Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 147 of 150
Found at i:44485849 original size:2 final size:2
Alignment explanation
Indices: 44485832--44485868 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
44485822 CATTTCCATC
* *
44485832 TA TA TA TG TA TG TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
44485869 GCTGGAACCT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:44487916 original size:18 final size:19
Alignment explanation
Indices: 44487872--44487918 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
44487862 AGCAAATAAA
44487872 GTTGGCATTGCAACTATTT
1 GTTGGCATTGCAACTATTT
44487891 GTTGGCATTGCAACTATTT
1 GTTGGCATTGCAACTATTT
44487910 G-TGGCATTG
1 GTTGGCATTG
44487919 GAGGCATTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 8 0.29
19 20 0.71
ACGTcount: A:0.19, C:0.15, G:0.26, T:0.40
Consensus pattern (19 bp):
GTTGGCATTGCAACTATTT
Found at i:44506975 original size:13 final size:13
Alignment explanation
Indices: 44506954--44506992 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
44506944 TTTATTCATT
*
44506954 TCTTCTTTTTTTC
1 TCTTTTTTTTTTC
*
44506967 TCTTTTTTTTCTC
1 TCTTTTTTTTTTC
44506980 TCTTTGTTTTTTT
1 TCTTT-TTTTTTT
44506993 AAAGAAGAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 16 0.73
14 6 0.27
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (13 bp):
TCTTTTTTTTTTC
Found at i:44520914 original size:26 final size:27
Alignment explanation
Indices: 44520860--44520916 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
44520850 TATTTTAAAA
** * *
44520860 TATTTTTAAAATACTTTTTTTATTTTT
1 TATTTTTAAAATAAATTTTTTAGTGTT
44520887 TATTTTTAAAATAAATTTTTT-GTGTT
1 TATTTTTAAAATAAATTTTTTAGTGTT
44520913 TATT
1 TATT
44520917 AAAAAAGGGC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 7 0.27
27 19 0.73
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.67
Consensus pattern (27 bp):
TATTTTTAAAATAAATTTTTTAGTGTT
Found at i:44522407 original size:55 final size:55
Alignment explanation
Indices: 44522323--44522543 Score: 262
Period size: 55 Copynumber: 4.0 Consensus size: 55
44522313 ATTGATTATC
* * * * * * * *
44522323 ATGTTGGAATAGTGCTTCTTTTGAGTCGATTCTTTGTATGTTTAAATCGATTGTC
1 ATGTTGGAATACTACTTCTTTTGAATCGATTGTGTATATGATTAAATCGATTGTT
** * * *
44522378 AAATTAGAACACTACTTCTTTTGAATCGATTGTGTATATGATTAAATTGATTGTT
1 ATGTTGGAATACTACTTCTTTTGAATCGATTGTGTATATGATTAAATCGATTGTT
* * * *
44522433 ATGTTGGAATACTGCTTCTTTTTAATTGATTGTGTATATGATTAAATTGATTGTT
1 ATGTTGGAATACTACTTCTTTTGAATCGATTGTGTATATGATTAAATCGATTGTT
* * *
44522488 ATGTTGGAATACTACTTCTCTTGAATCGATTGTTTATATGTTTAAATCGATTGTT
1 ATGTTGGAATACTACTTCTTTTGAATCGATTGTGTATATGATTAAATCGATTGTT
44522543 A
1 A
44522544 CATAACACAT
Statistics
Matches: 139, Mismatches: 27, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
55 139 1.00
ACGTcount: A:0.26, C:0.09, G:0.18, T:0.47
Consensus pattern (55 bp):
ATGTTGGAATACTACTTCTTTTGAATCGATTGTGTATATGATTAAATCGATTGTT
Found at i:44523745 original size:34 final size:36
Alignment explanation
Indices: 44523696--44523773 Score: 97
Period size: 37 Copynumber: 2.2 Consensus size: 36
44523686 TGTTTAAATT
* *
44523696 GATTGTCATGTTGGAATA-T-TGCTTCTTTTGAATC
1 GATTGTTATGGTGGAATACTATGCTTCTTTTGAATC
* *
44523730 GATTGTTATGGTGGAATACTACTTCTTCTTTTTAATC
1 GATTGTTATGGTGGAATACTA-TGCTTCTTTTGAATC
44523767 GATTGTT
1 GATTGTT
44523774 TATATGTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
34 16 0.43
35 1 0.03
37 20 0.54
ACGTcount: A:0.21, C:0.12, G:0.19, T:0.49
Consensus pattern (36 bp):
GATTGTTATGGTGGAATACTATGCTTCTTTTGAATC
Found at i:44523849 original size:55 final size:55
Alignment explanation
Indices: 44523726--44523905 Score: 191
Period size: 55 Copynumber: 3.2 Consensus size: 55
44523716 GCTTCTTTTG
* * * * *
44523726 AATCGATTGTTATGGTGGAATACTACTTCTTCTTTTTAATCGATTGTTTATATGTTTA
1 AATCGATTGTTATGTTGGAATACTA---CTTCTTTTGAATCAACTGTTTATATGTTCA
**
44523784 AATCGATTGTTATGTTGGAATA-TTGTTGCTTTTGAATCAACTGTTTATATGTTCA
1 AATCGATTGTTATGTTGGAATACTACTT-CTTTTGAATCAACTGTTTATATGTTCA
* * * * *
44523839 AATTGGTTGTTATGTTGGAATACTACTTCTTTTGAATCGATTGTTTATATGTTTA
1 AATCGATTGTTATGTTGGAATACTACTTCTTTTGAATCAACTGTTTATATGTTCA
* *
44523894 GATCAATTGTTA
1 AATCGATTGTTA
44523906 CGTAGCGCAT
Statistics
Matches: 102, Mismatches: 18, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
54 2 0.02
55 75 0.74
56 3 0.03
57 1 0.01
58 21 0.21
ACGTcount: A:0.25, C:0.09, G:0.17, T:0.49
Consensus pattern (55 bp):
AATCGATTGTTATGTTGGAATACTACTTCTTTTGAATCAACTGTTTATATGTTCA
Found at i:44525154 original size:123 final size:123
Alignment explanation
Indices: 44524928--44525302 Score: 579
Period size: 123 Copynumber: 3.0 Consensus size: 123
44524918 TTAGGGTTTT
* ** * * *
44524928 TAGGTCTTGGAAGAAATAATTTCGAGTTGATGTTTCTGATCAAATAGTATAAAATCGCTTCTAAC
1 TAGGTCATGGAAGAAATAATTT--TTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGC
* *
44524993 AGGATGCTATTTGAGAAGAATTTGTGAAATTGCGCCCTCGTGGACGCGCTTTTGCTACAG
64 AGGATGCTATTTGAGAAGAATTTGTAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
* * *
44525053 TAGGTCATGGAAGAAATAATTTTTTTGACGTTTCTAAGCAAATAATATAAAATCGCTTATAGCAG
1 TAGGTCATGGAAGAAATAATTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAG
* *
44525118 GATGCTATTTGAGAAGAATTTGTAAAATCGCACCCTCGTGGACGCGCTTTTGCTACAA
66 GATGCTATTTGAGAAGAATTTGTAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
*
44525176 TCGGTCATGGAAGAAATAATTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAG
1 TAGGTCATGGAAGAAATAATTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAG
* *
44525241 GATGCTATTTGAGAAGGATTTGTGAAAATCGCGCCCTCGTGGACGCGCTTTTTCTACAG
66 GATGCTATTTGAGAAGAATTTGT-AAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
44525300 TAG
1 TAG
44525303 TATGTTTAGG
Statistics
Matches: 227, Mismatches: 22, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
123 172 0.76
124 34 0.15
125 21 0.09
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (123 bp):
TAGGTCATGGAAGAAATAATTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAG
GATGCTATTTGAGAAGAATTTGTAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
Found at i:44529506 original size:16 final size:17
Alignment explanation
Indices: 44529480--44529513 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
44529470 TATATATATG
*
44529480 AAATAAAAATAAAGCTA
1 AAATAAAAATAAAACTA
44529497 AAAT-AAAATAAAACTA
1 AAATAAAAATAAAACTA
44529513 A
1 A
44529514 TTAATATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.74, C:0.06, G:0.03, T:0.18
Consensus pattern (17 bp):
AAATAAAAATAAAACTA
Found at i:44529570 original size:3 final size:3
Alignment explanation
Indices: 44529562--44529633 Score: 67
Period size: 3 Copynumber: 23.0 Consensus size: 3
44529552 AAAATAAAAC
* *
44529562 TAA TAA TAA TTAA TAA TAA TAA TAA TGA TAA TAA TAA TGAA -AA CAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA
44529608 TAA TAA -AA TAA TTAA CTAAA TAA TAA
1 TAA TAA TAA TAA -TAA -T-AA TAA TAA
44529634 AATTGCTAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
2 4 0.07
3 43 0.73
4 10 0.17
5 2 0.03
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:44530361 original size:17 final size:18
Alignment explanation
Indices: 44530326--44530365 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
44530316 CATATGTAAA
44530326 AAAAACGAAAGAAAGAAT
1 AAAAACGAAAGAAAGAAT
* *
44530344 AAAAATGAAATAAA-AAT
1 AAAAACGAAAGAAAGAAT
44530361 AAAAA
1 AAAAA
44530366 AACAAAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.78, C:0.03, G:0.10, T:0.10
Consensus pattern (18 bp):
AAAAACGAAAGAAAGAAT
Found at i:44530925 original size:23 final size:23
Alignment explanation
Indices: 44530900--44531148 Score: 274
Period size: 21 Copynumber: 11.3 Consensus size: 23
44530890 AGTAAAATTA
*
44530900 TTAACTTAGTTTAGGGTTTTTAA-
1 TTAA-TTAGGTTAGGGTTTTTAAT
* *
44530923 TTAACTTAGTTTAGGGTTTTTAAG
1 TTAA-TTAGGTTAGGGTTTTTAAT
* *
44530947 TTAA--GGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAT
*
44530968 TTAA--GGGTTTAGGGTTTTTAAT
1 TTAATTAGG-TTAGGGTTTTTAAT
44530990 TTAATTAGGTTAGGGTTTTTAAT
1 TTAATTAGGTTAGGGTTTTTAAT
*
44531013 TTAATT--GTTAGAGTTTTTAAT
1 TTAATTAGGTTAGGGTTTTTAAT
44531034 TTAATT--GTTAGGG-TTTTAAT
1 TTAATTAGGTTAGGGTTTTTAAT
*
44531054 TTAATTAGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAT
*
44531077 TTAA--GGGTTAGGGTTTTTAAT
1 TTAATTAGGTTAGGGTTTTTAAT
*
44531098 TTAATTAGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAT
*
44531121 TTAA--GGGTTAGGGTTTTTAAT
1 TTAATTAGGTTAGGGTTTTTAAT
44531142 TTAATTA
1 TTAATTA
44531149 AATAATATCA
Statistics
Matches: 201, Mismatches: 14, Indels: 22
0.85 0.06 0.09
Matches are distributed among these distances:
20 13 0.06
21 86 0.43
22 24 0.12
23 72 0.36
24 6 0.03
ACGTcount: A:0.26, C:0.01, G:0.23, T:0.50
Consensus pattern (23 bp):
TTAATTAGGTTAGGGTTTTTAAT
Found at i:44530950 original size:28 final size:23
Alignment explanation
Indices: 44530899--44531124 Score: 155
Period size: 23 Copynumber: 10.2 Consensus size: 23
44530889 AAGTAAAATT
44530899 ATTAACTTAGTTTAGGGTTTTTA
1 ATTAACTTAGTTTAGGGTTTTTA
44530922 ATTAACTTAGTTTAGGGTTTTTA
1 ATTAACTTAGTTTAGGGTTTTTA
* *
44530945 AGTTAA---GGGTTAGGGTTTTTA
1 A-TTAACTTAGTTTAGGGTTTTTA
**
44530966 AGTTAA--GGGTTTAGGGTTTTTA
1 A-TTAACTTAGTTTAGGGTTTTTA
*
44530988 ATTTAA-TTAGGTTAGGGTTTTTA
1 A-TTAACTTAGTTTAGGGTTTTTA
*
44531011 ATTTAA-TT-G-TTAGAGTTTTTA
1 A-TTAACTTAGTTTAGGGTTTTTA
44531032 ATTTAA-TT-G-TTAGGG-TTTTA
1 A-TTAACTTAGTTTAGGGTTTTTA
*
44531052 ATTTAA-TTAGGTTAGGGTTTTTA
1 A-TTAACTTAGTTTAGGGTTTTTA
* *
44531075 AGTTAA---GGGTTAGGGTTTTTA
1 A-TTAACTTAGTTTAGGGTTTTTA
*
44531096 ATTTAA-TTAGGTTAGGGTTTTTA
1 A-TTAACTTAGTTTAGGGTTTTTA
44531119 AGTTAA
1 A-TTAA
44531125 GGGTTAGGGT
Statistics
Matches: 181, Mismatches: 14, Indels: 16
0.86 0.07 0.08
Matches are distributed among these distances:
20 13 0.07
21 64 0.35
22 26 0.14
23 74 0.41
24 4 0.02
ACGTcount: A:0.26, C:0.01, G:0.23, T:0.50
Consensus pattern (23 bp):
ATTAACTTAGTTTAGGGTTTTTA
Found at i:44531039 original size:44 final size:43
