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 99 of 150
Found at i:31094726 original size:217 final size:216
Alignment explanation
Indices: 31094445--31095093 Score: 1012
Period size: 217 Copynumber: 3.0 Consensus size: 216
31094435 ACTAGATGCG
*
31094445 ATCTGCTCTCTGCAACTTC-AGAGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTC
1 ATCTGCTCACTGCAACTTCAAG-GAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTC
* * *
31094509 AGGAGGATAAGACTTACTTACTTAGTTTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGGG
65 AGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCG
* * * * *
31094574 ATTTGCTCTCTACAACTTCAGAGAGATAAGATCCAAAGTTTTAATTCGCTCCACTACAACTTCAG
130 ATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTAATCCGCTCCACTGCAACTTCAG
31094639 GGAGATAGGATTATCGGCTTTA
195 GGAGATAGGATTATCGGCTTTA
* * *
31094661 ATCTGCTTCACTGCCACTTCAAGGAGATAAGATTTGCCATCTTCAGTCTGCTTCACTGGAACTTC
1 ATCTGC-TCACTGCAACTTCAAGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTC
* *
31094726 AGGAAGATAGGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCG
65 AGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCG
* *
31094791 ATCTGCTCTCTGTAACTTCAGAGAGATAAGATCTAAGGTTTTAATCCGCTCCACTGCAACTTCAG
130 ATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTAATCCGCTCCACTGCAACTTCAG
*
31094856 GGAGATAGGATTATCGGCTCTA
195 GGAGATAGGATTATCGGCTTTA
* * * * *
31094878 ATCTTCTCGACTGCAACTTCAGGGAGATAAGATTTGCCATCTTTAGTCTACCTCACTACAACTTC
1 ATCTGCTC-ACTGCAACTTCAAGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTC
* *
31094943 AGGAGGATAAAACTTGCTTGCTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCG
65 AGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCG
*
31095008 ATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTAATCCTCTCCACTGCAACTTCAG
130 ATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTAATCCGCTCCACTGCAACTTCAG
* * *
31095073 GGATATAGGATCATTGGCTTT
195 GGAGATAGGATTATCGGCTTT
31095094 CGATCTGTTC
Statistics
Matches: 394, Mismatches: 36, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
216 8 0.02
217 384 0.97
218 2 0.01
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (216 bp):
ATCTGCTCACTGCAACTTCAAGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCA
GGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGA
TCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTAATCCGCTCCACTGCAACTTCAGG
GAGATAGGATTATCGGCTTTA
Found at i:31094768 original size:44 final size:44
Alignment explanation
Indices: 31094201--31095000 Score: 321
Period size: 44 Copynumber: 18.3 Consensus size: 44
31094191 ATCTGCTCCA
* * *
31094201 CAGGAAGATAAGA-TT-CATTTATTTAGTCTGCCCCACTGCAATTT
1 CAGGAAGATAAGACTTGC--TTACTTAGTCTGCTCCACTGCAACTT
** * *
31094245 CAGGGGGATAAGACTTGCTTTCTTGAGTCTGCTCCACTGCAAATT
1 CAGGAAGATAAGACTTGCTTACTT-AGTCTGCTCCACTGCAACTT
* * * * *
31094290 CAAGTAGATAAGACTATCGGTT--TTAATCTGCCCCACTGCAACTT
1 CAGGAAGATAAGACT-T-GCTTACTTAGTCTGCTCCACTGCAACTT
* * * *
31094334 CAGGAAGATAAGATTTG-TCATCTTCAGTCTGC-CTCACTACAACCT
1 CAGGAAGATAAGACTTGCTTA-CTT-AGTCTGCTC-CACTGCAACTT
* * *
31094379 CAGGAGGATAAGTCTTGCTTACTTAGTCTGCTCCACTACAACTT
1 CAGGAAGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTT
* * * * * *
31094423 CAGGGAGATAAGACTAG-ATGC-GA-TCTGCT-CTCTGCAACTT
1 CAGGAAGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTT
* *
31094463 CA-GAGAGATAAGATTTGC-CATCTTCAGTCTGC-CTCACTGCAACTT
1 CAGGA-AGATAAGACTTGCTTA-CTT-AGTCTGCTC-CACTGCAACTT
* * *
31094508 CAGGAGGATAAGACTTACTTACTTAGTTTGCTCCACTGCAACTT
1 CAGGAAGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTT
* * ** * * *
31094552 CAGGGAGATAAGACTAG---A-TGGGATTTGCT-CTCTACAACTT
1 CAGGAAGATAAGACTTGCTTACTTAG-TCTGCTCCACTGCAACTT
** * *
31094592 CA-GAGAGATAAGATCCAAAG-TT--TTAAT-TCGCTCCACTACAACTT
1 CAGGA-AGATAAGA--C-TTGCTTACTTAGTCT-GCTCCACTGCAACTT
* * * * * *
31094636 CAGGGAGATAGGATTATCGGC-T--TTAATCTGCTTCACTGCCACTT
1 CAGGAAGATAAGACT-T--GCTTACTTAGTCTGCTCCACTGCAACTT
* * * *
31094680 CAAGG-AGATAAGATTTGC-CATCTTCAGTCTGCTTCACTGGAACTT
1 C-AGGAAGATAAGACTTGCTTA-CTT-AGTCTGCTCCACTGCAACTT
*
31094725 CAGGAAGATAGGACTTGCTTACTTAGTCTGCTCCACTGCAACTT
1 CAGGAAGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTT
* * * * * * *
31094769 CAGGGAGATAAGACTAG-ATGC-GA-TCTGCT-CTCTGTAACTT
1 CAGGAAGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTT
* * * *
31094809 CA-GAGAGATAAGATCTAAGGTT--TTAATCCGCTCCACTGCAACTT
1 CAGGA-AGATAAGA-CT-TGCTTACTTAGTCTGCTCCACTGCAACTT
* * * * * *
31094853 CAGGGAGATAGGATTATCGGC-T-C-TAATCTTCTCGACTGCAACTT
1 CAGGAAGATAAGACT-T--GCTTACTTAGTCTGCTCCACTGCAACTT
* * * * *
31094897 CAGGGAGATAAGATTTGC-CATCTTTAGTCTAC-CTCACTACAACTT
1 CAGGAAGATAAGACTTGCTTA-C-TTAGTCTGCTC-CACTGCAACTT
* * *
31094942 CAGGAGGATAAAACTTGCTTGCTTAGTCTGCTCCACTGCAACTT
1 CAGGAAGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTT
*
31094986 CAGGGAGATAAGACT
1 CAGGAAGATAAGACT
31095001 AGATGCGATC
Statistics
Matches: 576, Mismatches: 117, Indels: 126
0.70 0.14 0.15
Matches are distributed among these distances:
39 3 0.01
40 61 0.11
41 27 0.05
42 8 0.01
43 23 0.04
44 280 0.49
45 163 0.28
46 8 0.01
47 3 0.01
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (44 bp):
CAGGAAGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTT
Found at i:31100450 original size:31 final size:31
Alignment explanation
Indices: 31100415--31100477 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
31100405 ATTAAAGAGT
31100415 AAGACTGAAAATTTGAGAAAACAAAAACATC
1 AAGACTGAAAATTTGAGAAAACAAAAACATC
*
31100446 AAGACTGAAAATTTGAGAAAATAAAAACATC
1 AAGACTGAAAATTTGAGAAAACAAAAACATC
31100477 A
1 A
31100478 CACTTATATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.59, C:0.11, G:0.13, T:0.17
Consensus pattern (31 bp):
AAGACTGAAAATTTGAGAAAACAAAAACATC
Found at i:31105122 original size:31 final size:32
Alignment explanation
Indices: 31105084--31105146 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
31105074 AAATAAAGAA
*
31105084 AAACAAAT-AAAAAACAGAAAAATAACAAAAG
1 AAACAAATAAAAAAACAGAAAAAGAACAAAAG
*
31105115 AAACAAATAAAAAAACAGAAAAAGGACAAAAG
1 AAACAAATAAAAAAACAGAAAAAGAACAAAAG
31105147 GCGACAGGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 8 0.28
32 21 0.72
ACGTcount: A:0.76, C:0.10, G:0.10, T:0.05
Consensus pattern (32 bp):
AAACAAATAAAAAAACAGAAAAAGAACAAAAG
Found at i:31108739 original size:17 final size:16
Alignment explanation
Indices: 31108713--31108755 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
31108703 ATAGTGGAAT
31108713 AAAATAATTTAAACAAA
1 AAAATAATTTAAA-AAA
* *
31108730 AAAATTATTTGAAAAA
1 AAAATAATTTAAAAAA
31108746 AAAATAATTT
1 AAAATAATTT
31108756 TTCGAAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 12 0.52
17 11 0.48
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (16 bp):
AAAATAATTTAAAAAA
Found at i:31108754 original size:19 final size:19
Alignment explanation
Indices: 31108727--31108771 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
