAGTATCGGTGTTGTGGT-
1 GGAATGTTAATTAA-AGAAGTATCGGTGTTGTGGTA
21580510 GGAATGTTAATTAAA
1 GGAATGTTAATTAAA
21580525 ATTGGACTGG
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
34 14 0.31
35 31 0.69
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.35
Consensus pattern (35 bp):
GGAATGTTAATTAAAGAAGTATCGGTGTTGTGGTA
Found at i:21595934 original size:17 final size:17
Alignment explanation
Indices: 21595912--21595964 Score: 81
Period size: 17 Copynumber: 3.2 Consensus size: 17
21595902 ATAGAAAGTC
21595912 AAAGATATGGGTATCAG
1 AAAGATATGGGTATCAG
*
21595929 AAAGATATGGGTATCAA
1 AAAGATATGGGTATCAG
*
21595946 AAAGATATGGCTATC-G
1 AAAGATATGGGTATCAG
21595962 AAA
1 AAA
21595965 TCTGGGATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
16 3 0.09
17 30 0.91
ACGTcount: A:0.45, C:0.08, G:0.25, T:0.23
Consensus pattern (17 bp):
AAAGATATGGGTATCAG
Found at i:21599502 original size:17 final size:17
Alignment explanation
Indices: 21599480--21599512 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
21599470 ATAGAAAGTC
21599480 AAAGATATGGGTATCAG
1 AAAGATATGGGTATCAG
21599497 AAAGATATGGGTATCA
1 AAAGATATGGGTATCA
21599513 AAATCTGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.06, G:0.27, T:0.24
Consensus pattern (17 bp):
AAAGATATGGGTATCAG
Found at i:21601337 original size:17 final size:17
Alignment explanation
Indices: 21601315--21601347 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
21601305 TAGTTGTCAC
21601315 TTGAATTAAATTAATTG
1 TTGAATTAAATTAATTG
*
21601332 TTGAATTAATTTAATT
1 TTGAATTAAATTAATT
21601348 TGATAGTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (17 bp):
TTGAATTAAATTAATTG
Done.