Alignment explanation
Indices: 44530910--44531148 Score: 306
Period size: 44 Copynumber: 5.5 Consensus size: 43
44530900 TTAACTTAGT
44530910 TTAGGGTTTTTAA-TTAACTTAGTTTAGGGTTTTTAAGTTAAGGG
1 TTAGGGTTTTTAATTTAA-TTAG-TTAGGGTTTTTAAGTTAAGGG
* ** * *
44530954 TTAGGGTTTTTAAGTTAA-GGGTTTAGGGTTTTTAATTTAATTAGG
1 TTAGGGTTTTTAATTTAATTAG-TTAGGGTTTTTAAGTTAA--GGG
* * **
44530999 TTAGGGTTTTTAATTTAATT-GTTAGAGTTTTTAATTTAATTG
1 TTAGGGTTTTTAATTTAATTAGTTAGGGTTTTTAAGTTAAGGG
44531041 TTAGGG-TTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGG
1 TTAGGGTTTTTAATTTAATTA-GTTAGGGTTTTTAAGTTAAGGG
44531084 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGG
1 TTAGGGTTTTTAATTTAATTA-GTTAGGGTTTTTAAGTTAAGGG
44531128 TTAGGGTTTTTAATTTAATTA
1 TTAGGGTTTTTAATTTAATTA
44531149 AATAATATCA
Statistics
Matches: 175, Mismatches: 13, Indels: 14
0.87 0.06 0.07
Matches are distributed among these distances:
41 13 0.07
42 7 0.04
43 43 0.25
44 88 0.50
45 24 0.14
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (43 bp):
TTAGGGTTTTTAATTTAATTAGTTAGGGTTTTTAAGTTAAGGG
Found at i:44531114 original size:108 final size:110
Alignment explanation
Indices: 44530910--44531148 Score: 362
Period size: 108 Copynumber: 2.2 Consensus size: 110
44530900 TTAACTTAGT
*
44530910 TTAGGGTTTTTAA-TTAACTTAGTTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGG
1 TTAGGGTTTTTAATTTAA-TTAGTTTAGGGTTTTTAAGTTAAAGGTTAGGGTTTTTAAGTTAAGG
* **
44530974 GTTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAATTTAATTG
65 GTTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGG
* *
44531020 TTAGAGTTTTTAATTTAATT-G-TTAGGG-TTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAG
1 TTAGGGTTTTTAATTTAATTAGTTTAGGGTTTTTAAGTTAA--AGGTTAGGGTTTTTAAGTTAAG
44531082 GG-TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGG
64 GGTTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGG
44531128 TTAGGGTTTTTAATTTAATTA
1 TTAGGGTTTTTAATTTAATTA
44531149 AATAATATCA
Statistics
Matches: 118, Mismatches: 7, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
107 10 0.08
108 66 0.56
109 24 0.20
110 14 0.12
111 4 0.03
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (110 bp):
TTAGGGTTTTTAATTTAATTAGTTTAGGGTTTTTAAGTTAAAGGTTAGGGTTTTTAAGTTAAGGG
TTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGG
Found at i:44531620 original size:18 final size:18
Alignment explanation
Indices: 44531580--44531614 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
44531570 GGACTCGGAA
44531580 AAGGATACATATAAGGGT
1 AAGGATACATATAAGGGT
44531598 AAGGATACATATAAGGG
1 AAGGATACATATAAGGG
44531615 CTAGGAAACG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.06, G:0.29, T:0.20
Consensus pattern (18 bp):
AAGGATACATATAAGGGT
Found at i:44532288 original size:14 final size:14
Alignment explanation
Indices: 44532271--44532299 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
44532261 TTATATACAT
44532271 AATACTAAATACCA
1 AATACTAAATACCA
44532285 AATACTAAATACCA
1 AATACTAAATACCA
44532299 A
1 A
44532300 TTGACTAGCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.21, G:0.00, T:0.21
Consensus pattern (14 bp):
AATACTAAATACCA
Found at i:44532502 original size:20 final size:20
Alignment explanation
Indices: 44532465--44532502 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
44532455 TTTATTTTTA
*
44532465 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
44532485 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
44532503 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:44533481 original size:51 final size:51
Alignment explanation
Indices: 44533425--44533545 Score: 215
Period size: 51 Copynumber: 2.4 Consensus size: 51
44533415 TATTTTTAAA
*
44533425 AAGGAAATTGAGAGCAAATTGAAATTAAATATGGATTTGAGAGAATTTTGG
1 AAGGAAATTGAGAGAAAATTGAAATTAAATATGGATTTGAGAGAATTTTGG
*
44533476 AAGGAAATTAAGAGAAAATTGAAATTAAATATGGATTTGAGAGAATTTTGG
1 AAGGAAATTGAGAGAAAATTGAAATTAAATATGGATTTGAGAGAATTTTGG
*
44533527 AAGGAAATTGAGAGGAAAT
1 AAGGAAATTGAGAGAAAAT
44533546 ACGAGAGAGC
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 66 1.00
ACGTcount: A:0.46, C:0.01, G:0.26, T:0.27
Consensus pattern (51 bp):
AAGGAAATTGAGAGAAAATTGAAATTAAATATGGATTTGAGAGAATTTTGG
Found at i:44533483 original size:29 final size:29
Alignment explanation
Indices: 44533451--44533534 Score: 74
Period size: 29 Copynumber: 3.1 Consensus size: 29
44533441 AATTGAAATT
44533451 AAATATGGATTTGAGAGAATTTTGGAAGG
1 AAATATGGATTTGAGAGAATTTTGGAAGG
** * **
44533480 AAAT-T--A----AGAGAAAATTGAAATT
1 AAATATGGATTTGAGAGAATTTTGGAAGG
44533502 AAATATGGATTTGAGAGAATTTTGGAAGG
1 AAATATGGATTTGAGAGAATTTTGGAAGG
44533531 AAAT
1 AAAT
44533535 TGAGAGGAAA
Statistics
Matches: 38, Mismatches: 10, Indels: 14
0.61 0.16 0.23
Matches are distributed among these distances:
22 15 0.39
23 1 0.03
25 1 0.03
26 1 0.03
28 1 0.03
29 19 0.50
ACGTcount: A:0.45, C:0.00, G:0.25, T:0.30
Consensus pattern (29 bp):
AAATATGGATTTGAGAGAATTTTGGAAGG
Found at i:44534339 original size:30 final size:31
Alignment explanation
Indices: 44534301--44534361 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
44534291 TTTTTATATA
44534301 TTATGTAATATATAATA-C-AAAAATTAAAT
1 TTATGTAATATATAATATCGAAAAATTAAAT
44534330 TTATAGTAATATATAATATCGTAAAAATTAAA
1 TTAT-GTAATATATAATATCG-AAAAATTAAA
44534362 AAAAACATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
29 4 0.14
30 13 0.46
31 1 0.04
33 10 0.36
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (31 bp):
TTATGTAATATATAATATCGAAAAATTAAAT
Found at i:44534443 original size:21 final size:22
Alignment explanation
Indices: 44534419--44534460 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
44534409 TATAAATTAT
*
44534419 TAAATAGTATT-AAAAATAATA
1 TAAATAATATTAAAAAATAATA
*
44534440 TAAATAATTTTAAAAAATAAT
1 TAAATAATATTAAAAAATAAT
44534461 TATATGGGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (22 bp):
TAAATAATATTAAAAAATAATA
Found at i:44535283 original size:76 final size:74
Alignment explanation
Indices: 44535197--44535387 Score: 310
Period size: 74 Copynumber: 2.6 Consensus size: 74
44535187 AACACAGTCT
*
44535197 GTATCTTCAGTTCATAAACATCCCAATAAACCATTGGGATTCAAACACAAAACCATCACACAAAC
1 GTATCTTCAGTTCATAAACATCCCAATAAACCATTGAGATTCAAACAC--AACCATCACACAAAC
* *
44535262 ACATATTGTCA
64 ACATACTGGCA
* **
44535273 GTATCTTCAGTTCATAAACATCCCAATAAACCATTGACATTCAAACACAACCATCACACAAATGC
1 GTATCTTCAGTTCATAAACATCCCAATAAACCATTGAGATTCAAACACAACCATCACACAAACAC
44535338 ATACTGGCA
66 ATACTGGCA
44535347 GTATCTTCAGTTCATAAACATCCCAATAAACCATTGAGATT
1 GTATCTTCAGTTCATAAACATCCCAATAAACCATTGAGATT
44535388 GTATTTCAAA
Statistics
Matches: 108, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
74 62 0.57
76 46 0.43
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.25
Consensus pattern (74 bp):
GTATCTTCAGTTCATAAACATCCCAATAAACCATTGAGATTCAAACACAACCATCACACAAACAC
ATACTGGCA
Found at i:44535502 original size:42 final size:42
Alignment explanation
Indices: 44535443--44535585 Score: 187
Period size: 42 Copynumber: 3.4 Consensus size: 42
44535433 ACTGGCTAGA
** **
44535443 TTCAGTTGGTTTTCTTTTAACCCAGCTTCGTCCTGATCCAGC
1 TTCAGTTTCTTTTCTTTTAAGTCAGCTTCGTCCTGATCCAGC
44535485 TTCAGTTTCTTTTCTTTTAAGTCAGCTTCGTCCTGATCCAGC
1 TTCAGTTTCTTTTCTTTTAAGTCAGCTTCGTCCTGATCCAGC
* * * **
44535527 TTCAGTTTCTTCTCTTTTAAGTCAGCTCCATCCTTCTCCAGC
1 TTCAGTTTCTTTTCTTTTAAGTCAGCTTCGTCCTGATCCAGC
44535569 TTCAGTCTGTCTTTTCT
1 TTCAGT-T-TCTTTTCT
44535586 AATATTAGCT
Statistics
Matches: 89, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
42 81 0.91
43 1 0.01
44 7 0.08
ACGTcount: A:0.13, C:0.29, G:0.13, T:0.45
Consensus pattern (42 bp):
TTCAGTTTCTTTTCTTTTAAGTCAGCTTCGTCCTGATCCAGC
Found at i:44535963 original size:43 final size:43
Alignment explanation
Indices: 44535798--44536400 Score: 705
Period size: 43 Copynumber: 14.1 Consensus size: 43
44535788 TTTTTTTTAC
* *
44535798 AACGCCGCTATAGACCATGTTCTTTAGCGGCGCTTAA--ATAAA
1 AACGCCACTATAGACCATGGTCTTTAGCGGCGCTTAAGCA-AAA
* * *
44535840 AACACCACTATAGACCGTGATCTTTAGCGGCGCTTAA--AAAA
1 AACGCCACTATAGACCATGGTCTTTAGCGGCGCTTAAGCAAAA
* * * *
44535881 AACGCCACTATAAACCGTGGTCTTTAGCGACGCTT-ACCAAAA
1 AACGCCACTATAGACCATGGTCTTTAGCGGCGCTTAAGCAAAA
* * * *
44535923 AATGCCACTATAGACCATGGTCTTTAGCGGTGCTTAACCAACA
1 AACGCCACTATAGACCATGGTCTTTAGCGGCGCTTAAGCAAAA
* * *
44535966 AACGCCACTACAGACCATGGTCTTTAGCGGCGCTTAACCAACA
1 AACGCCACTATAGACCATGGTCTTTAGCGGCGCTTAAGCAAAA
* * * *
44536009 AATGCCACTACAGACCATGGTCTTTAGCGGCGCTTAACCAACA
1 AACGCCACTATAGACCATGGTCTTTAGCGGCGCTTAAGCAAAA
* *
44536052 AACGCCACTATAGACCATGGTCTTTAGCGGCGCTTAGGCGAAA
1 AACGCCACTATAGACCATGGTCTTTAGCGGCGCTTAAGCAAAA
* * *
44536095 AACGCCACTATAGACCATGGTCTTTCGCGGCGCTTAGGCGAAA
1 AACGCCACTATAGACCATGGTCTTTAGCGGCGCTTAAGCAAAA
* * * * *
44536138 AACGCCAATATAGACCATGGTTTTTCGCGGCGCTTAGGAAAAA
1 AACGCCACTATAGACCATGGTCTTTAGCGGCGCTTAAGCAAAA
** * * *
44536181 AACGCCACTATAGACTGTGGTCTTTAGTGGCGC-TGACCAAAA
1 AACGCCACTATAGACCATGGTCTTTAGCGGCGCTTAAGCAAAA
* * * *
44536223 AATGCCACTATAGACCATGGTCTTTAGTGGCGCTTAGGCGAAA
1 AACGCCACTATAGACCATGGTCTTTAGCGGCGCTTAAGCAAAA
* * *
44536266 AACGCCACTATAGACCATGGTCTTTCGCGGCGCTTAGGCGAAA
1 AACGCCACTATAGACCATGGTCTTTAGCGGCGCTTAAGCAAAA
* * * * *
44536309 AATGCCACTATAGACCATTGTCTTTCGCGGCGCTTAGGAAAAA
1 AACGCCACTATAGACCATGGTCTTTAGCGGCGCTTAAGCAAAA
* * *
44536352 AATGCCACTATAGACCATGGTCTTTAGTGGCGCTTATGCAAAA
1 AACGCCACTATAGACCATGGTCTTTAGCGGCGCTTAAGCAAAA
44536395 AACGCC
1 AACGCC
44536401 GCTAATTTTG
Statistics
Matches: 498, Mismatches: 59, Indels: 7
0.88 0.10 0.01
Matches are distributed among these distances:
40 1 0.00
41 34 0.07
42 103 0.21
43 360 0.72
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (43 bp):
AACGCCACTATAGACCATGGTCTTTAGCGGCGCTTAAGCAAAA
Found at i:44536080 original size:171 final size:172
Alignment explanation
Indices: 44535798--44536400 Score: 786
Period size: 171 Copynumber: 3.5 Consensus size: 172
44535788 TTTTTTTTAC
* * * * * *
44535798 AACGCCGCTATAGACCATGTTCTTTAGCGGCGCTTAA-ATAAAAACACCACTATAGACCGTGATC