31108717 TAATTTAAAC
31108727 AAAAA-AATTATTT-GAAAA
1 AAAAATAATT-TTTCGAAAA
31108745 AAAAATAATTTTTCGAAAA
1 AAAAATAATTTTTCGAAAA
*
31108764 ATAAATAA
1 AAAAATAA
31108772 ATCTTTTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.29
Consensus pattern (19 bp):
AAAAATAATTTTTCGAAAA
Found at i:31111071 original size:26 final size:26
Alignment explanation
Indices: 31111042--31111093 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
31111032 TGAATTGAAG
31111042 ACTGATTATTCTTGATTGAATCATAT
1 ACTGATTATTCTTGATTGAATCATAT
31111068 ACTGATTATTCTTGATTGAATCATAT
1 ACTGATTATTCTTGATTGAATCATAT
31111094 TGATATGGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.46
Consensus pattern (26 bp):
ACTGATTATTCTTGATTGAATCATAT
Found at i:31113445 original size:112 final size:109
Alignment explanation
Indices: 31113237--31113522 Score: 394
Period size: 112 Copynumber: 2.6 Consensus size: 109
31113227 GTTAAATAAG
* * * * * *
31113237 AAATCGAAACCCAACACCTTAGGGTACG-TTCCTCAAATTTCCAAACGCAAAACATTGCCTTATT
1 AAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
** * * *
31113301 TTGAAAATTTTAAAAGAATATTTAGCCCTTTGGTTGAATGAGAA
66 TAAAAAATTTTAAAAGAATATTAAGCCATTTGGTTGAACGAGAA
*
31113345 AAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCCAAACGTAAAACATTGCCTTAT
1 AAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTT-CCAAACGCAAAACATTGCCTTAT
* *
31113410 ATTAAAAAAATTTTAAAAGGATATTAAGCCATTTGGTTGGACGAGAA
65 -TT-AAAAAATTTTAAAAGAATATTAAGCCATTTGGTTGAACGAGAA
* *
31113457 AAATCAACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAACATTGACTTATT
1 AAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
31113522 T
66 T
31113523 TGAAATATTT
Statistics
Matches: 157, Mismatches: 17, Indels: 6
0.87 0.09 0.03
Matches are distributed among these distances:
108 24 0.15
109 10 0.06
110 24 0.15
111 23 0.15
112 76 0.48
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (109 bp):
AAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
TAAAAAATTTTAAAAGAATATTAAGCCATTTGGTTGAACGAGAA
Found at i:31113873 original size:2 final size:2
Alignment explanation
Indices: 31113866--31113895 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
31113856 ATGTAAATAA
31113866 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31113896 GAGTAAGCAT
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):
AT
Found at i:31114118 original size:3 final size:3
Alignment explanation
Indices: 31114105--31114162 Score: 107
Period size: 3 Copynumber: 19.0 Consensus size: 3
31114095 GTGTATATAT
31114105 ATA AGTA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
31114151 ATA ATA ATA ATA
1 ATA ATA ATA ATA
31114163 TGACATTTGT
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 51 0.94
4 3 0.06
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:31115784 original size:20 final size:18
Alignment explanation
Indices: 31115737--31115843 Score: 62
Period size: 20 Copynumber: 5.8 Consensus size: 18
31115727 ATCTACAAAC
31115737 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
31115754 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
** *
31115774 ATTAAATTAATAAAATACT
1 ATTAAATTAAT-ATTTAAT
31115793 ATTAAGA-TAAGTA-TTAA-
1 ATTAA-ATTAA-TATTTAAT
*
31115810 ATTAAATTAAATATTAAACT
1 ATTAAATT-AATATTTAA-T
*
31115830 ATTAAAATAATATT
1 ATTAAATTAATATT
31115844 ATTTTTGGAA
Statistics
Matches: 70, Mismatches: 8, Indels: 22
0.70 0.08 0.22
Matches are distributed among these distances:
16 1 0.01
17 16 0.23
18 8 0.11
19 20 0.29
20 25 0.36
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.40
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:31115980 original size:21 final size:21
Alignment explanation
Indices: 31115931--31115980 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
31115921 CCGATGACCA
31115931 ACCGCCGTTGGCCACCGGGAC
1 ACCGCCGTTGGCCACCGGGAC
* *
31115952 GCCACCGTTGCTGCCACC-GG-C
1 ACCGCCGTTG--GCCACCGGGAC
31115973 ACCGCCGT
1 ACCGCCGT
31115981 GTCCGGTGGT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
21 15 0.65
22 2 0.09
23 6 0.26
ACGTcount: A:0.12, C:0.46, G:0.30, T:0.12
Consensus pattern (21 bp):
ACCGCCGTTGGCCACCGGGAC
Found at i:31119696 original size:63 final size:63
Alignment explanation
Indices: 31119597--31119754 Score: 244
Period size: 63 Copynumber: 2.5 Consensus size: 63
31119587 ATTTTGTGGG
* * **
31119597 TGCCATAGAGTCTTTCACCCATGGTCTTACACTGATCCTTCATCCTGGTTTGCTATCATATAA
1 TGCCATAGAGTCTTTCATCCATGGTCTTACACTGATCCTCCATCCTGGCGTGCTATCATATAA
*
31119660 TGCCATAGAGTCTTTCATCTATGGTCTTACACTGATCCTCCATCCTGGCGTGCTATCATATAA
1 TGCCATAGAGTCTTTCATCCATGGTCTTACACTGATCCTCCATCCTGGCGTGCTATCATATAA
* * *
31119723 TGTCATAAAGTCTTTCATCCATGGCCTTACAC
1 TGCCATAGAGTCTTTCATCCATGGTCTTACAC
31119755 ATTATACCTA
Statistics
Matches: 86, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
63 86 1.00
ACGTcount: A:0.23, C:0.27, G:0.15, T:0.35
Consensus pattern (63 bp):
TGCCATAGAGTCTTTCATCCATGGTCTTACACTGATCCTCCATCCTGGCGTGCTATCATATAA
Found at i:31119773 original size:44 final size:44
Alignment explanation
Indices: 31119723--31119807 Score: 120
Period size: 44 Copynumber: 1.9 Consensus size: 44
31119713 TATCATATAA
31119723 TGTCATA-AAGTCTTTCATCCATGGCCTTACACAT-TATACCTAGT
1 TGTCATAGAA-TCTTTCATCCATGGCCTTACAC-TGTATACCTAGT
* *
31119767 TGTCATAGAATCTTTCATCTATGGTCTTACACTGTATACCT
1 TGTCATAGAATCTTTCATCCATGGCCTTACACTGTATACCT
31119808 TATATCTTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
43 1 0.03
44 34 0.92
45 2 0.05
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.39
Consensus pattern (44 bp):
TGTCATAGAATCTTTCATCCATGGCCTTACACTGTATACCTAGT
Found at i:31122399 original size:12 final size:12
Alignment explanation
Indices: 31122382--31122410 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
31122372 TAGGTTTCCA
31122382 AAAATGGAAATG
1 AAAATGGAAATG
31122394 AAAATGGAAATG
1 AAAATGGAAATG
31122406 AAAAT
1 AAAAT
31122411 AAAAATAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.21, T:0.17
Consensus pattern (12 bp):
AAAATGGAAATG
Found at i:31122410 original size:18 final size:18
Alignment explanation
Indices: 31122383--31122422 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
31122373 AGGTTTCCAA
* * *
31122383 AAATGGAAATGAAAATGG
1 AAATGAAAATAAAAATAG
31122401 AAATGAAAATAAAAATAG
1 AAATGAAAATAAAAATAG
31122419 AAAT
1 AAAT
31122423 TTGCAATCCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.65, C:0.00, G:0.17, T:0.17
Consensus pattern (18 bp):
AAATGAAAATAAAAATAG
Found at i:31128363 original size:3 final size:3
Alignment explanation
Indices: 31128355--31128389 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
31128345 CGATTCATAT
31128355 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
31128390 TTAGTTGGGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:31132248 original size:29 final size:29
Alignment explanation
Indices: 31132167--31132242 Score: 107
Period size: 29 Copynumber: 2.6 Consensus size: 29
31132157 AAGTATTATA