1 AACGCCACTATAGACCATGGTCTTTAGCGGCGCTTAAGAAAAAAACGCCACTATAGACCATGGTC
* * * * *
44535862 TTTAGCGGCGCTTAA--AAAAAACGCCACTATAAACCGTGGTCTTTAGCGACGCTTA-CCAAAAA
66 TTTAGCGGCGCTTAACCAAAAAACGCCACTATAGACCATGGTCTTTAGCGGCGCTTAGGCGAAAA
* * * * *
44535924 ATGCCACTATAGACCATGGTCTTTAGCGGTGCTTA-ACCAACA
131 ACGCCACTATAGACCATGGTCTTTCGCGGCGCTTAGGCGAA-A
* ** * * *
44535966 AACGCCACTACAGACCATGGTCTTTAGCGGCGCTTAACCAACAAATGCCACTACAGACCATGGTC
1 AACGCCACTATAGACCATGGTCTTTAGCGGCGCTTAAGAAAAAAACGCCACTATAGACCATGGTC
*
44536031 TTTAGCGGCGCTTAACCAACAAACGCCACTATAGACCATGGTCTTTAGCGGCGCTTAGGCGAAAA
66 TTTAGCGGCGCTTAACCAAAAAACGCCACTATAGACCATGGTCTTTAGCGGCGCTTAGGCGAAAA
44536096 ACGCCACTATAGACCATGGTCTTTCGCGGCGCTTAGGCGAAA
131 ACGCCACTATAGACCATGGTCTTTCGCGGCGCTTAGGCGAAA
* * * * **
44536138 AACGCCAATATAGACCATGGTTTTTCGCGGCGCTTAGGAAAAAAACGCCACTATAGACTGTGGTC
1 AACGCCACTATAGACCATGGTCTTTAGCGGCGCTTAAGAAAAAAACGCCACTATAGACCATGGTC
* * * *
44536203 TTTAGTGGCGC-TGACCAAAAAATGCCACTATAGACCATGGTCTTTAGTGGCGCTTAGGCGAAAA
66 TTTAGCGGCGCTTAACCAAAAAACGCCACTATAGACCATGGTCTTTAGCGGCGCTTAGGCGAAAA
44536267 ACGCCACTATAGACCATGGTCTTTCGCGGCGCTTAGGCGAAA
131 ACGCCACTATAGACCATGGTCTTTCGCGGCGCTTAGGCGAAA
* * * * *
44536309 AATGCCACTATAGACCATTGTCTTTCGCGGCGCTTAGGAAAAAAATGCCACTATAGACCATGGTC
1 AACGCCACTATAGACCATGGTCTTTAGCGGCGCTTAAGAAAAAAACGCCACTATAGACCATGGTC
* **
44536374 TTTAGTGGCGCTTATGCAAAAAACGCC
66 TTTAGCGGCGCTTAACCAAAAAACGCC
44536401 GCTAATTTTG
Statistics
Matches: 379, Mismatches: 50, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
168 34 0.09
169 34 0.09
171 196 0.52
172 112 0.30
173 3 0.01
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (172 bp):
AACGCCACTATAGACCATGGTCTTTAGCGGCGCTTAAGAAAAAAACGCCACTATAGACCATGGTC
TTTAGCGGCGCTTAACCAAAAAACGCCACTATAGACCATGGTCTTTAGCGGCGCTTAGGCGAAAA
ACGCCACTATAGACCATGGTCTTTCGCGGCGCTTAGGCGAAA
Found at i:44536836 original size:21 final size:21
Alignment explanation
Indices: 44536812--44536851 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
44536802 TTTCGTTGAA
44536812 CCTCAACTTCTCTCGCTGCTG
1 CCTCAACTTCTCTCGCTGCTG
**
44536833 CCTCTGCTTCTCTCGCTGC
1 CCTCAACTTCTCTCGCTGC
44536852 CGCATCTGCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.05, C:0.45, G:0.15, T:0.35
Consensus pattern (21 bp):
CCTCAACTTCTCTCGCTGCTG
Found at i:44536837 original size:87 final size:87
Alignment explanation
Indices: 44536745--44536928 Score: 273
Period size: 87 Copynumber: 2.1 Consensus size: 87
44536735 ACTCGCTTTA
44536745 GCCTCTGCTTCTCTCGCTGCCGCATCTGCTTTAAGCTGCT-GCTGGAGTTCTTCAT-GCTTTCGT
1 GCCTCTGCTTCTCTCGCTGCCGCATCTGCTTTAAGCTG-TAGCTGGAGTTCTTCATAGCTTT-GT
*
44536808 TGAACCTCAACTTCTCTCGCTGCT
64 TGAACCTCAACTTCTCTCGATGCT
* * *
44536832 GCCTCTGCTTCTCTCGCTGCCGCATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATCTTTTTTG
1 GCCTCTGCTTCTCTCGCTGCCGCATCTGCTTTAAGCTGTAGCTGGAGTTCTTCATAGCTTTGTTG
* *
44536897 AACCTCAGCTTCTCTCGATGTT
66 AACCTCAACTTCTCTCGATGCT
*
44536919 GCCTCCGCTT
1 GCCTCTGCTT
44536929 TAAGTTGTGT
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
86 1 0.01
87 83 0.94
88 4 0.05
ACGTcount: A:0.11, C:0.32, G:0.19, T:0.39
Consensus pattern (87 bp):
GCCTCTGCTTCTCTCGCTGCCGCATCTGCTTTAAGCTGTAGCTGGAGTTCTTCATAGCTTTGTTG
AACCTCAACTTCTCTCGATGCT
Found at i:44536859 original size:21 final size:21
Alignment explanation
Indices: 44536818--44536862 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
44536808 TGAACCTCAA
* *
44536818 CTTCTCTCGCTGCTGCCTCTG
1 CTTCTCTCGCTGCCGCATCTG
44536839 CTTCTCTCGCTGCCGCATCTG
1 CTTCTCTCGCTGCCGCATCTG
44536860 CTT
1 CTT
44536863 TAAGTTGTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.02, C:0.42, G:0.18, T:0.38
Consensus pattern (21 bp):
CTTCTCTCGCTGCCGCATCTG
Found at i:44542637 original size:9 final size:9
Alignment explanation
Indices: 44542623--44542867 Score: 113
Period size: 9 Copynumber: 26.6 Consensus size: 9
44542613 TGTCGTATTA
44542623 ATGTAAGTT
1 ATGTAAGTT
*
44542632 ATGTAATTT
1 ATGTAAGTT
*
44542641 ATGTATAATATT
1 ATG--TAA-GTT
44542653 AATGTAAGTT
1 -ATGTAAGTT
44542663 ATGTAAG-T
1 ATGTAAGTT
44542671 -TGTAAGTT
1 ATGTAAGTT
*
44542679 ATGTAATTT
1 ATGTAAGTT
*
44542688 ATGTATAATATT
1 ATG--TAA-GTT
44542700 AATGTAAGTT
1 -ATGTAAGTT
44542710 ATGTAAG-T
1 ATGTAAGTT
44542718 -TGTAAGTT
1 ATGTAAGTT
*
44542726 ATGTATA-AT
1 ATGTA-AGTT
44542735 AT-TAA-TT
1 ATGTAAGTT
44542742 AAT-TAAGTT
1 -ATGTAAGTT
*
44542751 ATGTAATTT
1 ATGTAAGTT
*
44542760 ATGTATAATATT
1 ATG--TAA-GTT
44542772 AATGTAAGTT
1 -ATGTAAGTT
*
44542782 ATGTAATTT
1 ATGTAAGTT
*
44542791 ATGTATAATATT
1 ATG--TAA-GTT
44542803 AATGTAAGTT
1 -ATGTAAGTT
44542813 ATGTAAG-T
1 ATGTAAGTT
44542821 -TGTAAGTT
1 ATGTAAGTT
*
44542829 ATGTATA-AT
1 ATGTA-AGTT
44542838 AT-TAA-TT
1 ATGTAAGTT
44542845 AAT-TAAGTT
1 -ATGTAAGTT
*
44542854 ATGTAATTT
1 ATGTAAGTT
44542863 ATGTA
1 ATGTA
44542868 TAATATTAAT
Statistics
Matches: 189, Mismatches: 17, Indels: 60
0.71 0.06 0.23
Matches are distributed among these distances:
7 22 0.12
8 24 0.13
9 89 0.47
10 10 0.05
11 24 0.13
12 8 0.04
13 12 0.06
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.47
Consensus pattern (9 bp):
ATGTAAGTT
Found at i:44542676 original size:16 final size:15
Alignment explanation
Indices: 44542624--44542833 Score: 88
Period size: 16 Copynumber: 13.9 Consensus size: 15
44542614 GTCGTATTAA
44542624 TGTAAGTTATGTAAT
1 TGTAAGTTATGTAAT
* *
44542639 T-TATGTATAATATTAA-
1 TGTAAGT-T-AT-GTAAT
44542655 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAA-T
44542671 TGTAAGTTATGTAAT
1 TGTAAGTTATGTAAT
* *
44542686 T-TATGTATAATATTAA-
1 TGTAAGT-T-AT-GTAAT
44542702 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAA-T
44542718 TGTAAGTTATGT-AT
1 TGTAAGTTATGTAAT
**
44542732 AAT-A-TTAAT-TAA-
1 TGTAAGTT-ATGTAAT
44542744 T-TAAGTTATGTAAT
1 TGTAAGTTATGTAAT
* *
44542758 T-TATGTATAATATTAA-
1 TGTAAGT-T-AT-GTAAT
44542774 TGTAAGTTATGTAAT
1 TGTAAGTTATGTAAT
* *
44542789 T-TATGTATAATATTAA-
1 TGTAAGT-T-AT-GTAAT
44542805 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAA-T
44542821 TGTAAGTTATGTA
1 TGTAAGTTATGTA
44542834 TAATATTAAT
Statistics
Matches: 147, Mismatches: 19, Indels: 57
0.66 0.09 0.26
Matches are distributed among these distances:
11 1 0.01
12 6 0.04
13 9 0.06
14 31 0.21
15 17 0.12
16 55 0.37
17 28 0.19
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (15 bp):
TGTAAGTTATGTAAT
Found at i:44542685 original size:47 final size:48
Alignment explanation
Indices: 44542624--44542730 Score: 200
Period size: 47 Copynumber: 2.3 Consensus size: 48
44542614 GTCGTATTAA
44542624 TGTAAGTTATGTAAT-TTATGTATAATATTAATGTAAGTTATGTAAGT
1 TGTAAGTTATGTAATATTATGTATAATATTAATGTAAGTTATGTAAGT
44542671 TGTAAGTTATGTAAT-TTATGTATAATATTAATGTAAGTTATGTAAGT
1 TGTAAGTTATGTAATATTATGTATAATATTAATGTAAGTTATGTAAGT
44542718 TGTAAGTTATGTA
1 TGTAAGTTATGTA
44542731 TAATATTAAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 60 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.47
Consensus pattern (48 bp):
TGTAAGTTATGTAATATTATGTATAATATTAATGTAAGTTATGTAAGT
Found at i:44542759 original size:72 final size:71
Alignment explanation
Indices: 44542663--44542879 Score: 261
Period size: 72 Copynumber: 3.1 Consensus size: 71
44542653 AATGTAAGTT
44542663 ATGTAAGTTGTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTAAGTTGTAAGTTAT
1 ATGTAAG-T-TAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTAA--TGTAA-TTAT
44542728 GTATAATATTA
61 GTATAATATTA
44542739 AT-TAA-TTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTAA--T--TTATGTATA
1 ATGTAAGTTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTAATGTAATTATGTATA
44542798 ATATTA
66 ATATTA
* * * * *
44542804 ATGTAAGTTATGTAAGTTGTAAGTTATGTATAATATTAAT-TAA-TTAAGTTATGTAATTTATGT
1 ATGTAAGTTAAGTTA--TGTAATTTATGTATAATATTAATGTAAGTTATGTAATGTAA-TTATGT
44542867 ATAATATTA
63 ATAATATTA
44542876 ATGT
1 ATGT
44542880 GGCTTCTACG
Statistics
Matches: 127, Mismatches: 5, Indels: 22
0.82 0.03 0.14
Matches are distributed among these distances:
65 17 0.13
66 3 0.02
67 12 0.09
68 4 0.03
69 23 0.18
72 62 0.49
73 1 0.01
75 3 0.02
76 2 0.02
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.47
Consensus pattern (71 bp):
ATGTAAGTTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTAATGTAATTATGTATA
ATATTA
Found at i:44542794 original size:103 final size:103
Alignment explanation
Indices: 44542671--44542879 Score: 418
Period size: 103 Copynumber: 2.0 Consensus size: 103
44542661 TTATGTAAGT
44542671 TGTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTAAGTTGTAAGTTATGTATAATA
1 TGTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTAAGTTGTAAGTTATGTATAATA
44542736 TTAATTAATTAAGTTATGTAATTTATGTATAATATTAA
66 TTAATTAATTAAGTTATGTAATTTATGTATAATATTAA
44542774 TGTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTAAGTTGTAAGTTATGTATAATA
1 TGTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTAAGTTGTAAGTTATGTATAATA
44542839 TTAATTAATTAAGTTATGTAATTTATGTATAATATTAA
66 TTAATTAATTAAGTTATGTAATTTATGTATAATATTAA
44542877 TGT
1 TGT
44542880 GGCTTCTACG
Statistics
Matches: 106, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 106 1.00
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (103 bp):
TGTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTAAGTTGTAAGTTATGTATAATA
TTAATTAATTAAGTTATGTAATTTATGTATAATATTAA
Found at i:44543434 original size:47 final size:47
Alignment explanation
Indices: 44543359--44543452 Score: 143
Period size: 47 Copynumber: 2.0 Consensus size: 47
44543349 AACGCTAGAC
*
44543359 CACCTCCACATGCATTAATCAAATCCTAAATTATATTTTAGAAGGGG
1 CACCTCCACATGCATTAATCAAACCCTAAATTATATTTTAGAAGGGG
* * * *
44543406 CACCTCCATATGCATTAATCAAGCCCTAAATTATCTTTTGGAAGGGG
1 CACCTCCACATGCATTAATCAAACCCTAAATTATATTTTAGAAGGGG
44543453 AATCGAAGCA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (47 bp):
CACCTCCACATGCATTAATCAAACCCTAAATTATATTTTAGAAGGGG
Found at i:44544552 original size:16 final size:16
Alignment explanation
Indices: 44544533--44544573 Score: 64
Period size: 16 Copynumber: 2.5 Consensus size: 16
44544523 TATTTATTTA
44544533 TTTATTACCTGTATCT
1 TTTATTACCTGTATCT
*
44544549 TTTATTAACTGTATCT
1 TTTATTACCTGTATCT
44544565 TTTAATTAC
1 TTT-ATTAC
44544574 TAAGTATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.24, C:0.15, G:0.05, T:0.56
Consensus pattern (16 bp):
TTTATTACCTGTATCT
Found at i:44546028 original size:13 final size:14
Alignment explanation
Indices: 44545993--44546033 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
44545983 GCCACCCCTA
*
44545993 AAGT-CTAAACCGT
1 AAGTCCTAAACCAT
*
44546006 AAGTCATAAACCAT
1 AAGTCCTAAACCAT
44546020 AA-TCCTAAACCAT
1 AAGTCCTAAACCAT
44546033 A
1 A
44546034 TCTTTGAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 15 0.62
14 9 0.38
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.22
Consensus pattern (14 bp):
AAGTCCTAAACCAT
Found at i:44553365 original size:18 final size:19
Alignment explanation
Indices: 44553330--44553367 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
44553320 GATAATTCTA
44553330 AAAAAATTATTTAAATTTTC
1 AAAAAATTATTT-AATTTTC
44553350 AAAAAATTATTT-ATTTTC
1 AAAAAATTATTTAATTTTC
44553368 TAAATATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.33
20 12 0.67
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (19 bp):
AAAAAATTATTTAATTTTC
Found at i:44557166 original size:20 final size:20
Alignment explanation
Indices: 44557141--44557179 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
44557131 TAAGCCCAAT
44557141 AAACCATTAAACTTACCACC
1 AAACCATTAAACTTACCACC
44557161 AAACCATTAAACTTACCAC
1 AAACCATTAAACTTACCAC
44557180 TAAAGATAAG
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:0.46, C:0.33, G:0.00, T:0.21
Consensus pattern (20 bp):
AAACCATTAAACTTACCACC
Found at i:44560400 original size:17 final size:17
Alignment explanation
Indices: 44560380--44560417 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
44560370 TTAAAGTTCA
44560380 CAAGGAAGTAAAGGCTG
1 CAAGGAAGTAAAGGCTG
*
44560397 CAAGGAAGTAGAGGCTG
1 CAAGGAAGTAAAGGCTG
44560414 CAAG
1 CAAG
44560418 TTCCTGGGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.39, C:0.13, G:0.37, T:0.11
Consensus pattern (17 bp):
CAAGGAAGTAAAGGCTG
Found at i:44560705 original size:33 final size:33
Alignment explanation
Indices: 44560658--44560725 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
44560648 ATATACATAT
*
44560658 ATTCATACCTAACACTAATCTCATTTAACTCGA
1 ATTCATACCCAACACTAATCTCATTTAACTCGA
*
44560691 ATTCATACCCAACACTCATCTCATTTAACTCGA
1 ATTCATACCCAACACTAATCTCATTTAACTCGA
44560724 AT
1 AT
44560726 AACATAGATG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.32
Consensus pattern (33 bp):
ATTCATACCCAACACTAATCTCATTTAACTCGA
Found at i:44562855 original size:42 final size:41
Alignment explanation
Indices: 44562710--44563030 Score: 356
Period size: 41 Copynumber: 7.8 Consensus size: 41
44562700 AAGGTTAATA
* * * * **
44562710 CATTCGCGGCGCTTAGATACAAACGCCGCTGA-ATACAGGAG
1 CATTAGCGGCGCTTAGACAAAAACGCCGCT-ATAGACCCGAG
* * * * * * *
44562751 AATTAGCGGCGCATATATAAAAACGCCGCTAAAAACCTGAG
1 CATTAGCGGCGCTTAGACAAAAACGCCGCTATAGACCCGAG
* * *
44562792 CATTAGCGGCGCATAGGCGAAAACGCCGCTATAGACCCAGAG
1 CATTAGCGGCGCTTAGACAAAAACGCCGCTATAGACCC-GAG
* * *
44562834 CATTAGCGGCGCTTAGACGAAAACGCCGCTAAAGACTCGGAG
1 CATTAGCGGCGCTTAGACAAAAACGCCGCTATAGAC-CCGAG
* * * * *
44562876 CATTAGCGGCACTTAGACGAAAGCGCCGCTAAAGACTCGGAG
1 CATTAGCGGCGCTTAGACAAAAACGCCGCTATAGAC-CCGAG
44562918 CATTAGCGGCGCTTAGACAAAAACGCCGCTATAGACCCGAG
1 CATTAGCGGCGCTTAGACAAAAACGCCGCTATAGACCCGAG
* *
44562959 CATTAGCGGCGCTTAGACAAAGACGCTGCTATAGACCCGAG
1 CATTAGCGGCGCTTAGACAAAAACGCCGCTATAGACCCGAG
*
44563000 CATTAGCGGCGCTTAGATAAAAACGCCGCTA
1 CATTAGCGGCGCTTAGACAAAAACGCCGCTA
44563031 AATGTTTAAA
Statistics
Matches: 245, Mismatches: 32, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
40 1 0.00
41 132 0.54
42 111 0.45
43 1 0.00
ACGTcount: A:0.32, C:0.26, G:0.26, T:0.16
Consensus pattern (41 bp):
CATTAGCGGCGCTTAGACAAAAACGCCGCTATAGACCCGAG
Found at i:44562905 original size:84 final size:82
Alignment explanation
Indices: 44562752--44563032 Score: 375
Period size: 84 Copynumber: 3.4 Consensus size: 82
44562742 ATACAGGAGA
* * * * * * * *
44562752 ATTAGCGGCGCATATATAAAAACGCCGCTAAAAACCTGAGCATTAGCGGCGCATAGGCGAAAACG
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGACCCGAGCATTAGCGGCGCTTAGACGAAAGCG
44562817 CCGCTATAGACCCAGAGC
66 CCGCTATAGACCC-GAGC
* * *
44562835 ATTAGCGGCGCTTAGACGAAAACGCCGCTAAAGACTCGGAGCATTAGCGGCACTTAGACGAAAGC
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGAC-CCGAGCATTAGCGGCGCTTAGACGAAAGC
* *
44562900 GCCGCTAAAGACTCGGAGC
65 GCCGCTATAGAC-CCGAGC
*
44562919 ATTAGCGGCGCTTAGACAAAAACGCCGCTATAGACCCGAGCATTAGCGGCGCTTAGAC-AAAGAC
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGACCCGAGCATTAGCGGCGCTTAGACGAAAG-C
*
44562983 GCTGCTATAGACCCGAGC
65 GCCGCTATAGACCCGAGC
*
44563001 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAA
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAA
44563033 TGTTTAAAAA
Statistics
Matches: 174, Mismatches: 21, Indels: 7
0.86 0.10 0.03
Matches are distributed among these distances:
82 39 0.22
83 62 0.36
84 72 0.41
85 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.26, T:0.15
Consensus pattern (82 bp):
ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGACCCGAGCATTAGCGGCGCTTAGACGAAAGCG
CCGCTATAGACCCGAGC
Found at i:44563180 original size:40 final size:40
Alignment explanation
Indices: 44563114--44563191 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 40
44563104 AATTCCTATT
*
44563114 TTTAGCGGCGCTTCCGTATAAACGCCGCTGATGCTCTACC
1 TTTAGCGGCGCTTCCGTATAAACGCCGCTAATGCTCTACC
** *
44563154 TTTAGCGGCGCTTTGGCTA-AATCGCCGCTAATGCTCTA
1 TTTAGCGGCGCTTCCG-TATAAACGCCGCTAATGCTCTA
44563192 TTTTTTGTGG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 31 0.94
41 2 0.06
ACGTcount: A:0.18, C:0.29, G:0.23, T:0.29
Consensus pattern (40 bp):
TTTAGCGGCGCTTCCGTATAAACGCCGCTAATGCTCTACC
Found at i:44564363 original size:2 final size:2
Alignment explanation
Indices: 44564356--44564383 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
44564346 GTAAAAATTA
44564356 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
44564384 TGAATTAAAT
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:44569183 original size:22 final size:24
Alignment explanation
Indices: 44569131--44569189 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 24
44569121 AGATATACCT
*
44569131 ATATATATATATAAAAGAGTATTC
1 ATATATATATATAAAAGAGTATTA
*
44569155 ATGTATATAT-TAAATA-AGT-TTA
1 ATATATATATATAAA-AGAGTATTA
44569177 ATATATATATATA
1 ATATATATATATA
44569190 TGTATACGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
22 11 0.37
23 9 0.30
24 10 0.33
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.42
Consensus pattern (24 bp):
ATATATATATATAAAAGAGTATTA
Found at i:44569313 original size:29 final size:29
Alignment explanation
Indices: 44569281--44569336 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
44569271 ATGAGTGGAA
44569281 ATATAATGATAATAATAATAACATTAATG
1 ATATAATGATAATAATAATAACATTAATG
* * * *
44569310 ATATGATGATAGTAGTAATAAGATTAA
1 ATATAATGATAATAATAATAACATTAA
44569337 AATAATTAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.52, C:0.02, G:0.12, T:0.34
Consensus pattern (29 bp):
ATATAATGATAATAATAATAACATTAATG
Found at i:44571120 original size:27 final size:26
Alignment explanation
Indices: 44571069--44571121 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
44571059 CTCTCTCTTT
*
44571069 TTTCTCTTTATTTTCCATTATCTTCTG
1 TTTCTCTTTATTTTCCA-TACCTTCTG
44571096 TTTCTCCTTCTATTTTCC-TACCTTCT
1 TTTCT-CTT-TATTTTCCATACCTTCT
44571122 CCATGTCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 12 0.52
28 3 0.13
29 8 0.35
ACGTcount: A:0.09, C:0.28, G:0.02, T:0.60
Consensus pattern (26 bp):
TTTCTCTTTATTTTCCATACCTTCTG
Found at i:44592554 original size:44 final size:46
Alignment explanation
Indices: 44592489--44592586 Score: 137
Period size: 47 Copynumber: 2.1 Consensus size: 46
44592479 TTTATGAGAT
* * *
44592489 TATATGTTCATGGTAAAAATAAG-AAACTAATGCAACATTTCGATA
1 TATATGTTCATAGTAAAAATAAGAAAACTAATGCAACATTTCAACA
44592534 TATATGTTCA-AGTAAAAATAAGATCAAACTAATGCAACATTTCAACA
1 TATATGTTCATAGTAAAAATAAGA--AAACTAATGCAACATTTCAACA
44592581 TATATG
1 TATATG
44592587 ATACATTCAA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
44 11 0.23
45 10 0.21
47 26 0.55
ACGTcount: A:0.46, C:0.12, G:0.11, T:0.31
Consensus pattern (46 bp):
TATATGTTCATAGTAAAAATAAGAAAACTAATGCAACATTTCAACA
Found at i:44592599 original size:47 final size:47
Alignment explanation
Indices: 44592512--44592608 Score: 117
Period size: 47 Copynumber: 2.1 Consensus size: 47
44592502 TAAAAATAAG
* * *
44592512 AAACTAATGCAACATTTCGATATATATGTTCAAGTAAAAAT-AAGATC
1 AAACTAATGCAACATTTCAACATATATGTACAAGTAAAAATCAA-ATC
* *
44592559 AAACTAATGCAACATTTCAACATATATGATAC-ATTCAAAATCAAATC
1 AAACTAATGCAACATTTCAACATATATG-TACAAGTAAAAATCAAATC
44592606 AAA
1 AAA
44592609 TCAAATAAAG
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
47 39 0.91
48 4 0.09
ACGTcount: A:0.49, C:0.15, G:0.07, T:0.28
Consensus pattern (47 bp):
AAACTAATGCAACATTTCAACATATATGTACAAGTAAAAATCAAATC
Found at i:44597627 original size:55 final size:55
Alignment explanation
Indices: 44597543--44597771 Score: 262
Period size: 55 Copynumber: 4.2 Consensus size: 55
44597533 CTTCTTTTGG
* * * * * * *
44597543 ATCGATTATCATGTTGGAATAGTGCTTCTTTTGAGTCAATTCTTTATATGTTTAA
1 ATCGATTGTCATGTTGGAATACTACTTCTTTTGAATCGATTCTGTATATGATTAA
* * *
44597598 ATCGATTGTCAAGTTGGAACACTACTTCTTTTGAATCGATTGTGTATATGATTAA
1 ATCGATTGTCATGTTGGAATACTACTTCTTTTGAATCGATTCTGTATATGATTAA
* * * * * *
44597653 ATTGATTGTTATGTTGGAATACTGCTTCTTTTTAATTGATTGTGTATATGATTAA
1 ATCGATTGTCATGTTGGAATACTACTTCTTTTGAATCGATTCTGTATATGATTAA
* * * *
44597708 ATCGATTATTATGTTGGAATATTACTTCTTTTGAATCGATTGCT-TATATGTTTAA
1 ATCGATTGTCATGTTGGAATACTACTTCTTTTGAATCGATT-CTGTATATGATTAA
44597763 ATCGATTGT
1 ATCGATTGT
44597772 TACATAACAC
Statistics
Matches: 147, Mismatches: 26, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