*
31132167 TAGCTCAGGCGAGCAACCTGGTGTAATTT
1 TAGCTCAGACGAGCAACCTGGTGTAATTT
* * *
31132196 TAACTCGGACGAGCAATCTGGTGTAATTT
1 TAGCTCAGACGAGCAACCTGGTGTAATTT
*
31132225 TAGCTCAAACGAGCAACC
1 TAGCTCAGACGAGCAACC
31132243 CCGTGTGGTG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (29 bp):
TAGCTCAGACGAGCAACCTGGTGTAATTT
Found at i:31132428 original size:57 final size:57
Alignment explanation
Indices: 31132364--31132491 Score: 202
Period size: 57 Copynumber: 2.2 Consensus size: 57
31132354 GTCAATTTGA
* *
31132364 TATGTCATTGAAATGAATGATGGGTAACTGGAATCACCTTATAGATTGTTAATGGAT
1 TATGTCATTGAAATGAATGATGGGTAACTGGAATCACCTTATAGACTGCTAATGGAT
* * *
31132421 TATGTCATTGAAATGAATTATGTGTTACTGGAATCACCTTATAGACTGCTAATGGAT
1 TATGTCATTGAAATGAATGATGGGTAACTGGAATCACCTTATAGACTGCTAATGGAT
*
31132478 TATGCCATTGAAAT
1 TATGTCATTGAAAT
31132492 AAATCATGTA
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 65 1.00
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.36
Consensus pattern (57 bp):
TATGTCATTGAAATGAATGATGGGTAACTGGAATCACCTTATAGACTGCTAATGGAT
Found at i:31132519 original size:57 final size:57
Alignment explanation
Indices: 31132364--31132519 Score: 159
Period size: 57 Copynumber: 2.7 Consensus size: 57
31132354 GTCAATTTGA
* * * ** * * *
31132364 TATGTCATTGAAATGAATGATGGGTAACTGGAATCACCTTATAGATTGTTAATGGAT
1 TATGCCATTGAAATAAATCATGTATAACTGGAATAACCTTATAGACTGCTAATGGAT
* * * * * *
31132421 TATGTCATTGAAATGAATTATGTGTTACTGGAATCACCTTATAGACTGCTAATGGAT
1 TATGCCATTGAAATAAATCATGTATAACTGGAATAACCTTATAGACTGCTAATGGAT
* * *
31132478 TATGCCATTGAAATAAATCATGTATAATTGGTATAATCTTAT
1 TATGCCATTGAAATAAATCATGTATAACTGGAATAACCTTAT
31132520 GGATTGATGA
Statistics
Matches: 85, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
57 85 1.00
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.37
Consensus pattern (57 bp):
TATGCCATTGAAATAAATCATGTATAACTGGAATAACCTTATAGACTGCTAATGGAT
Found at i:31133948 original size:18 final size:17
Alignment explanation
Indices: 31133925--31133963 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
31133915 TTTTTTTAGC
*
31133925 AATTTTATACATTTATA
1 AATTTTATAAATTTATA
31133942 GAATTTTATAAATTTATA
1 -AATTTTATAAATTTATA
31133960 AATT
1 AATT
31133964 CCTATTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (17 bp):
AATTTTATAAATTTATA
Found at i:31134399 original size:31 final size:31
Alignment explanation
Indices: 31134355--31134434 Score: 99
Period size: 31 Copynumber: 2.6 Consensus size: 31
31134345 ATTTGAGAAA
* * *
31134355 CCCTTGTTCGAGCATTTTCAAAAA-GATATGT
1 CCCTTATTTGAGCATTTTCAAAAATG-TATGG
*
31134386 CCCTTATTTGAGCATTTTCAAAAATGTTTGG
1 CCCTTATTTGAGCATTTTCAAAAATGTATGG
*
31134417 CCCTTATTTGACCATTTT
1 CCCTTATTTGAGCATTTT
31134435 GAAAGGGTTG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
31 42 0.98
32 1 0.02
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.41
Consensus pattern (31 bp):
CCCTTATTTGAGCATTTTCAAAAATGTATGG
Found at i:31134455 original size:29 final size:31
Alignment explanation
Indices: 31134413--31134471 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 31
31134403 TCAAAAATGT
*
31134413 TTGGCCCTTATTTGACCA-TTTTG-AAAGGG
1 TTGGCCCTTATTTGAACACTTTTGTAAAGGG
31134442 TTGG-CCTTCATTTGAACACTTTTGTAAAGG
1 TTGGCCCTT-ATTTGAACACTTTTGTAAAGG
31134472 TTAGGTCATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 4 0.15
29 12 0.46
30 5 0.19
31 5 0.19
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.39
Consensus pattern (31 bp):
TTGGCCCTTATTTGAACACTTTTGTAAAGGG
Found at i:31136795 original size:44 final size:44
Alignment explanation
Indices: 31136726--31136809 Score: 132
Period size: 44 Copynumber: 1.9 Consensus size: 44
31136716 ACTCTGTTTT
* * *
31136726 TAGTTTCCCACTTAAACTTTGATTAGTGTAGGTTATTTTAATAG
1 TAGTTTCCCACTTAAACTCTAATTAGTGTAGCTTATTTTAATAG
*
31136770 TAGTTTTCCACTTAAACTCTAATTAGTGTAGCTTATTTTA
1 TAGTTTCCCACTTAAACTCTAATTAGTGTAGCTTATTTTA
31136810 TTCTTATTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.46
Consensus pattern (44 bp):
TAGTTTCCCACTTAAACTCTAATTAGTGTAGCTTATTTTAATAG
Found at i:31138522 original size:21 final size:21
Alignment explanation
Indices: 31138485--31138527 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
31138475 TCATACATTG
*
31138485 TTTTAAAATTTATTATTTTTA
1 TTTTAAAATTTATTATTATTA
*
31138506 TTTTCAAATTCTA-TATTATTA
1 TTTTAAAATT-TATTATTATTA
31138527 T
1 T
31138528 GTGTTTCATC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTTAAAATTTATTATTATTA
Found at i:31139013 original size:16 final size:15
Alignment explanation
Indices: 31138990--31139019 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
31138980 ATATTGCAAC
31138990 TTAAAAATGTTGTTA
1 TTAAAAATGTTGTTA
31139005 TTAATAAATGTTGTT
1 TTAA-AAATGTTGTT
31139020 GTATTTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (15 bp):
TTAAAAATGTTGTTA
Found at i:31142899 original size:24 final size:25
Alignment explanation
Indices: 31142845--31142897 Score: 92
Period size: 23 Copynumber: 2.2 Consensus size: 25
31142835 AGCTATTTAA
31142845 AATTTACTAAAATTAAAAAAAATAT
1 AATTTACTAAAATTAAAAAAAATAT
31142870 AATTTACTAAAA-T-AAAAAAATAT
1 AATTTACTAAAATTAAAAAAAATAT
31142893 AATTT
1 AATTT
31142898 TAATAATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 15 0.54
24 1 0.04
25 12 0.43
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (25 bp):
AATTTACTAAAATTAAAAAAAATAT
Found at i:31142905 original size:22 final size:22
Alignment explanation
Indices: 31142845--31142907 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 22
31142835 AGCTATTTAA
31142845 AATTTACTAAAATTAAAAAAAATAT
1 AATTTA-TAAAA-T-AAAAAAATAT
31142870 AATTTACTAAAATAAAAAAATAT
1 AATTTA-TAAAATAAAAAAATAT
31142893 AATTT-TAATAATAAA
1 AATTTATAA-AATAAA
31142908 TATAAATTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
21 3 0.08
22 6 0.16
23 15 0.41
24 1 0.03
25 12 0.32
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (22 bp):
AATTTATAAAATAAAAAAATAT
Found at i:31143282 original size:29 final size:29
Alignment explanation
Indices: 31143251--31143306 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
31143241 ATTTTAAATA
31143251 AAAATTAAAT-ATTTCTTATATTTTTATT
1 AAAATTAAATAATTTCTTATATTTTTATT
* * *
31143279 AAAATTTAATAATTTTTTATTTTTTTAT
1 AAAATTAAATAATTTCTTATATTTTTAT
31143307 CATTTTTTGC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 9 0.38
29 15 0.62
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (29 bp):
AAAATTAAATAATTTCTTATATTTTTATT
Found at i:31152804 original size:84 final size:84
Alignment explanation
Indices: 31152691--31152854 Score: 217
Period size: 84 Copynumber: 2.0 Consensus size: 84
31152681 CAACTAAATC
* * *
31152691 AAGCGAAAGACCCAAAAATAAAAGAAAAACTGTGA-AGGGAAGAGAATAATAAAAGGAATAAAGA
1 AAGCGAAAGACCCAAAAATAAAAGAAAAACTATGAGA-GGAAAAGAAGAATAAAAGGAATAAAGA
* *
31152755 ACAATGAAATACCATAAACG
65 AAAAAGAAATACCATAAACG
* *
31152775 AAGCGGAAGACCCAGAATAA-AAAAG-AAAACTATGAGAGTAAAAGAAGAATAAAAGGAATAAAG
1 AAGCGAAAGACCCA-AA-AATAAAAGAAAAACTATGAGAGGAAAAGAAGAATAAAAGGAATAAAG
31152838 AAAAAAGAAATACCATA
64 AAAAAAGAAATACCATA
31152855 TTGTGAGCCC
Statistics
Matches: 70, Mismatches: 7, Indels: 6
0.84 0.08 0.07
Matches are distributed among these distances:
84 60 0.86
85 8 0.11
86 2 0.03
ACGTcount: A:0.61, C:0.10, G:0.19, T:0.10
Consensus pattern (84 bp):
AAGCGAAAGACCCAAAAATAAAAGAAAAACTATGAGAGGAAAAGAAGAATAAAAGGAATAAAGAA
AAAAGAAATACCATAAACG
Found at i:31162488 original size:41 final size:42
Alignment explanation
Indices: 31162443--31162533 Score: 98
Period size: 41 Copynumber: 2.2 Consensus size: 42
31162433 TCCACCAGGC
** *
31162443 TTCGTGCCGA-TGAATT-ATATCAGGCTTTTAGCCTAGAAGGT
1 TTCGTGCCGAGTGAATTGA-ATCAGGCCCTGAGCCTAGAAGGT
* * *
31162484 TTCGTGTC-AGTGTATTGAATCAGGCCCTGAGCCTAGTAGGT
1 TTCGTGCCGAGTGAATTGAATCAGGCCCTGAGCCTAGAAGGT
31162525 TTCGTGCCG
1 TTCGTGCCG
31162534 GTGTATTTGT
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
40 1 0.03
41 38 0.95
42 1 0.03
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.33
Consensus pattern (42 bp):
TTCGTGCCGAGTGAATTGAATCAGGCCCTGAGCCTAGAAGGT
Found at i:31167416 original size:19 final size:19
Alignment explanation
Indices: 31167392--31167432 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
31167382 TATTTTAAAG
*
31167392 TTATTTAGATAGATAAATC
1 TTATTTAGATAGACAAATC
*
31167411 TTATTTAGGTAGACAAATC
1 TTATTTAGATAGACAAATC
31167430 TTA
1 TTA
31167433 GAATAAATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.41
Consensus pattern (19 bp):
TTATTTAGATAGACAAATC
Found at i:31171258 original size:19 final size:19
Alignment explanation
Indices: 31171220--31171260 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
31171210 TATTTTAAAG
* **
31171220 TTATTTATGTAGATTTATC
1 TTATTTAGGTAGATAAATC
31171239 TTATTTAGGTAGATAAATC
1 TTATTTAGGTAGATAAATC
31171258 TTA
1 TTA
31171261 GAATAAATCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.12, T:0.51
Consensus pattern (19 bp):
TTATTTAGGTAGATAAATC
Found at i:31171346 original size:41 final size:41
Alignment explanation
Indices: 31171298--31171379 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
31171288 ATATTTTATT
*
31171298 TTATGTTTTAGTAGTTTATTAGAATAAGGGAATTATTTTCC
1 TTATGTTTTAGTAGTTTATTAGAATAAGAGAATTATTTTCC
31171339 TTATGTTTTAGTAGTTTATTAGAATAAGAGAATTATTTTCC
1 TTATGTTTTAGTAGTTTATTAGAATAAGAGAATTATTTTCC
31171380 CAATTAAGTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.30, C:0.05, G:0.16, T:0.49
Consensus pattern (41 bp):
TTATGTTTTAGTAGTTTATTAGAATAAGAGAATTATTTTCC
Found at i:31183867 original size:30 final size:30
Alignment explanation
Indices: 31183831--31183988 Score: 237
Period size: 30 Copynumber: 5.3 Consensus size: 30
31183821 GACGCAAATA
31183831 GGGAGACCTGCTCCTGCTTCTTCGATTTCT
1 GGGAGACCTGCTCCTGCTTCTTCGATTTCT
* *
31183861 GGGAGACCTACTCCTGCTTCTTCGGTTTCT
1 GGGAGACCTGCTCCTGCTTCTTCGATTTCT
31183891 GGGAGACCTGCTCCTGCTTCTAT-GATTTCT
1 GGGAGACCTGCTCCTGCTTCT-TCGATTTCT
* *
31183921 AGGAGACCTGCTCCTGCTTCTACGATTTCT
1 GGGAGACCTGCTCCTGCTTCTTCGATTTCT
* * *
31183951 GGGAGACCTGCTTCTGCTTCTCCGGTTTCT
1 GGGAGACCTGCTCCTGCTTCTTCGATTTCT
31183981 GGGAGACC
1 GGGAGACC
31183989 AACTAAAACA
Statistics
Matches: 116, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
30 115 0.99
31 1 0.01
ACGTcount: A:0.12, C:0.29, G:0.25, T:0.34
Consensus pattern (30 bp):
GGGAGACCTGCTCCTGCTTCTTCGATTTCT
Found at i:31184936 original size:20 final size:22
Alignment explanation
Indices: 31184897--31184938 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
31184887 AATTCTAAAC
31184897 TTGCTAAACATACAACAGATAA
1 TTGCTAAACATACAACAGATAA
*
31184919 TTGC-AAAC-TACAAGAGATAA
1 TTGCTAAACATACAACAGATAA
31184939 AGAGTCGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 11 0.58
21 4 0.21
22 4 0.21
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (22 bp):
TTGCTAAACATACAACAGATAA
Found at i:31197117 original size:22 final size:20
Alignment explanation
Indices: 31197081--31197139 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 20
31197071 GGCCCGGCCC
31197081 ATTT-TTTTAATAAATACCAAAA
1 ATTTATTTTAA-AAATA--AAAA
31197103 ATTTATTTTAAAAATTAAAAA
1 ATTTATTTTAAAAA-TAAAAA
**
31197124 AAGTATTTTAAAAATA
1 ATTTATTTTAAAAATA
31197140 TTTTAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 2 0.06
21 16 0.48
22 7 0.21
23 8 0.24
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (20 bp):
ATTTATTTTAAAAATAAAAA
Found at i:31197161 original size:28 final size:28
Alignment explanation
Indices: 31197106--31197192 Score: 138
Period size: 28 Copynumber: 3.0 Consensus size: 28
31197096 ACCAAAAATT
31197106 TATTTTAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATT--AAAAA-TATTTTAAAAA
31197138 TATTTTAAAATTAAAAATATTTTAAAAA
1 TATTTTAAAATTAAAAATATTTTAAAAA
31197166 TATTTTAAAATTAAAAATATTTTAAAA
1 TATTTTAAAATTAAAAATATTTTAAAA
31197193 TTAAAAAATA
Statistics
Matches: 55, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
28 38 0.69
29 5 0.09
31 6 0.11
32 6 0.11
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (28 bp):
TATTTTAAAATTAAAAATATTTTAAAAA
Found at i:31197187 original size:45 final size:46
Alignment explanation
Indices: 31197131--31197228 Score: 155
Period size: 45 Copynumber: 2.2 Consensus size: 46
31197121 AAAAAGTATT
* *
31197131 TTAAAAATATTTTAAAATT-AAAAATATTTTAAAAA-TATTTTAAAA
1 TTAAAAATATTTTAAAATTAAAAAATA-ATAAAAAAGTATTTTAAAA
31197176 TTAAAAATATTTTAAAATTAAAAAATAATAAAAAAGTATTTTAAAA
1 TTAAAAATATTTTAAAATTAAAAAATAATAAAAAAGTATTTTAAAA
31197222 TTAAAAA
1 TTAAAAA
31197229 ATAATAAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
45 25 0.51
46 24 0.49
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (46 bp):
TTAAAAATATTTTAAAATTAAAAAATAATAAAAAAGTATTTTAAAA
Found at i:31197192 original size:11 final size:11
Alignment explanation
Indices: 31197121--31197175 Score: 66
Period size: 11 Copynumber: 5.4 Consensus size: 11
31197111 TAAAAATTAA
31197121 AAAAAGTATTTT
1 AAAAA-TATTTT
31197133 AAAAATATTTT
1 AAAAATATTTT
31197144 --AAA-A--TT
1 AAAAATATTTT
31197150 AAAAATATTTT
1 AAAAATATTTT
31197161 AAAAATATTTT
1 AAAAATATTTT
31197172 AAAA
1 AAAA
31197176 TTAAAAATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
6 2 0.05
8 4 0.11
9 4 0.11
11 23 0.61
12 5 0.13
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:31197202 original size:18 final size:17
Alignment explanation
Indices: 31197131--31197199 Score: 96
Period size: 17 Copynumber: 4.4 Consensus size: 17
31197121 AAAAAGTATT
31197131 TTAAAAATATTTTAAAA
1 TTAAAAATATTTTAAAA
31197148 TTAAAAATA--TT----
1 TTAAAAATATTTTAAAA
31197159 TTAAAAATATTTTAAAA
1 TTAAAAATATTTTAAAA
31197176 TTAAAAATATTTTAAAA
1 TTAAAAATATTTTAAAA
31197193 TTAAAAA
1 TTAAAAA
31197200 ATAATAAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
11 9 0.20
13 2 0.04
15 2 0.04
17 33 0.72
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TTAAAAATATTTTAAAA
Found at i:31197220 original size:29 final size:29
Alignment explanation