55 146 0.99
56 1 0.01
ACGTcount: A:0.27, C:0.10, G:0.17, T:0.47
Consensus pattern (55 bp):
ATCGATTGTCATGTTGGAATACTACTTCTTTTGAATCGATTCTGTATATGATTAA
Found at i:44597746 original size:110 final size:110
Alignment explanation
Indices: 44597543--44597773 Score: 293
Period size: 110 Copynumber: 2.1 Consensus size: 110
44597533 CTTCTTTTGG
* * * * * * *
44597543 ATCGATTATCATGTTGGAATAGTGCTTCTTTTGAGTCAATTCTTTATATGTTTAAATCGATTGTC
1 ATCGATTGTTATGTTGGAATACTGCTTCTTTTGAATCAATTCTGTATATGATTAAATCGATTATC
44597608 AAGTTGGAACACTACTTCTTTTGAATCGATTG-TGTATATGATTAA
66 AAGTTGGAACACTACTTCTTTTGAATCGATTGCT-TATATGATTAA
* * ** * *
44597653 ATTGATTGTTATGTTGGAATACTGCTTCTTTTTAATTGATTGTGTATATGATTAAATCGATTATT
1 ATCGATTGTTATGTTGGAATACTGCTTCTTTTGAATCAATTCTGTATATGATTAAATCGATTATC
* * * *
44597718 ATGTTGGAATATTACTTCTTTTGAATCGATTGCTTATATGTTTAA
66 AAGTTGGAACACTACTTCTTTTGAATCGATTGCTTATATGATTAA
44597763 ATCGATTGTTA
1 ATCGATTGTTA
44597774 CATAACACAT
Statistics
Matches: 102, Mismatches: 18, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
110 101 0.99
111 1 0.01
ACGTcount: A:0.27, C:0.10, G:0.17, T:0.47
Consensus pattern (110 bp):
ATCGATTGTTATGTTGGAATACTGCTTCTTTTGAATCAATTCTGTATATGATTAAATCGATTATC
AAGTTGGAACACTACTTCTTTTGAATCGATTGCTTATATGATTAA
Found at i:44598872 original size:28 final size:29
Alignment explanation
Indices: 44598828--44598884 Score: 98
Period size: 28 Copynumber: 2.0 Consensus size: 29
44598818 TGTTAATATT
*
44598828 CATTTGGTCCTTTATCAATACTTGCACAA
1 CATTTGGTCCCTTATCAATACTTGCACAA
44598857 CATTT-GTCCCTTATCAATACTTGCACAA
1 CATTTGGTCCCTTATCAATACTTGCACAA
44598885 AAATAACTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 22 0.81
29 5 0.19
ACGTcount: A:0.28, C:0.26, G:0.09, T:0.37
Consensus pattern (29 bp):
CATTTGGTCCCTTATCAATACTTGCACAA
Found at i:44599063 original size:55 final size:55
Alignment explanation
Indices: 44598999--44599138 Score: 210
Period size: 55 Copynumber: 2.5 Consensus size: 55
44598989 ACTACTTTTT
* *
44598999 CTTCTTTTGAATCGATTGTTTATATGTTTAAATCGGTTGTTGTGTTGGAATACT-
1 CTTCTTTTGAATCGATTGTTTATATGTTTAAATCGATTGTTATGTTGGAATACTA
* * * *
44599053 GTTGCTTTTGAATCCATTGTTTATATGTTCAAATTGATTGTTATGTTGGAATACTA
1 CTT-CTTTTGAATCGATTGTTTATATGTTTAAATCGATTGTTATGTTGGAATACTA
44599109 CTTCTTTTGAATCGATTGTTTATATGTTTA
1 CTTCTTTTGAATCGATTGTTTATATGTTTA
44599139 GATCATTTGT
Statistics
Matches: 75, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
54 2 0.03
55 71 0.95
56 2 0.03
ACGTcount: A:0.22, C:0.09, G:0.18, T:0.51
Consensus pattern (55 bp):
CTTCTTTTGAATCGATTGTTTATATGTTTAAATCGATTGTTATGTTGGAATACTA
Found at i:44601329 original size:76 final size:74
Alignment explanation
Indices: 44601229--44601437 Score: 292
Period size: 74 Copynumber: 2.8 Consensus size: 74
44601219 CTAGAAAAGT
* *
44601229 CAAACACAAATACAGTCTGTATCTTCAGTTCATAAACATCCCAATAAACCATTGGGATTCAAACA
1 CAAACAC--ATACTGTCTGTATCTTCAGTTCATAAACATCCCAATAAACCATTGAGATTCAAACA
44601294 CAAAACCATCACA
64 C--AACCATCACA
* * *
44601307 CAAACACATATTGTCTGCATCTTCAGTTCATAAACATCCCAATAAACCATTGACATTCAAACACA
1 CAAACACATACTGTCTGTATCTTCAGTTCATAAACATCCCAATAAACCATTGAGATTCAAACACA
44601372 ACCATCACA
66 ACCATCACA
** * * *
44601381 CAAATGCATACTGGCAGTATCTTCAGTTCATAAACATCCCAATACACCATTGAGATT
1 CAAACACATACTGTCTGTATCTTCAGTTCATAAACATCCCAATAAACCATTGAGATT
44601438 GTATTTCAAA
Statistics
Matches: 118, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
74 59 0.50
76 52 0.44
78 7 0.06
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.24
Consensus pattern (74 bp):
CAAACACATACTGTCTGTATCTTCAGTTCATAAACATCCCAATAAACCATTGAGATTCAAACACA
ACCATCACA
Found at i:44601551 original size:42 final size:42
Alignment explanation
Indices: 44601490--44601626 Score: 211
Period size: 42 Copynumber: 3.3 Consensus size: 42
44601480 CAACCTGGCT
** * *
44601490 AGCTTCAGTTGGTTTTCTTTTAACTCAGCTTCGTCCTGATCC
1 AGCTTCAGTTTCTTCTCTTTTAAGTCAGCTTCGTCCTGATCC
44601532 AGCTTCAGTTTCTTCTCTTTTAAGTCAGCTTCGTCCTGATCC
1 AGCTTCAGTTTCTTCTCTTTTAAGTCAGCTTCGTCCTGATCC
* **
44601574 AGCTTCAGTTTCTTCTCTTTTAAGTCAGCTTCATCCTTCTCC
1 AGCTTCAGTTTCTTCTCTTTTAAGTCAGCTTCGTCCTGATCC
44601616 AGCTTCAGTTT
1 AGCTTCAGTTT
44601627 GTCTTTTCTA
Statistics
Matches: 88, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 88 1.00
ACGTcount: A:0.15, C:0.28, G:0.14, T:0.44
Consensus pattern (42 bp):
AGCTTCAGTTTCTTCTCTTTTAAGTCAGCTTCGTCCTGATCC
Found at i:44608408 original size:57 final size:57
Alignment explanation
Indices: 44608318--44608433 Score: 223
Period size: 57 Copynumber: 2.0 Consensus size: 57
44608308 AACAAATGGA
*
44608318 CTCCCAATCTACTTTTGGATGCCCAGCATAACCACCCCAAATGAACTGCCTTGCTAT
1 CTCCCAATCTACTTTTGGATGCCCAGCAGAACCACCCCAAATGAACTGCCTTGCTAT
44608375 CTCCCAATCTACTTTTGGATGCCCAGCAGAACCACCCCAAATGAACTGCCTTGCTAT
1 CTCCCAATCTACTTTTGGATGCCCAGCAGAACCACCCCAAATGAACTGCCTTGCTAT
44608432 CT
1 CT
44608434 TCTCTCCTTT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.26, C:0.35, G:0.13, T:0.26
Consensus pattern (57 bp):
CTCCCAATCTACTTTTGGATGCCCAGCAGAACCACCCCAAATGAACTGCCTTGCTAT
Found at i:44610265 original size:24 final size:24
Alignment explanation
Indices: 44610219--44610265 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
44610209 ATGTGTGGTA
*
44610219 CAAATTGAAAAAAATAAACAAAAT
1 CAAATTGAAAAAAACAAACAAAAT
*
44610243 CAAATTGAAACAACACAAA-AAAA
1 CAAATTGAAA-AAAACAAACAAAA
44610266 GGGACTTGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.70, C:0.13, G:0.04, T:0.13
Consensus pattern (24 bp):
CAAATTGAAAAAAACAAACAAAAT
Found at i:44613918 original size:16 final size:17
Alignment explanation
Indices: 44613897--44613936 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
44613887 ATAATTATAA
44613897 TTAAAATA-AATCCAAT
1 TTAAAATACAATCCAAT
*
44613913 TTAAAATACAATCGAAT
1 TTAAAATACAATCCAAT
44613930 TTAAAAT
1 TTAAAAT
44613937 CAAAGTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.55, C:0.10, G:0.03, T:0.33
Consensus pattern (17 bp):
TTAAAATACAATCCAAT
Found at i:44623277 original size:36 final size:36
Alignment explanation
Indices: 44623209--44623281 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 36
44623199 AACGGTCTCA
* * *
44623209 AGCAACTTGCTTTTTGCACGGTCGTCACAGCGTAAG
1 AGCAACTTGCTTTTTACACGATCGTCAAAGCGTAAG
*
44623245 AGCAACTTGCTTTTTACAC-ATTGTTCAAAGCGTAAG
1 AGCAACTTGCTTTTTACACGATCG-TCAAAGCGTAAG
44623281 A
1 A
44623282 TCCCTATTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 2 0.06
36 30 0.94
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (36 bp):
AGCAACTTGCTTTTTACACGATCGTCAAAGCGTAAG
Found at i:44625125 original size:33 final size:33
Alignment explanation
Indices: 44625086--44625157 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
44625076 TCATTTTACT
* * * *
44625086 TTAAAAAAAT-T-CTTAACAATAATTCTAAATTT
1 TTAAAAAAATATATTTAA-AATAAATATAAATTA
44625118 TTAAAAAAATATATTTAAAATAAATATAAATTA
1 TTAAAAAAATATATTTAAAATAAATATAAATTA
44625151 TTAAAAA
1 TTAAAAA
44625158 TTATGTTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
32 10 0.29
33 20 0.59
34 4 0.12
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (33 bp):
TTAAAAAAATATATTTAAAATAAATATAAATTA
Found at i:44625136 original size:14 final size:15
Alignment explanation
Indices: 44625117--44625145 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
44625107 ATTCTAAATT
44625117 TTTAAAA-AAATATA
1 TTTAAAATAAATATA
44625131 TTTAAAATAAATATA
1 TTTAAAATAAATATA
44625146 AATTATTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
TTTAAAATAAATATA
Found at i:44625157 original size:32 final size:33
Alignment explanation
Indices: 44625086--44625170 Score: 81
Period size: 33 Copynumber: 2.7 Consensus size: 33
44625076 TCATTTTACT
* * *
44625086 TTAAAAAA-AT-TCTTAACAATAATTCTAAATTT
1 TTAAAAAATATATCTTAA-AATAAATATAAATTA
44625118 TTAAAAAAATATAT-TTAAAATAAATATAAATTA
1 TT-AAAAAATATATCTTAAAATAAATATAAATTA
*
44625151 TT-AAAAAT-TATGTTAAAATA
1 TTAAAAAATATATCTTAAAATA
44625171 TTAAATAAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
30 3 0.07
31 14 0.30
32 2 0.04
33 20 0.43
34 6 0.13
35 1 0.02
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (33 bp):
TTAAAAAATATATCTTAAAATAAATATAAATTA
Found at i:44625388 original size:28 final size:27
Alignment explanation
Indices: 44625345--44625402 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
44625335 TTTCCTTTAG
* *
44625345 AAATCAAAGCTTGATTTCAGTTAAAA-CA
1 AAATCAAACCTAGATTT-A-TTAAAACCA
44625373 AAATCAAACCTAGATTTATTAAAACCA
1 AAATCAAACCTAGATTTATTAAAACCA
44625400 AAA
1 AAA
44625403 CTTACATTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 6 0.22
27 6 0.22
28 15 0.56
ACGTcount: A:0.52, C:0.16, G:0.07, T:0.26
Consensus pattern (27 bp):
AAATCAAACCTAGATTTATTAAAACCA
Found at i:44625971 original size:20 final size:20
Alignment explanation
Indices: 44625946--44625986 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
44625936 TGTGAAAGTT
*
44625946 AGTAATAGCTAAGGGGAGGC
1 AGTAATAACTAAGGGGAGGC
44625966 AGTAATAACTAAGGGGAGGC
1 AGTAATAACTAAGGGGAGGC
44625986 A
1 A
44625987 AAAATAAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.39, C:0.10, G:0.37, T:0.15
Consensus pattern (20 bp):
AGTAATAACTAAGGGGAGGC
Found at i:44625992 original size:20 final size:20
Alignment explanation
Indices: 44625949--44625993 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
44625939 GAAAGTTAGT
* **
44625949 AATAGCTAAGGGGAGGCAGT
1 AATAACTAAGGGGAGGCAAA
44625969 AATAACTAAGGGGAGGCAAA
1 AATAACTAAGGGGAGGCAAA
44625989 AATAA
1 AATAA
44625994 GTAATCAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.47, C:0.09, G:0.31, T:0.13
Consensus pattern (20 bp):
AATAACTAAGGGGAGGCAAA
Found at i:44626349 original size:11 final size:11
Alignment explanation
Indices: 44626312--44626353 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
44626302 TAGAATTTTT
44626312 ATTTTTAA-AA
1 ATTTTTAACAA
44626322 ATATTTTAACATA
1 AT-TTTTAACA-A
*
44626335 ATTTTTAACAC
1 ATTTTTAACAA
44626346 ATTTTTAA
1 ATTTTTAA
44626354 TGATTTTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 2 0.07
11 14 0.50
12 9 0.32