Indices: 31197178--31197247 Score: 133
Period size: 29 Copynumber: 2.4 Consensus size: 29
31197168 TTTTAAAATT
31197178 AAAAA-TATTTTAAAATTAAAAAATAATA
1 AAAAAGTATTTTAAAATTAAAAAATAATA
31197206 AAAAAGTATTTTAAAATTAAAAAATAATA
1 AAAAAGTATTTTAAAATTAAAAAATAATA
31197235 AAAAAGTATTTTA
1 AAAAAGTATTTTA
31197248 TATCGGGCCG
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (29 bp):
AAAAAGTATTTTAAAATTAAAAAATAATA
Found at i:31197261 original size:5 final size:5
Alignment explanation
Indices: 31197251--31197282 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
31197241 TATTTTATAT
31197251 CGGGC CGGGC CGGGC CGGGC CGGGC TCGGGC C
1 CGGGC CGGGC CGGGC CGGGC CGGGC -CGGGC C
31197283 AAAAAAGTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.00, C:0.41, G:0.56, T:0.03
Consensus pattern (5 bp):
CGGGC
Found at i:31198011 original size:5 final size:5
Alignment explanation
Indices: 31198001--31198053 Score: 52
Period size: 5 Copynumber: 10.0 Consensus size: 5
31197991 GGTCTACCTG
* * *
31198001 TAAAA TAAAA TAAAA TAGAAG GAAGAA GAAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TA-AAA TAA-AA -TAAAA TAAAA TAAAA TAAAA
31198049 TAAAA
1 TAAAA
31198054 AAATGTGCAA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
5 32 0.80
6 6 0.15
7 2 0.05
ACGTcount: A:0.75, C:0.00, G:0.09, T:0.15
Consensus pattern (5 bp):
TAAAA
Found at i:31212192 original size:30 final size:31
Alignment explanation
Indices: 31212158--31212216 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
31212148 GCTTCTGAAG
*
31212158 CTGAGCCTTTAGCTCCATAAGCT-CTTTAAT
1 CTGAGCATTTAGCTCCATAAGCTCCTTTAAT
*
31212188 CTGAGCATTTCGCTCCATAAGCTCCTTTA
1 CTGAGCATTTAGCTCCATAAGCTCCTTTA
31212217 GTGTCATACG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.22, C:0.29, G:0.14, T:0.36
Consensus pattern (31 bp):
CTGAGCATTTAGCTCCATAAGCTCCTTTAAT
Found at i:31215832 original size:47 final size:47
Alignment explanation
Indices: 31215763--31215869 Score: 187
Period size: 47 Copynumber: 2.3 Consensus size: 47
31215753 CACAAGATAG
*
31215763 CTAATAATCGAATTCATTGATAACACTAACACCCTTCCAAACTCTTA
1 CTAATAATCGAACTCATTGATAACACTAACACCCTTCCAAACTCTTA
31215810 CTAATAATCGAACTCATTGATAACACTAACACCCTTCCAAACTCTTA
1 CTAATAATCGAACTCATTGATAACACTAACACCCTTCCAAACTCTTA
**
31215857 CCGATAATCGAAC
1 CTAATAATCGAAC
31215870 CACAACCCCA
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 57 1.00
ACGTcount: A:0.38, C:0.29, G:0.06, T:0.27
Consensus pattern (47 bp):
CTAATAATCGAACTCATTGATAACACTAACACCCTTCCAAACTCTTA
Found at i:31217893 original size:22 final size:22
Alignment explanation
Indices: 31217859--31217912 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
31217849 AAATGATAGC
* * *
31217859 AAAATAGTGAAAAAATAA-CAAT
1 AAAATAG-CAAAAAAAAAGCAAA
*
31217881 AAAATAGCAAAAAAAAAGTAAA
1 AAAATAGCAAAAAAAAAGCAAA
31217903 AAAATAGCAA
1 AAAATAGCAA
31217913 GGAAAAGCAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 8 0.30
22 19 0.70
ACGTcount: A:0.72, C:0.06, G:0.09, T:0.13
Consensus pattern (22 bp):
AAAATAGCAAAAAAAAAGCAAA
Found at i:31217895 original size:11 final size:11
Alignment explanation
Indices: 31217868--31217912 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
31217858 CAAAATAGTG
*
31217868 AAAAAATAACA
1 AAAAAATAGCA
*
31217879 ATAAAATAGCA
1 AAAAAATAGCA
* *
31217890 AAAAAAAAGTA
1 AAAAAATAGCA
31217901 AAAAAATAGCA
1 AAAAAATAGCA
31217912 A
1 A
31217913 GGAAAAGCAG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.76, C:0.07, G:0.07, T:0.11
Consensus pattern (11 bp):
AAAAAATAGCA
Found at i:31218787 original size:46 final size:40
Alignment explanation
Indices: 31218676--31219152 Score: 449
Period size: 37 Copynumber: 11.8 Consensus size: 40
31218666 TTTGACATAT
*
31218676 GACCTCTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCTA
1 GACCACTTATCACTTTGTCACTTGATCAGATAAGTGT-G-TA
*
31218716 GGCTACCACTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAA
1 -G--ACCACTTATCACTTTGTCACTTGATCAGATAAGTGT-G-T--A
*
31218763 GCTACCACTTATCACTTTATCACTTGATCAGATAA--GTGTA
1 G--ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTGTA
*
31218803 G-CCACTTATCACTTTGTCTCTTGATCAGATAA--GTGTA
1 GACCACTTATCACTTTGTCACTTGATCAGATAAGTGTGTA
**
31218840 -ACCACTTATCACTTTGTTTCTTGATCAGATAA--GTGTA
1 GACCACTTATCACTTTGTCACTTGATCAGATAAGTGTGTA
*
31218877 G-CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAA
1 GACCACTTATCACTTTGTCACTTGATCAGATAAGTGT-G-T--A
*
31218920 GCTACCACTTATCACTTTGTCTCTTGATCAGATAAGT-T-TA
1 G--ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTGTA
31218960 G--CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAA
1 GACCACTTATCACTTTGTCACTTGATCAGATAAGTGT-G-T--A
*
31219002 GCTACCACTTATCACTTTGTCTCTTGATCAGATAAGT-T-TA
1 G--ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTGTA
31219042 G--CACTTATCACTTTGTCACTTGATCAGATAA--GTGTA
1 GACCACTTATCACTTTGTCACTTGATCAGATAAGTGTGTA
31219078 -ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAA
1 GACCACTTATCACTTTGTCACTTGATCAGATAAGTGT-G-T---A
*
31219122 CTACCACTTATCACTTTGTCACTTGATCAGA
1 -GACCACTTATCACTTTGTCACTTGATCAGA
31219153 AGTACTCAAA
Statistics
Matches: 385, Mismatches: 11, Indels: 75
0.82 0.02 0.16
Matches are distributed among these distances:
35 1 0.00
36 62 0.16
37 130 0.34
39 4 0.01
40 9 0.02
41 3 0.01
42 5 0.01
43 14 0.04
44 7 0.02
45 23 0.06
46 126 0.33
47 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.36
Consensus pattern (40 bp):
GACCACTTATCACTTTGTCACTTGATCAGATAAGTGTGTA
Found at i:31218863 original size:74 final size:79
Alignment explanation
Indices: 31218721--31219116 Score: 519
Period size: 82 Copynumber: 5.0 Consensus size: 79
31218711 AGCTAGGCTA
* * *
31218721 CCACTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCACTTATCACTTTATCAC
1 CCACTTATCACTTTGTCACTTGATCAGATAAG-GTAGCT-AA-C-ACCACTTATCACTTTGTCTC
31218786 TTGATCAGATAAGTGTAG
62 TTGATCAGATAAGTGTAG
* *
31218804 CCACTTATCACTTTGTCTCTTGATCAGATAA-GT-G-T-A-ACCACTTATCACTTTGTTTCTTGA
1 CCACTTATCACTTTGTCACTTGATCAGATAAGGTAGCTAACACCACTTATCACTTTGTCTCTTGA
31218864 TCAGATAAGTGTAG
66 TCAGATAAGTGTAG
*
31218878 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTC
1 CCACTTATCACTTTGTCACTTGATCAGATAAG-GTAGCT-AA-C-ACCACTTATCACTTTGTCTC
*
31218943 TTGATCAGATAAGTTTAG
62 TTGATCAGATAAGTGTAG
31218961 -CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTC
1 CCACTTATCACTTTGTCACTTGATCAGATAAG-GTAGCT-AA-C-ACCACTTATCACTTTGTCTC
*
31219025 TTGATCAGATAAGTTTAG
62 TTGATCAGATAAGTGTAG
*
31219043 -CACTTATCACTTTGTCACTTGATCAGATAA-GT-G-T-A-ACCACTTATCACTTTGTCACTTGA
1 CCACTTATCACTTTGTCACTTGATCAGATAAGGTAGCTAACACCACTTATCACTTTGTCTCTTGA
31219102 TCAGATAAGTGTAG
66 TCAGATAAGTGTAG
31219116 C
1 C
31219117 TAAAACTACC
Statistics
Matches: 293, Mismatches: 10, Indels: 29
0.88 0.03 0.09
Matches are distributed among these distances:
73 36 0.12
74 66 0.23
76 3 0.01
77 2 0.01
78 2 0.01
79 2 0.01
80 4 0.01
81 2 0.01
82 111 0.38
83 65 0.22
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (79 bp):