13 3 0.11
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (11 bp):
ATTTTTAACAA
Found at i:44627786 original size:38 final size:39
Alignment explanation
Indices: 44627733--44627806 Score: 114
Period size: 38 Copynumber: 1.9 Consensus size: 39
44627723 ATACTCCACC
* * *
44627733 AATTATAAGTTACAGGTGAATATTTCCT-AAATATTCTG
1 AATTATAAGTAACAGGTAAATATCTCCTAAAATATTCTG
44627771 AATTATAAGTAACAGGTAAATATCTCCTAAAATATT
1 AATTATAAGTAACAGGTAAATATCTCCTAAAATATT
44627807 TGAGTAGGGA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 25 0.78
39 7 0.22
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (39 bp):
AATTATAAGTAACAGGTAAATATCTCCTAAAATATTCTG
Found at i:44633020 original size:34 final size:35
Alignment explanation
Indices: 44632945--44633031 Score: 97
Period size: 34 Copynumber: 2.5 Consensus size: 35
44632935 ACACTGCATG
* * * *
44632945 ACTGTATATTGATACTATGATGGGCTAAGATCCTA
1 ACTGCATATTGATACTGTGATGGGCTAAGAGCCCA
* *
44632980 AC-GCATACTGATACTGTGATGGGCTAAG-GCCCC
1 ACTGCATATTGATACTGTGATGGGCTAAGAGCCCA
44633013 ACTGCATATTTGATACTGT
1 ACTGCATA-TTGATACTGT
44633032 ACTGAGTTAG
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
33 4 0.09
34 28 0.65
35 11 0.26
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.31
Consensus pattern (35 bp):
ACTGCATATTGATACTGTGATGGGCTAAGAGCCCA
Found at i:44637926 original size:42 final size:42
Alignment explanation
Indices: 44637879--44638012 Score: 180
Period size: 42 Copynumber: 3.2 Consensus size: 42
44637869 AGGGAAGGCG
* *
44637879 AACTGAAGGTGGAGAAGGGAGAAGCTGATTTAAAAGAAAACA
1 AACTGAAGGTGGAGAAGGGAGAAGCTGAGTTAAAAGAAAACC
*
44637921 AACTGAAGGTGGAGAAGGGTGAAGCTGAGTTAAAAGAAAACC
1 AACTGAAGGTGGAGAAGGGAGAAGCTGAGTTAAAAGAAAACC
* * * *
44637963 AACTGAAGCTAGAGAA-GGACAAAGCTGAGTTAGAAGAAAACC
1 AACTGAAGGTGGAGAAGGGA-GAAGCTGAGTTAAAAGAAAACC
*
44638005 TACTGAAG
1 AACTGAAG
44638013 CTAGCGGGAT
Statistics
Matches: 82, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
41 2 0.02
42 80 0.98
ACGTcount: A:0.46, C:0.10, G:0.30, T:0.14
Consensus pattern (42 bp):
AACTGAAGGTGGAGAAGGGAGAAGCTGAGTTAAAAGAAAACC
Found at i:44638178 original size:76 final size:76
Alignment explanation
Indices: 44638069--44638383 Score: 531
Period size: 76 Copynumber: 4.1 Consensus size: 76
44638059 TGAAATACTT
* *
44638069 TCTCAATGGTTTATTGAGGATGTTGATGAACTGAAGATACAAACAGTATGTGTTTGTGTGATGGT
1 TCTCAATGGTTTATTG-GGATGTTTATGAACTGAAGATACAGACAGTATGTGTTTGTGTGATGGT
44638134 TTTGTGTTTGAA
65 TTTGTGTTTGAA
*
44638146 TCTCAATGGTTTATTGGGATGTTTATGAACTGAAGATACAGACAGTCTGTGTTTGTGTGATGGTT
1 TCTCAATGGTTTATTGGGATGTTTATGAACTGAAGATACAGACAGTATGTGTTTGTGTGATGGTT
*
44638211 TTGTGTTTGGA
66 TTGTGTTTGAA
* * **
44638222 TCTCAATGGTTTATTAGGATGTTTATGAACTGAAGATAGAGACAGTATGCATTTGTGTGATGGTT
1 TCTCAATGGTTTATTGGGATGTTTATGAACTGAAGATACAGACAGTATGTGTTTGTGTGATGGTT
44638287 TTGTGTTTGAA
66 TTGTGTTTGAA
* *
44638298 TCTCAATGGTTTATTGGGATGTTTATGAACTGAAGATACAGACACTATGTGTTTATGTGATGGTT
1 TCTCAATGGTTTATTGGGATGTTTATGAACTGAAGATACAGACAGTATGTGTTTGTGTGATGGTT
44638363 TTGTGTTTGAA
66 TTGTGTTTGAA
44638374 TCTCAATGGT
1 TCTCAATGGT
44638384 CTAACTGAGA
Statistics
Matches: 222, Mismatches: 16, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
76 206 0.93
77 16 0.07
ACGTcount: A:0.24, C:0.08, G:0.27, T:0.41
Consensus pattern (76 bp):
TCTCAATGGTTTATTGGGATGTTTATGAACTGAAGATACAGACAGTATGTGTTTGTGTGATGGTT
TTGTGTTTGAA
Found at i:44644957 original size:4 final size:4
Alignment explanation
Indices: 44644948--44644974 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
44644938 TCTTCTCCTA
44644948 TATC TATC TATC TATC TATC TATC TAT
1 TATC TATC TATC TATC TATC TATC TAT
44644975 ATATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.22, G:0.00, T:0.52
Consensus pattern (4 bp):
TATC
Found at i:44644979 original size:2 final size:2
Alignment explanation
Indices: 44644972--44645004 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
44644962 TCTATCTATC
44644972 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
44645005 TCCTAAGGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:44646344 original size:76 final size:76
Alignment explanation
Indices: 44646217--44646531 Score: 481
Period size: 76 Copynumber: 4.1 Consensus size: 76
44646207 TGAAATACAT
* * * *
44646217 TCTCAATGGTTTATCGAGGATGTTGATGAACTGAAGATACAAACAGTATGTGTTTGTGTGATGGT
1 TCTCAATGGTTTATTG-GGATGTTTATGAACTAAAGATACAGACAGTATGTGTTTGTGTGATGGT
44646282 TTTGTGTTTGAA
65 TTTGTGTTTGAA
*
44646294 TCTCAATGGTTTATTGGAATGTTTATGAACTAAAGATACAGACAGTATGTGTTTGTGTGATGGTT
1 TCTCAATGGTTTATTGGGATGTTTATGAACTAAAGATACAGACAGTATGTGTTTGTGTGATGGTT
*
44646359 TTGTGTTTGGA
66 TTGTGTTTGAA
* * *
44646370 TCTCAATGGTTTATTGGGATGTTTATGAACTGAAGATACAGACAATATGCGTTTGTGTGATGGTT
1 TCTCAATGGTTTATTGGGATGTTTATGAACTAAAGATACAGACAGTATGTGTTTGTGTGATGGTT
44646435 TTGTGTTTGAA
66 TTGTGTTTGAA
* * *
44646446 TCTCAATGGTTTATTGGGATGTTTATGAACTGCAAA-CT-CAGACAGTATGTGTTTATGTGATGA
1 TCTCAATGGTTTATTGGGATGTTTATGAACT--AAAGATACAGACAGTATGTGTTTGTGTGATGG
44646509 TTTTGTGTTTGAA
64 TTTTGTGTTTGAA
44646522 TCTCAATGGT
1 TCTCAATGGT
44646532 CGAAGTGAGA
Statistics
Matches: 219, Mismatches: 17, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
76 201 0.92
77 16 0.07
78 2 0.01
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (76 bp):
TCTCAATGGTTTATTGGGATGTTTATGAACTAAAGATACAGACAGTATGTGTTTGTGTGATGGTT
TTGTGTTTGAA
Found at i:44646736 original size:12 final size:12
Alignment explanation
Indices: 44646719--44646744 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
44646709 CAAAACAGGC
44646719 TTTTAGCGGCGT
1 TTTTAGCGGCGT
44646731 TTTTAGCGGCGT
1 TTTTAGCGGCGT
44646743 TT
1 TT
44646745 AGATAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.15, G:0.31, T:0.46
Consensus pattern (12 bp):
TTTTAGCGGCGT
Found at i:44647019 original size:114 final size:113
Alignment explanation
Indices: 44646812--44647021 Score: 314
Period size: 114 Copynumber: 1.8 Consensus size: 113
44646802 AAAATAAGCA
* * * * *
44646812 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCCAACGACGTCGTTTCCCGAGCTTT
1 TTAGCGGCATTTTCGAAAAAGCGCCGCAAAAAACCTAAGCCCAACGACATCGTTTCCCAAGCTTT
*
44646877 CGGGGATTTAGCGGCGTTTTTATGAAAGCGCTGCTAATGCTCAGGGCT
66 CGGGGATTTAGCGGCGTTTTTATAAAAGCGCTGCTAATGCTCAGGGCT
* * *
44646925 TTAGCGGCATTTTCGAAAAAGCGCCGCAAAAAAACCTAAGCCCAACTACATCGTTTTCTAAGCTT
1 TTAGCGGCATTTTCGAAAAAGCGCCGC-AAAAAACCTAAGCCCAACGACATCGTTTCCCAAGCTT
44646990 TCGGGGATTTAGCGGCGTTTTTGA-AAAAGCGC
65 TCGGGGATTTAGCGGCGTTTTT-ATAAAAGCGC
44647022 AGCAAAAAAC
Statistics
Matches: 86, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
113 24 0.28
114 61 0.71
115 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.26
Consensus pattern (113 bp):
TTAGCGGCATTTTCGAAAAAGCGCCGCAAAAAACCTAAGCCCAACGACATCGTTTCCCAAGCTTT
CGGGGATTTAGCGGCGTTTTTATAAAAGCGCTGCTAATGCTCAGGGCT
Found at i:44647056 original size:72 final size:74
Alignment explanation
Indices: 44646924--44647090 Score: 248
Period size: 73 Copynumber: 2.3 Consensus size: 74
44646914 TGCTCAGGGC
* * * * *
44646924 TTTAGCGGCATTTTCGAAAAAGCGCCGCAAAAAAACCTAAGCCCAACTACATCGTTTTCTAAG-C
1 TTTAGCGGCGTTTTTGAAAAAGCGCAGCAAAAAAACCTAAGCCCAACGACACCGTTTTCTAAGTC
44646988 TTTCGGGGA
66 TTTCGGGGA
* *
44646997 TTTAGCGGCGTTTTTGAAAAAGCGCAGC-AAAAAACCTAAGCCCAACGACGCCGTTTTCTAAGTT
1 TTTAGCGGCGTTTTTGAAAAAGCGCAGCAAAAAAACCTAAGCCCAACGACACCGTTTTCTAAGTC
44647061 TTTCGGGGA
66 TTTCGGGGA
44647070 TTTAGCGGCGTTTTTAGAAAA
1 TTTAGCGGCGTTTTT-GAAAA
44647091 GCGAGTCGGG
Statistics
Matches: 85, Mismatches: 7, Indels: 3
0.89 0.07 0.03
Matches are distributed among these distances:
72 31 0.36
73 49 0.58
74 5 0.06
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.27
Consensus pattern (74 bp):
TTTAGCGGCGTTTTTGAAAAAGCGCAGCAAAAAAACCTAAGCCCAACGACACCGTTTTCTAAGTC
TTTCGGGGA
Found at i:44648124 original size:22 final size:23
Alignment explanation
Indices: 44648085--44648127 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
44648075 GGCCTTCTGA
44648085 CGCCGCCACGGTCACGTCGCCAT
1 CGCCGCCACGGTCACGTCGCCAT
44648108 CGCCG-CAC-GTCACCGTCGCC
1 CGCCGCCACGGTCA-CGTCGCC
44648128 CACTTGCTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.21
22 10 0.53
23 5 0.26
ACGTcount: A:0.12, C:0.51, G:0.26, T:0.12
Consensus pattern (23 bp):
CGCCGCCACGGTCACGTCGCCAT
Found at i:44658314 original size:3 final size:3
Alignment explanation
Indices: 44658306--44658346 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
44658296 GAGGAGTATT
44658306 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
44658347 TTTTTTTTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:44658813 original size:22 final size:21
Alignment explanation
Indices: 44658770--44658819 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
44658760 TATAAAAATG
*
44658770 AAAAT-AA-AATAAAATAGTA
1 AAAATAAATAATAAAATAGGA
44658789 AAAATAAATAATAATAATAGGA
1 AAAATAAATAATAA-AATAGGA
*
44658811 AAATTAAAT
1 AAAATAAAT
44658820 TTTTTTTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 5 0.19
20 2 0.08
21 5 0.19
22 14 0.54
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.24
Consensus pattern (21 bp):
AAAATAAATAATAAAATAGGA
Found at i:44663745 original size:2 final size:2
Alignment explanation
Indices: 44663738--44663774 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
44663728 TTTATACTTC
44663738 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
44663775 CCTCCTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:44665420 original size:89 final size:89
Alignment explanation
Indices: 44665315--44665482 Score: 284
Period size: 89 Copynumber: 1.9 Consensus size: 89
44665305 TCAATATAGC
* *
44665315 TCAAAGAAAAATTAAATTCATTAAATAGTAGCTTGCAGACATTACTTGGGAACAAATCATCCCTC
1 TCAAAGAAAAATTAAATTCATTAAATAGTAGCTTGCAAACATTACTTCGGAACAAATCATCCCTC
44665380 CAACTTCCCAAGTTCTGAAAATAT
66 CAACTTCCCAAGTTCTGAAAATAT
*
44665404 TCAAAGAGAAAA-TAAATTCATTAAATAGTAGCTTGCAAACATTACTTCGGAACAAATCATCCGT
1 TCAAAGA-AAAATTAAATTCATTAAATAGTAGCTTGCAAACATTACTTCGGAACAAATCATCCCT
*
44665468 CCAACTTCCCGAGTT
65 CCAACTTCCCAAGTT
44665483 GTCAAGATCA
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
89 70 0.95
90 4 0.05
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.27
Consensus pattern (89 bp):
TCAAAGAAAAATTAAATTCATTAAATAGTAGCTTGCAAACATTACTTCGGAACAAATCATCCCTC
CAACTTCCCAAGTTCTGAAAATAT
Found at i:44670461 original size:42 final size:42
Alignment explanation
Indices: 44670375--44670461 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
44670365 GAACGAAGAA
* *
44670375 TTTAATTTAAAGATTTTTGAAGGAGAAGAATGGATTTGAGGG
1 TTTAATTTAAAGATTTTTGAAGGAAAAGAATGAATTTGAGGG
* *
44670417 TTTAATTTAAGGATTTTTGAA-GACAAAGCATGAATTT-AGTGG
1 TTTAATTTAAAGATTTTTGAAGGA-AAAGAATGAATTTGAG-GG
44670459 TTT
1 TTT
44670462 GAATGAATGG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
41 4 0.10
42 35 0.90
ACGTcount: A:0.34, C:0.02, G:0.24, T:0.39
Consensus pattern (42 bp):
TTTAATTTAAAGATTTTTGAAGGAAAAGAATGAATTTGAGGG
Found at i:44672148 original size:18 final size:17
Alignment explanation
Indices: 44672092--44672146 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 17
44672082 AAAATTGAAA
*
44672092 TATTAAAAACAACCATT
1 TATTAAAAACAACCGTT
44672109 T-TTAATAAATCTAAACCGTT
1 TATTAA-AAA-C--AACCGTT
44672129 TATTAAAAACAACCGTT
1 TATTAAAAACAACCGTT
44672146 T
1 T
44672147 TACGAGGTGA
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
16 4 0.12
17 12 0.38
18 1 0.03
19 1 0.03
20 10 0.31
21 4 0.12
ACGTcount: A:0.45, C:0.16, G:0.04, T:0.35
Consensus pattern (17 bp):
TATTAAAAACAACCGTT
Found at i:44678305 original size:16 final size:17
Alignment explanation
Indices: 44678284--44678320 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
44678274 TTAAATGTTA
44678284 AATTATCTTTAA-TTTT
1 AATTATCTTTAATTTTT
*
44678300 AATTATTTTTAATTTTT
1 AATTATCTTTAATTTTT
44678317 AATT
1 AATT
44678321 TAATATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (17 bp):
AATTATCTTTAATTTTT
Found at i:44679667 original size:76 final size:76
Alignment explanation
Indices: 44679536--44679774 Score: 379
Period size: 76 Copynumber: 3.1 Consensus size: 76
44679526 TGAAATACAT
* *
44679536 TCTCAATGGTTTATTGAGGATGTTGATGAACTAAAGATACAGACAGTATGTGTTTGTGTGATGGT
1 TCTCAATGGTTTATTG-GGATGTTTATGAACTGAAGATACAGACAGTATGTGTTTGTGTGATGGT
44679601 TTTGTGTTTGGA
65 TTTGTGTTTGGA
* *
44679613 TCTGAATGGTTTATTGGGATGTTTATGAACTGAAGATACAGACAGTATGCGTTTGTGTGATGGTT
1 TCTCAATGGTTTATTGGGATGTTTATGAACTGAAGATACAGACAGTATGTGTTTGTGTGATGGTT
44679678 TTGTGTTTGGA
66 TTGTGTTTGGA
* * * *
44679689 TCTCAATGGTTTATTGGGATATTTATGAACTGAAGATACAGACAGTATGTGTTTATTTGATGATT
1 TCTCAATGGTTTATTGGGATGTTTATGAACTGAAGATACAGACAGTATGTGTTTGTGTGATGGTT
* *
44679754 TAGTGTTTGAA
66 TTGTGTTTGGA
44679765 TCTCAATGGT
1 TCTCAATGGT
44679775 CTAAGTGAGA
Statistics
Matches: 150, Mismatches: 12, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
76 135 0.90
77 15 0.10
ACGTcount: A:0.25, C:0.07, G:0.27, T:0.41
Consensus pattern (76 bp):
TCTCAATGGTTTATTGGGATGTTTATGAACTGAAGATACAGACAGTATGTGTTTGTGTGATGGTT
TTGTGTTTGGA
Found at i:44683092 original size:17 final size:17
Alignment explanation
Indices: 44683070--44683103 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
44683060 ATATTTAATA
44683070 TATATTTGATTAAAAAT
1 TATATTTGATTAAAAAT
44683087 TATATTTGATTAAAAAT
1 TATATTTGATTAAAAAT
44683104 ATAAAATATA
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:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (17 bp):
TATATTTGATTAAAAAT
Found at i:44683106 original size:16 final size:16
Alignment explanation
Indices: 44683069--44683106 Score: 67
Period size: 17 Copynumber: 2.3 Consensus size: 16
44683059 TATATTTAAT
44683069 ATATATTTGATTAAAA
1 ATATATTTGATTAAAA
44683085 ATTATATTTGATTAAAA
1 A-TATATTTGATTAAAA
44683102 ATATA
1 ATATA
44683107 AAATATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (16 bp):
ATATATTTGATTAAAA
Found at i:44688960 original size:30 final size:30
Alignment explanation
Indices: 44688926--44688988 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
44688916 ACTTATTTTA
*
44688926 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTATTATTATTTTAAAGACAT
*
44688956 TTGTTAATTTTATTATTATTTTAGAGACAT
1 TTGTTAATTTTATTATTATTTTAAAGACAT
44688986 TTG
1 TTG
44688989 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.29, C:0.03, G:0.11, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTATTATTATTTTAAAGACAT
Found at i:44690540 original size:9 final size:8
Alignment explanation
Indices: 44690528--44690588 Score: 50
Period size: 9 Copynumber: 6.9 Consensus size: 8
44690518 TTTTATGTTT
44690528 ATTTTTTGA
1 ATTTTTT-A
44690537 ATTTTTATAA
1 ATTTTT-T-A
*
44690547 ATATTTTA
1 ATTTTTTA
44690555 TATTTTTTA
1 -ATTTTTTA
44690564 ATTTTTTTA
1 A-TTTTTTA
*
44690573 ATTTTTAA
1 ATTTTTTA
44690581 ATTATTTT
1 ATT-TTTT
44690589 TTGAGGTGAC
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
8 11 0.26
9 25 0.58
10 7 0.16
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.69
Consensus pattern (8 bp):
ATTTTTTA
Found at i:44701383 original size:15 final size:15
Alignment explanation
Indices: 44701363--44701398 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
44701353 AACTAAAGGG
* *
44701363 GATGATGATGACGAC
1 GATGATGATGAAGAA
44701378 GATGATGATGAAGAA
1 GATGATGATGAAGAA
44701393 GATGAT
1 GATGAT
44701399 TGGGTTTCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.39, C:0.06, G:0.33, T:0.22
Consensus pattern (15 bp):
GATGATGATGAAGAA
Found at i:44708896 original size:20 final size:20
Alignment explanation
Indices: 44708871--44708939 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
44708861 TAAATATATT
44708871 TATTTTTTAAAATTTTAAAA
1 TATTTTTTAAAATTTTAAAA
* **
44708891 TATTTTTTACATACTTTTTTAA
1 TATTTTTTA-A-AATTTTAAAA
44708913 T-TTTTTT--AATTTTAAAA
1 TATTTTTTAAAATTTTAAAA
44708930 TATTTTTTAA
1 TATTTTTTAA
44708940 TTTTTTTAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
17 8 0.21
18 6 0.16
20 9 0.24
21 7 0.18
22 8 0.21
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTTTTTAAAATTTTAAAA
Found at i:44708925 original size:27 final size:26
Alignment explanation
Indices: 44708895--44708963 Score: 102
Period size: 27 Copynumber: 2.5 Consensus size: 26
44708885 TTAAAATATT
*
44708895 TTTTACATACTTTTTTAATTTTTTTAA
1 TTTTAAATA-TTTTTTAATTTTTTTAA
44708922 TTTTAAAATATTTTTTAATTTTTTTAA
1 TTTT-AAATATTTTTTAATTTTTTTAA
44708949 TTTTAAAATATTTTT
1 TTTT-AAATATTTTT
44708964 AAAATACTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
27 36 0.90
28 4 0.10
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (26 bp):
TTTTAAATATTTTTTAATTTTTTTAA
Found at i:44708936 original size:11 final size:11
Alignment explanation
Indices: 44708922--44709041 Score: 50
Period size: 11 Copynumber: 11.9 Consensus size: 11
44708912 ATTTTTTTAA
44708922 TTTTAAAATAT
1 TTTTAAAATAT
*
44708933 TTTT-TAAT-T
1 TTTTAAAATAT
*
44708942 TTTT-TAA--T
1 TTTTAAAATAT
44708950 TTT-AAAATAT
1 TTTTAAAATAT
44708960 TTTTAAAATACT
1 TTTTAAAATA-T
**
44708972 TTTTTTAAT-T
1 TTTTAAAATAT
* *
44708982 TTTT---TTAA
1 TTTTAAAATAT
*
44708990 TTTTAAAATAC
1 TTTTAAAATAT
44709001 TTTTAAAATACT
1 TTTTAAAATA-T
**
44709013 TTTTTTAAT-T
1 TTTTAAAATAT
44709023 TTTT-AAA-AT
1 TTTTAAAATAT
44709032 TTTTAAAATA
1 TTTTAAAATA
44709042 AAAATGGGTC
Statistics
Matches: 84, Mismatches: 12, Indels: 26
0.69 0.10 0.21
Matches are distributed among these distances:
7 1 0.01
8 10 0.12
9 15 0.18
10 20 0.24
11 23 0.27
12 15 0.18
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:44709033 original size:41 final size:40
Alignment explanation
Indices: 44708922--44709041 Score: 181
Period size: 41 Copynumber: 3.0 Consensus size: 40
44708912 ATTTTTTTAA
*
44708922 TTTTAAAATA--TTTTTTAATTTTTTTAATTTTAAAATAT
1 TTTTAAAATACTTTTTTTAATTTTTTTAATTTTAAAATAC
44708960 TTTTAAAATACTTTTTTTAATTTTTTTTAATTTTAAAATAC
1 TTTTAAAATACTTTTTTTAA-TTTTTTTAATTTTAAAATAC
*
44709001 TTTTAAAATACTTTTTTTAATTTTTTAAAATTTTTAAAATA
1 TTTTAAAATACTTTTTTTAATTTTTT-TAA-TTTTAAAATA
44709042 AAAATGGGTC
Statistics
Matches: 75, Mismatches: 2, Indels: 6
0.90 0.02 0.07
Matches are distributed among these distances:
38 10 0.13
40 14 0.19
41 41 0.55
42 10 0.13
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (40 bp):
TTTTAAAATACTTTTTTTAATTTTTTTAATTTTAAAATAC
Found at i:44709036 original size:31 final size:30
Alignment explanation
Indices: 44708981--44709041 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 30
44708971 TTTTTTTAAT
44708981 TTTTTTTAATTTTAAAATACTTTTAAAATAC
1 TTTTTTTAATTTTAAAATA-TTTTAAAATAC
44709012 TTTTTTTAATTTTTTAAAAT-TTTTAAAATA
1 TTTTTTTAA--TTTTAAAATATTTTAAAATA
44709042 AAAATGGGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
31 19 0.68
33 9 0.32
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (30 bp):
TTTTTTTAATTTTAAAATATTTTAAAATAC
Found at i:44709332 original size:21 final size:22
Alignment explanation
Indices: 44709307--44709356 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
44709297 AGTAAAGTTT
44709307 TTTTACTCATATTTTC-TACTG
1 TTTTACTCATATTTTCTTACTG
* ** *
44709328 TTTTAATGTTATTTTCTTATTG
1 TTTTACTCATATTTTCTTACTG
44709350 TTTTACT
1 TTTTACT
44709357 TCTATGTTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.18, C:0.12, G:0.06, T:0.64
Consensus pattern (22 bp):
TTTTACTCATATTTTCTTACTG
Found at i:44712833 original size:16 final size:17
Alignment explanation
Indices: 44712812--44712862 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
44712802 ATATGATATT
*
44712812 TAAATAATTTAATATAA
1 TAAATAATTAAATATAA
*
44712829 T-AATACATAAAATAT-A
1 TAAATA-ATTAAATATAA
*
44712845 TAAATAATTCAATATAA
1 TAAATAATTAAATATAA
44712862 T
1 T
44712863 GATACATAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
16 13 0.48
17 14 0.52
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (17 bp):
TAAATAATTAAATATAA
Found at i:44712844 original size:17 final size:17
Alignment explanation
Indices: 44712822--44712879 Score: 66
Period size: 17 Copynumber: 3.5 Consensus size: 17
44712812 TAAATAATTT
44712822 AATATAATAATACATAA
1 AATATAATAATACATAA
**
44712839 AATAT-ATAAATA-ATTC