CCACTTATCACTTTGTCACTTGATCAGATAAGGTAGCTAACACCACTTATCACTTTGTCTCTTGA
TCAGATAAGTGTAG
Found at i:31218965 original size:36 final size:36
Alignment explanation
Indices: 31218925--31219116 Score: 240
Period size: 36 Copynumber: 5.0 Consensus size: 36
31218915 CTAAAGCTAC
*
31218925 CACTTATCACTTTGTCTCTTGATCAGATAAGTTTAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTTTAG
31218961 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGT-T---T--AG
*
31219003 CTACCACTTATCACTTTGTCTCTTGATCAGATAAGTTTAG
1 ----CACTTATCACTTTGTCACTTGATCAGATAAGTTTAG
* *
31219043 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGT-TTAG
*
31219080 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTTTAG
31219116 C
1 C
31219117 TAAAACTACC
Statistics
Matches: 137, Mismatches: 8, Indels: 22
0.82 0.05 0.13
Matches are distributed among these distances:
36 64 0.47
37 35 0.26
40 3 0.02
42 3 0.02
45 1 0.01
46 31 0.23
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.37
Consensus pattern (36 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTTTAG
Found at i:31223436 original size:16 final size:16
Alignment explanation
Indices: 31223412--31223451 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
31223402 TTTTTGGAAA
* * *
31223412 TTATCTAATTAATTTT
1 TTATTTAATTAAATAT
31223428 TTATTTAATTAAATAT
1 TTATTTAATTAAATAT
31223444 TTATTTAA
1 TTATTTAA
31223452 ATTTTAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (16 bp):
TTATTTAATTAAATAT
Found at i:31230696 original size:16 final size:16
Alignment explanation
Indices: 31230672--31230709 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
31230662 TTTGGTTCGC
* *
31230672 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
31230688 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
31230704 TGTAAT
1 TGTAAT
31230710 AGCAAATCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.34, T:0.34
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:31230794 original size:39 final size:43
Alignment explanation
Indices: 31230689--31230797 Score: 109
Period size: 45 Copynumber: 2.6 Consensus size: 43
31230679 GATTAGAGGT
31230689 GTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 GTAA-GGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
* * * ***
31230733 TGTAATGGAATAAAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 -GTAA-GGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
31230777 -T-A-GAATAGAGGTGTAATAGCA
1 GTAAGGAATAGAGGTGTAATAGCA
31230798 TAATGGAAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
39 15 0.28
41 1 0.02
42 1 0.02
44 16 0.30
45 21 0.39
ACGTcount: A:0.36, C:0.06, G:0.28, T:0.31
Consensus pattern (43 bp):
GTAAGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
Found at i:31230960 original size:16 final size:16
Alignment explanation
Indices: 31230923--31230964 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
31230913 TTAATCATAT
*
31230923 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
31230939 TT-AAATATATTATAA
1 TTAAAATATATTATAA
31230954 TTAAAATATAT
1 TTAAAATATAT
31230965 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:31230971 original size:14 final size:15
Alignment explanation
Indices: 31230932--31231093 Score: 58
Period size: 15 Copynumber: 10.9 Consensus size: 15
31230922 TTTAAACATA
*
31230932 ATTATTATTAAATAT
1 ATTATAATTAAATAT
31230947 ATTATAATTAAAATAT
1 ATTATAATT-AAATAT
* *
31230963 ATAATTTAATAAAAT-T
1 AT--TATAATTAAATAT
*
31230979 CTTAATAATT-AATATT
1 ATT-ATAATTAAATA-T
* * *
31230995 CTTAT-A-TGAATTT
1 ATTATAATTAAATAT
*
31231008 ACTTA-AATCATAATAT
1 A-TTATAATTA-AATAT
* *
31231024 ATGATACTGTAAA-AT
1 ATTATAAT-TAAATAT
31231039 A-TA-AATTAACATA-
1 ATTATAATTAA-ATAT
*
31231052 ATTATTATTAAATAT
1 ATTATAATTAAATAT
31231067 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
31231081 A-TATAATTTAATA
1 ATTATAATTAAATA
31231094 AAATTCTTAA
Statistics
Matches: 109, Mismatches: 19, Indels: 39
0.65 0.11 0.23
Matches are distributed among these distances:
12 3 0.03
13 15 0.14
14 23 0.21
15 35 0.32
16 23 0.21
17 5 0.05
18 5 0.05
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:31231071 original size:120 final size:121
Alignment explanation
Indices: 31230921--31231218 Score: 503
Period size: 120 Copynumber: 2.5 Consensus size: 121
31230911 ATTTAATCAT
*
31230921 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
* * *
31230986 ATTAATATTCTTATATGAATTTACTTAAATCATAATATATGATACTGTAAAATATAA
66 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGA-AA
31231043 A-TT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
31231106 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAA
66 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAA
* * *
31231162 ATTTGAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
31231219 TAAAATAATT
Statistics
Matches: 168, Mismatches: 6, Indels: 6
0.93 0.03 0.03
Matches are distributed among these distances:
119 3 0.02
120 160 0.95
121 4 0.02
122 1 0.01
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.43
Consensus pattern (121 bp):
ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAA
Found at i:31231288 original size:26 final size:28
Alignment explanation
Indices: 31231259--31231319 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
31231249 TATGAATTTG
*
31231259 TATAATTTAA-AATAAT-TATTATTACA
1 TATAATTTAATAATAATATATAATTACA
*
31231285 TATAATTTAATAATAATATATAATTTCA
1 TATAATTTAATAATAATATATAATTACA
*
31231313 TAAAATT
1 TATAATT
31231320 CTTGATAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (28 bp):
TATAATTTAATAATAATATATAATTACA
Found at i:31234134 original size:3 final size:3
Alignment explanation
Indices: 31234120--31234149 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
31234110 CCAAAATCCT
*
31234120 TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
31234150 CCCACTATTT
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:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:31237201 original size:7 final size:8
Alignment explanation
Indices: 31237184--31237217 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
31237174 GGACCAGTCC
31237184 AATTAAAA
1 AATTAAAA
31237192 AATT-AAA
1 AATTAAAA
31237199 AATTCAAAA
1 AATT-AAAA
31237208 AATTAAAA
1 AATTAAAA
31237216 AA
1 AA
31237218 CCTGGTTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
7 7 0.29
8 10 0.42
9 7 0.29
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (8 bp):
AATTAAAA
Found at i:31239272 original size:40 final size:40
Alignment explanation
Indices: 31239192--31239273 Score: 94
Period size: 40 Copynumber: 2.0 Consensus size: 40
31239182 AACATAAGTA
* * *
31239192 ATAAGTAATAACTAACCCAAAAGTCTGGAAATCTGTTTTT
1 ATAAGTAACAACTAACCCAAAAGTCTAGAAATCTGCTTTT
* * *
31239232 ATAAGTAACAAGTAATCCAAAAGTC-AGAAGGTCTGCTTTT
1 ATAAGTAACAACTAACCCAAAAGTCTAGAA-ATCTGCTTTT
31239272 AT
1 AT
31239274 TTTCTAAAGC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
39 3 0.09
40 32 0.91
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (40 bp):
ATAAGTAACAACTAACCCAAAAGTCTAGAAATCTGCTTTT
Found at i:31239353 original size:74 final size:72
Alignment explanation
Indices: 31239262--31239425 Score: 206
Period size: 74 Copynumber: 2.2 Consensus size: 72
31239252 AAGTCAGAAG
* *
31239262 GTCTGCTTTTATTTTCTAAAGC-TTATGTTTGGTGCTAAGTACA-AAGTAAAACATAAGTAACAA
1 GTCTGTTTTTATTTTCTAAA-CTTTATGTTTGGTGCAAAGTACAGAA--AAAACATAAGTAACAA
*
31239325 GTAACCCAAAA
63 GTAACAC-AAA
* * * *
31239336 GTCTGTTTTTATCTTCTAAACTTTATTTTTTGTGCAAAGTACAGAAAAAACCTAAGTAACAAGTA
1 GTCTGTTTTTATTTTCTAAACTTTATGTTTGGTGCAAAGTACAGAAAAAACATAAGTAACAAGTA
31239401 ACACAAA
66 ACACAAA
*
31239408 GTCCGTTTTTATTTTCTA
1 GTCTGTTTTTATTTTCTA
31239426 TTATTACAGA
Statistics
Matches: 79, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
72 19 0.24
73 22 0.28
74 36 0.46
75 2 0.03
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (72 bp):
GTCTGTTTTTATTTTCTAAACTTTATGTTTGGTGCAAAGTACAGAAAAAACATAAGTAACAAGTA
ACACAAA
Found at i:31239559 original size:161 final size:161
Alignment explanation
Indices: 31239383--31239704 Score: 617
Period size: 161 Copynumber: 2.0 Consensus size: 161
31239373 AGTACAGAAA
*
31239383 AAACCTAAGTAACAAGTAACACAAAGTCCGTTTTTATTTTCTATTATTACAGATGAAAAGACGAG
1 AAACCTAAGTAACAAGTAACACAAAGTCCGTTTTTATTTTCTATTATTACAGATGAAAAGACAAG
31239448 CAAGATACAATAGCCAACCACACAAAGGCACGTCCATAGTTCAAAGACTAATTTCTTTGAGTGTG
66 CAAGATACAATAGCCAACCACACAAAGGCACGTCCATAGTTCAAAGACTAATTTCTTTGAGTGTG
31239513 CCTAGATGTTTGGAGGAACAGGGGGTGAGGT
131 CCTAGATGTTTGGAGGAACAGGGGGTGAGGT
31239544 AAACCTAAGTAACAAGTAACACAAAGTCCGTTTTTATTTTCTATTATTACAGATGAAAAGACAAG
1 AAACCTAAGTAACAAGTAACACAAAGTCCGTTTTTATTTTCTATTATTACAGATGAAAAGACAAG
31239609 CAAGATACAATAGCCAACCACACAAAGGCACGTCCATAGTTCAAAGACTAATTTCTTTGAGTGTG
66 CAAGATACAATAGCCAACCACACAAAGGCACGTCCATAGTTCAAAGACTAATTTCTTTGAGTGTG
* *
31239674 CCTGGGTGTTTGGAGGAACAGGGGGTGAGGT
131 CCTAGATGTTTGGAGGAACAGGGGGTGAGGT
31239705 GAGGGCTTAG
Statistics
Matches: 158, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
161 158 1.00
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.25
Consensus pattern (161 bp):
AAACCTAAGTAACAAGTAACACAAAGTCCGTTTTTATTTTCTATTATTACAGATGAAAAGACAAG
CAAGATACAATAGCCAACCACACAAAGGCACGTCCATAGTTCAAAGACTAATTTCTTTGAGTGTG
CCTAGATGTTTGGAGGAACAGGGGGTGAGGT
Found at i:31242171 original size:66 final size:66
Alignment explanation
Indices: 31242064--31242198 Score: 225
Period size: 66 Copynumber: 2.0 Consensus size: 66
31242054 TGAGTGTCCA
* * * *
31242064 AAAATTACATGAAGACCATCTCAACAAGTTTTGTGATTATCTCCAAAGAACATTACTTCCTATAA
1 AAAATTACATGAAGACAATCTCAACAAGTTTTGTGACTATCTCCAAAGAACATTAATTCCTACAA
31242129 C
66 C
*
31242130 AAAATTACATGAAGACAATCTCAACGAGTTTTGTGACTATCTCCAAAGAACATTAATTCCTACAA
1 AAAATTACATGAAGACAATCTCAACAAGTTTTGTGACTATCTCCAAAGAACATTAATTCCTACAA
31242195 C
66 C
31242196 AAA
1 AAA
31242199 CTTAAAAGGG
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.41, C:0.21, G:0.10, T:0.28
Consensus pattern (66 bp):
AAAATTACATGAAGACAATCTCAACAAGTTTTGTGACTATCTCCAAAGAACATTAATTCCTACAA
C
Found at i:31247682 original size:42 final size:42
Alignment explanation
Indices: 31247603--31247744 Score: 230
Period size: 42 Copynumber: 3.4 Consensus size: 42
31247593 GGTTAGACTT
* *
31247603 CTAAAGAACATAGTCTTTAGCGGCGTTTCTTTTTAAGCGCCG
1 CTAAAGAACATGGTCTTTAGCGGCGTTTCTTTCTAAGCGCCG
* * * *
31247645 CTAAAGAACATGGTCTATAGTGGCATTTGTTTCTAAGCGCCG
1 CTAAAGAACATGGTCTTTAGCGGCGTTTCTTTCTAAGCGCCG
31247687 CTAAAGAACATGGTCTTTAGCGGCGTTTCTTTCTAAGCGCCG
1 CTAAAGAACATGGTCTTTAGCGGCGTTTCTTTCTAAGCGCCG
31247729 CTAAAGAACATGGTCT
1 CTAAAGAACATGGTCT
31247745 CCATTATTTT
Statistics
Matches: 90, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 90 1.00
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (42 bp):
CTAAAGAACATGGTCTTTAGCGGCGTTTCTTTCTAAGCGCCG
Found at i:31253603 original size:9 final size:9
Alignment explanation
Indices: 31253589--31254179 Score: 442
Period size: 9 Copynumber: 64.8 Consensus size: 9
31253579 TTTTTATATA
31253589 TTATGTAAG
1 TTATGTAAG
31253598 TTATGTACTAAG
1 TTATG---TAAG
*
31253610 TTTTGT-A-
1 TTATGTAAG
31253617 TTATGTAAG
1 TTATGTAAG
31253626 TTATGTAAG
1 TTATGTAAG
*
31253635 TTGTGT-A-
1 TTATGTAAG
*
31253642 TTATGTGAG
1 TTATGTAAG
31253651 TTATGTAAG
1 TTATGTAAG
31253660 TTATGTAAG
1 TTATGTAAG
* *
31253669 TTATTTAAT
1 TTATGTAAG
31253678 TTATGTAAG
1 TTATGTAAG
*
31253687 TTTATATATAAG
1 --T-TATGTAAG
*
31253699 TTATGTAGG
1 TTATGTAAG
*
31253708 CTATGT-A-
1 TTATGTAAG
* *
31253715 TTATCTAAA
1 TTATGTAAG
*
31253724 TAATGTAAG
1 TTATGTAAG
*
31253733 TTA-GGAAGG
1 TTATGTAA-G
31253742 TTATGT-A-
1 TTATGTAAG
31253749 TTATGTAAG
1 TTATGTAAG
*
31253758 TTATTTAAG
1 TTATGTAAG
* *
31253767 TTATTTAAT
1 TTATGTAAG
31253776 TTATGTAAG
1 TTATGTAAG
31253785 TTATGTAAG
1 TTATGTAAG
*
31253794 TTA-GGAAG
1 TTATGTAAG
31253802 TTTATGTAAG
1 -TTATGTAAG
* *
31253812 TTATTTAGAAAAAA
1 TTA--T-G--TAAG
31253826 TTATGTAAG
1 TTATGTAAG
31253835 TTATGTACTAAG
1 TTATG---TAAG
31253847 TTATGT-A-
1 TTATGTAAG
*
31253854 TTATGTAAA
1 TTATGTAAG
*
31253863 TAATGTAAG
1 TTATGTAAG
*
31253872 TTATTTAAG
1 TTATGTAAG
31253881 TTATGTAAG
1 TTATGTAAG
31253890 TTATGTAAG
1 TTATGTAAG
*
31253899 TTATTTAAG
1 TTATGTAAG
31253908 TTATGTAAG
1 TTATGTAAG
* *
31253917 TTATTTAAT
1 TTATGTAAG
31253926 TTATGTAAG
1 TTATGTAAG
31253935 TTATGTAAG
1 TTATGTAAG
*
31253944 TTATTTAAG
1 TTATGTAAG
31253953 TTATGTAAG
1 TTATGTAAG
* *
31253962 TTATTTAAT
1 TTATGTAAG
* *
31253971 TTATTTAAT
1 TTATGTAAG
31253980 TTATGTAAG
1 TTATGTAAG
*
31253989 TTATTTAAG
1 TTATGTAAG
31253998 TTATGTAAG
1 TTATGTAAG
* *
31254007 TTATTTAAT
1 TTATGTAAG
* *
31254016 TTATTTAAT
1 TTATGTAAG
31254025 TTATGTAAG
1 TTATGTAAG
31254034 TTATGTAAG
1 TTATGTAAG
* **
31254043 TTATTTATT
1 TTATGTAAG
*
31254052 TTATGTAAA
1 TTATGTAAG
* *
31254061 TTATTTAGAAAAAA
1 TTA--T-G--TAAG
31254075 TTATGTAAG
1 TTATGTAAG
31254084 TTATGTACTAAG
1 TTATG---TAAG
31254096 TTATGT-A-
1 TTATGTAAG
*
31254103 TTATGTAAA
1 TTATGTAAG
*
31254112 TAATGTAAG
1 TTATGTAAG
*
31254121 TTA-GGAAGG
1 TTATGTAA-G
31254130 TTATGT-A-
1 TTATGTAAG
31254137 TTATGTAAG
1 TTATGTAAG
*
31254146 TTATTTAAG
1 TTATGTAAG
31254155 TTATGTAAG
1 TTATGTAAG
31254164 TTATGTAAG
1 TTATGTAAG
31254173 TTATGTA
1 TTATGTA
31254180 GGCCATGTAT
Statistics
Matches: 469, Mismatches: 71, Indels: 84
0.75 0.11 0.13
Matches are distributed among these distances:
7 38 0.08
8 21 0.04
9 350 0.75
10 7 0.01
11 5 0.01
12 37 0.08
14 11 0.02
ACGTcount: A:0.35, C:0.01, G:0.17, T:0.48
Consensus pattern (9 bp):
TTATGTAAG
Found at i:31254187 original size:18 final size:18
Alignment explanation
Indices: 31254137--31254188 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 18
31254127 AGGTTATGTA
** *
31254137 TTATGTAAGTTATTTAAG
1 TTATGTAAGCCATGTAAG
**
31254155 TTATGTAAGTTATGTAAG
1 TTATGTAAGCCATGTAAG
*
31254173 TTATGTAGGCCATGTA
1 TTATGTAAGCCATGTA
31254189 TTATGTTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.31, C:0.04, G:0.21, T:0.44