1 AATATAAT-AATACATAA
*
44712855 AATATAATGATACATAA
1 AATATAATAATACATAA
44712872 AATATAAT
1 AATATAAT
44712880 TTAATCTAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
16 12 0.36
17 21 0.64
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (17 bp):
AATATAATAATACATAA
Found at i:44712853 original size:33 final size:33
Alignment explanation
Indices: 44712807--44712877 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
44712797 AAATTATATG
* *
44712807 ATATTTAAATAATTTAATATAATAATACATAAA
1 ATATATAAATAATTCAATATAATAATACATAAA
*
44712840 ATATATAAATAATTCAATATAATGATACATAAA
1 ATATATAAATAATTCAATATAATAATACATAAA
44712873 ATATA
1 ATATA
44712878 ATTTAATCTA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (33 bp):
ATATATAAATAATTCAATATAATAATACATAAA
Found at i:44719204 original size:19 final size:21
Alignment explanation
Indices: 44719166--44719204 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
44719156 CAAAAAGATA
*
44719166 TTTTTAAGAATAATTTTTGTT
1 TTTTTAAGAATAATTATTGTT
44719187 TTTTTAAGAA-AA-TATTGT
1 TTTTTAAGAATAATTATTGT
44719205 CATTAATAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 2 0.12
21 10 0.59
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.56
Consensus pattern (21 bp):
TTTTTAAGAATAATTATTGTT
Found at i:44719439 original size:31 final size:31
Alignment explanation
Indices: 44719376--44719452 Score: 75
Period size: 31 Copynumber: 2.5 Consensus size: 31
44719366 TTTATCTAAG
* *
44719376 TTAGACCTTGAACTTCACAATTATTTTTATA
1 TTAGACCTTGAACTTCACAATTATTCTCATA
* * * *
44719407 TTAGAGCTTGAACTTGATAATTGTTCTCATA
1 TTAGACCTTGAACTTCACAATTATTCTCATA
*
44719438 TTGGGACC-TGAACTT
1 TT-AGACCTTGAACTT
44719453 TGGGGTTTTT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
31 34 0.92
32 3 0.08
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.42
Consensus pattern (31 bp):
TTAGACCTTGAACTTCACAATTATTCTCATA
Found at i:44723392 original size:2 final size:2
Alignment explanation
Indices: 44723385--44723409 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
44723375 AAGATCATAC
44723385 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
44723410 TGGCCAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:44724475 original size:12 final size:12
Alignment explanation
Indices: 44724458--44724485 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
44724448 GGTCATTCGG
44724458 GTGAAGGCACCA
1 GTGAAGGCACCA
44724470 GTGAAGGCACCA
1 GTGAAGGCACCA
44724482 GTGA
1 GTGA
44724486 TGCCAGAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.21, G:0.36, T:0.11
Consensus pattern (12 bp):
GTGAAGGCACCA
Found at i:44730198 original size:16 final size:18
Alignment explanation
Indices: 44730174--44730210 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
44730164 CGATGGGGAA
*
44730174 AAAGGTGAAGA-AAA-AT
1 AAAGATGAAGATAAAGAT
44730190 AAAGATGAAGATAAAGAT
1 AAAGATGAAGATAAAGAT
44730208 AAA
1 AAA
44730211 AGCTATCGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 10 0.56
17 3 0.17
18 5 0.28
ACGTcount: A:0.65, C:0.00, G:0.22, T:0.14
Consensus pattern (18 bp):
AAAGATGAAGATAAAGAT
Found at i:44736429 original size:25 final size:25
Alignment explanation
Indices: 44736395--44736442 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
44736385 TTTTCAATAA
44736395 TTTAGAATTTAGTCCTTATATTTCT
1 TTTAGAATTTAGTCCTTATATTTCT
* * *
44736420 TTTATAATTTAGTTCTTTTATTT
1 TTTAGAATTTAGTCCTTATATTT
44736443 TTCTAATTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.23, C:0.08, G:0.06, T:0.62
Consensus pattern (25 bp):
TTTAGAATTTAGTCCTTATATTTCT
Found at i:44741690 original size:6 final size:6
Alignment explanation
Indices: 44741678--44741708 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
44741668 AGAGGAAAAG
*
44741678 GATGAA GAAGAA GATGAA GATGAA GATGAA G
1 GATGAA GATGAA GATGAA GATGAA GATGAA G
44741709 GGAGTATTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.35, T:0.13
Consensus pattern (6 bp):
GATGAA
Found at i:44752283 original size:16 final size:16
Alignment explanation
Indices: 44752260--44752298 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
44752250 ACCCAAAATG
*
44752260 ATTT-AAACTTTAAAA
1 ATTTAAAACTCTAAAA
44752275 ATTTAAAACTCTAAAA
1 ATTTAAAACTCTAAAA
44752291 ATTCTAAA
1 ATT-TAAA
44752299 TTATCCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 4 0.19
16 13 0.62
17 4 0.19
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.36
Consensus pattern (16 bp):
ATTTAAAACTCTAAAA
Found at i:44759683 original size:10 final size:10
Alignment explanation
Indices: 44759670--44759696 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
44759660 ATTTAAGTAA
44759670 TTTTATATAT
1 TTTTATATAT
44759680 TTTTATATAT
1 TTTTATATAT
44759690 TTTTATA
1 TTTTATA
44759697 CGCTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
TTTTATATAT
Found at i:44763721 original size:39 final size:39
Alignment explanation
Indices: 44763667--44763745 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
44763657 GCCCAATGGC
44763667 TTTTACTGTATGGCCAATGAACAAAGGATTAGGTGAGGA
1 TTTTACTGTATGGCCAATGAACAAAGGATTAGGTGAGGA
44763706 TTTTACTGTATGGCCAATGAACAAAGGATTAGGTGAGGA
1 TTTTACTGTATGGCCAATGAACAAAGGATTAGGTGAGGA
44763745 T
1 T
44763746 AAAGTTTTCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.33, C:0.10, G:0.28, T:0.29
Consensus pattern (39 bp):
TTTTACTGTATGGCCAATGAACAAAGGATTAGGTGAGGA
Found at i:44773554 original size:18 final size:19
Alignment explanation
Indices: 44773504--44773554 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 19
44773494 AAATTTACTG
*
44773504 ATTCAAATTCATATTCAGATA
1 ATTCAAA-TCA-ATACAGATA
*
44773525 ATTCAAA-AAATACAGAT-
1 ATTCAAATCAATACAGATA
44773542 ATTCAAATCAATA
1 ATTCAAATCAATA
44773555 TCATTCCTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
17 7 0.27
18 11 0.42
19 1 0.04
21 7 0.27
ACGTcount: A:0.51, C:0.14, G:0.04, T:0.31
Consensus pattern (19 bp):
ATTCAAATCAATACAGATA
Found at i:44778654 original size:13 final size:13
Alignment explanation
Indices: 44778638--44778680 Score: 61
Period size: 12 Copynumber: 3.3 Consensus size: 13
44778628 AAATATTTTC
44778638 AATAAAATTTAAA
1 AATAAAATTTAAA
44778651 AAT-AAATTTAAA
1 AATAAAATTTAAA
*
44778663 AATAAATATTTTAA
1 AATAAA-ATTTAAA
44778677 AATA
1 AATA
44778681 TAATAATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 12 0.44
13 5 0.19
14 10 0.37
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
AATAAAATTTAAA
Found at i:44778685 original size:15 final size:15
Alignment explanation
Indices: 44778645--44778685 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
44778635 TTCAATAAAA
44778645 TTTAAAA-ATAA-AT
1 TTTAAAATATAATAT
*
44778658 TTAAAAATA-AATAT
1 TTTAAAATATAATAT
44778672 TTTAAAATATAATA
1 TTTAAAATATAATA
44778686 ATAAATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 8 0.35
14 11 0.48
15 4 0.17
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TTTAAAATATAATAT
Found at i:44778688 original size:22 final size:22
Alignment explanation
Indices: 44778654--44778695 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
44778644 ATTTAAAAAT
*
44778654 AAATTTAAAAATAAATATTTTA
1 AAATATAAAAATAAATATTTTA
*
44778676 AAATATAATAATAAATATTT
1 AAATATAAAAATAAATATTT
44778696 ATGTATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
AAATATAAAAATAAATATTTTA
Found at i:44779207 original size:2 final size:2
Alignment explanation
Indices: 44779200--44779229 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
44779190 CTATTATGGT
44779200 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
44779230 ACACTTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:44793421 original size:2 final size:2
Alignment explanation
Indices: 44793414--44793440 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
44793404 CCTGATTATG
44793414 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
44793441 GATTTTAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:44794220 original size:26 final size:27
Alignment explanation
Indices: 44794188--44794255 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 27
44794178 CAAAAAATAC
44794188 AAAAAAATTTTAAAATTCAAAATATTT
1 AAAAAAATTTTAAAATTCAAAATATTT
* * * * *
44794215 ATAAAAATTCTAAAATT-TATATTTTT
1 AAAAAAATTTTAAAATTCAAAATATTT
*
44794241 TAAAAAATTTTAAAA
1 AAAAAAATTTTAAAA
44794256 AAATATATAA
Statistics
Matches: 33, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
26 18 0.55
27 15 0.45
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (27 bp):
AAAAAAATTTTAAAATTCAAAATATTT
Found at i:44794221 original size:19 final size:18
Alignment explanation
Indices: 44794190--44794235 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
44794180 AAAAATACAA
44794190 AAAAATTT-T-AAAATTC
1 AAAAATTTATAAAAATTC
44794206 AAAATATTTATAAAAATTC
1 AAAA-ATTTATAAAAATTC
*
44794225 TAAAATTTATA
1 AAAAATTTATA
44794236 TTTTTTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 4 0.15
17 4 0.15
18 8 0.31
19 10 0.38
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (18 bp):
AAAAATTTATAAAAATTC
Found at i:44794256 original size:27 final size:26
Alignment explanation
Indices: 44794189--44794255 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 26
44794179 AAAAAATACA
44794189 AAAAAATTTTAAAATTCAAAATATTT
1 AAAAAATTTTAAAATTCAAAATATTT
* * * * *
44794215 ATAAAAATTCTAAAATTTATATTTTTT
1 A-AAAAATTTTAAAATTCAAAATATTT
44794242 AAAAAATTTTAAAA
1 AAAAAATTTTAAAA
44794256 AAATATATAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
26 13 0.38
27 21 0.62
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (26 bp):
AAAAAATTTTAAAATTCAAAATATTT
Found at i:44794616 original size:5 final size:5
Alignment explanation
Indices: 44794606--44794645 Score: 62
Period size: 5 Copynumber: 8.0 Consensus size: 5
44794596 AATTTTTCAC
* *
44794606 TCGAT TCGAT TCGAT TCGAT TCGAT TCGAC TCGAC TCGAT
1 TCGAT TCGAT TCGAT TCGAT TCGAT TCGAT TCGAT TCGAT
44794646 CGAACGCTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.35
Consensus pattern (5 bp):
TCGAT
Done.