Consensus pattern (18 bp):
TTATGTAAGCCATGTAAG
Found at i:31254187 original size:27 final size:27
Alignment explanation
Indices: 31254137--31254188 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
31254127 AGGTTATGTA
* **
31254137 TTATGTAAGTTATTTAAGTTATGTAAG
1 TTATGTAAGTTATGTAAGCCATGTAAG
*
31254164 TTATGTAAGTTATGTAGGCCATGTA
1 TTATGTAAGTTATGTAAGCCATGTA
31254189 TTATGTTATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.31, C:0.04, G:0.21, T:0.44
Consensus pattern (27 bp):
TTATGTAAGTTATGTAAGCCATGTAAG
Found at i:31254258 original size:35 final size:37
Alignment explanation
Indices: 31254214--31254325 Score: 135
Period size: 35 Copynumber: 3.1 Consensus size: 37
31254204 AGTTATGCAA
31254214 GTTTATATATTGTATGTTATTTAAGTTATGTATA-A-
1 GTTTATATATTGTATGTTATTTAAGTTATGTATATAT
*
31254249 G-TTATTATATTGTATGTTATTATATAAGTT-TCTATATAT
1 GTTTA-TATATTGTATGTTA-T-T-TAAGTTATGTATATAT
*
31254288 GTTTATATATTGTATGTTATTTAACTTATGTAT-TAT
1 GTTTATATATTGTATGTTATTTAAGTTATGTATATAT
31254324 GT
1 GT
31254326 AAGTTTATAT
Statistics
Matches: 66, Mismatches: 3, Indels: 15
0.79 0.04 0.18
Matches are distributed among these distances:
34 3 0.05
35 15 0.23
36 11 0.17
37 11 0.17
38 8 0.12
39 15 0.23
40 3 0.05
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.56
Consensus pattern (37 bp):
GTTTATATATTGTATGTTATTTAAGTTATGTATATAT
Found at i:31254304 original size:39 final size:36
Alignment explanation
Indices: 31254190--31254308 Score: 129
Period size: 35 Copynumber: 3.2 Consensus size: 36
31254180 GGCCATGTAT
* **
31254190 TATGTTATTATATAAGTTATGCAAGTTTATATATTG
1 TATGTTATTATATAAGTTTTATAAGTTTATATATTG
31254226 TATGTTA-T-T-TAAGTTATGTATAAG-TTATTATATTG
1 TATGTTATTATATAAGTT-T-TATAAGTTTA-TATATTG
31254261 TATGTTATTATATAAGTTTCTATATATGTTTATATATTG
1 TATGTTATTATATAAGTTT-TATA-A-GTTTATATATTG
31254300 TATGTTATT
1 TATGTTATT
31254309 TAACTTATGT
Statistics
Matches: 70, Mismatches: 4, Indels: 15
0.79 0.04 0.17
Matches are distributed among these distances:
33 6 0.09
34 4 0.06
35 19 0.27
36 8 0.11
37 6 0.09
38 7 0.10
39 17 0.24
40 3 0.04
ACGTcount: A:0.31, C:0.02, G:0.13, T:0.55
Consensus pattern (36 bp):
TATGTTATTATATAAGTTTTATAAGTTTATATATTG
Found at i:31254445 original size:17 final size:16
Alignment explanation
Indices: 31254404--31254447 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
31254394 TAAATTTTGA
* *
31254404 AAAAATTATAGATTTT
1 AAAAATTATATATATT
31254420 AAAAA-TATATATATT
1 AAAAATTATATATATT
31254435 AAAAATGTATATA
1 AAAAAT-TATATA
31254448 AATATTTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 13 0.54
16 5 0.21
17 6 0.25
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.39
Consensus pattern (16 bp):
AAAAATTATATATATT
Found at i:31254694 original size:23 final size:23
Alignment explanation
Indices: 31254650--31254694 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
31254640 ATAAAATTGG
* *
31254650 AATATAAGTTATATGTCCATATT
1 AATATAAGTTATATATCAATATT
* *
31254673 AATATATGTTATATATTAATAT
1 AATATAAGTTATATATCAATAT
31254695 ATGTCCCAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.47
Consensus pattern (23 bp):
AATATAAGTTATATATCAATATT
Found at i:31257968 original size:21 final size:21
Alignment explanation
Indices: 31257935--31258002 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
31257925 ATCATAAATT
**
31257935 CTAAACCTTAAACCCCAAAAAC
1 CTAAACCCCAAACCCC-AAAAC
* *
31257957 C-AAACCCCAAACCTCAAATC
1 CTAAACCCCAAACCCCAAAAC
* * *
31257977 CTAAACCCCAAATCTCAAACC
1 CTAAACCCCAAACCCCAAAAC
31257998 CTAAA
1 CTAAA
31258003 AGTCAAAACA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
20 5 0.13
21 33 0.85
22 1 0.03
ACGTcount: A:0.47, C:0.40, G:0.00, T:0.13
Consensus pattern (21 bp):
CTAAACCCCAAACCCCAAAAC
Found at i:31259403 original size:120 final size:114
Alignment explanation
Indices: 31259198--31259497 Score: 289
Period size: 120 Copynumber: 2.6 Consensus size: 114
31259188 TTTTTCCTAG
* * * * * * * * **
31259198 CGCCACTAATTCTAATCTACCTCAAGACTAAACGCTGCATTTTAGATAAGATATTTTGCAACGC-
1 CGCCACTAACTCTAATATACCTCAAAACCAAACACTGCGTTTTGGTTAAGATATTTTGCGGCGCT
* * * *
31259262 -GTTCAGACAAGCGCCGCTAATACTGTGCTTTAGCGGCGTGTTCTCCAAAG
66 TGTT--GTCAAACGTCGCTAATACTGTGCTTTAGCGGCGTGTTCTCCAAAA
* * *
31259312 CGCCACTAACTCTAATCTACCTCAAGACCAAGACCAAACGGTGCGTTTTGGTTAAGATCTTTTGC
1 CGCCACTAACTCTAATATACCTCAAAACCAA-A-C--AC--TGCGTTTTGGTTAAGATATTTTGC
* * **
31259377 GGCGCTTGTTGTCAAACGTCGCTAATACTGTTCTTTAGCGGCGTTTTCTTGAAAA
60 GGCGCTTGTTGTCAAACGTCGCTAATACTGTGCTTTAGCGGCGTGTTCTCCAAAA
* * * *
31259432 CGCCACTAATTTTAATATACCTCAAAACCAAACACTGCGTTTTGGTTAAGGTATTTTGTGGCGCT
1 CGCCACTAACTCTAATATACCTCAAAACCAAACACTGCGTTTTGGTTAAGATATTTTGCGGCGCT
31259497 T
66 T
31259498 ACAAATAAAC
Statistics
Matches: 154, Mismatches: 24, Indels: 16
0.79 0.12 0.08
Matches are distributed among these distances:
114 57 0.37
115 1 0.01
116 3 0.02
118 2 0.01
119 1 0.01
120 87 0.56
122 3 0.02
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (114 bp):
CGCCACTAACTCTAATATACCTCAAAACCAAACACTGCGTTTTGGTTAAGATATTTTGCGGCGCT
TGTTGTCAAACGTCGCTAATACTGTGCTTTAGCGGCGTGTTCTCCAAAA
Found at i:31259995 original size:38 final size:38
Alignment explanation
Indices: 31259945--31260017 Score: 128
Period size: 38 Copynumber: 1.9 Consensus size: 38
31259935 GAGCTTGTTT
*
31259945 GAATAGTTGAATGAATGCATGTTTGGTTGTTGTTTGAG
1 GAATAGTTGAATGAATGCATGTTTGATTGTTGTTTGAG
*
31259983 GAATGGTTGAATGAATGCATGTTTGATTGTTGTTT
1 GAATAGTTGAATGAATGCATGTTTGATTGTTGTTT
31260018 ACGGTGTCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.23, C:0.03, G:0.30, T:0.44
Consensus pattern (38 bp):
GAATAGTTGAATGAATGCATGTTTGATTGTTGTTTGAG
Found at i:31268965 original size:42 final size:42
Alignment explanation
Indices: 31268862--31268980 Score: 141
Period size: 42 Copynumber: 2.8 Consensus size: 42
31268852 AGTTAACTCA
* *
31268862 TATGAGTTTCCGTTTAA-CCCTAATGGGTTTCAGTTCAGCTCT
1 TATGAGCTTCCGTTTAACCCCT-ATGGGTTTCCGTTCAGCTCT
* ** *
31268904 TTTGAGCTTCAATTTAACCCCTACGGGTTTCCGTTCAGCTCT
1 TATGAGCTTCCGTTTAACCCCTATGGGTTTCCGTTCAGCTCT
* * *
31268946 TATGAGCTTCCGTTCAACCCTTGTGGGTTTCCGTT
1 TATGAGCTTCCGTTTAACCCCTATGGGTTTCCGTT
31268981 TAGCACTTCT
Statistics
Matches: 63, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
42 59 0.94
43 4 0.06
ACGTcount: A:0.16, C:0.25, G:0.19, T:0.39
Consensus pattern (42 bp):
TATGAGCTTCCGTTTAACCCCTATGGGTTTCCGTTCAGCTCT
Found at i:31268977 original size:21 final size:21
Alignment explanation
Indices: 31268862--31268980 Score: 67
Period size: 21 Copynumber: 5.7 Consensus size: 21
31268852 AGTTAACTCA
* *
31268862 TATGAGTTTCCGTTTAACCCT
1 TATGGGTTTCCGTTCAACCCT
* * * *
31268883 AATGGGTTTCAGTTCAGCTCT
1 TATGGGTTTCCGTTCAACCCT
* * * ** * *
31268904 TTTGAGCTTCAATTTAACCCC
1 TATGGGTTTCCGTTCAACCCT
* * *
31268925 TACGGGTTTCCGTTCAGCTCT
1 TATGGGTTTCCGTTCAACCCT
* *
31268946 TATGAGCTTCCGTTCAACCCT
1 TATGGGTTTCCGTTCAACCCT
*
31268967 TGTGGGTTTCCGTT
1 TATGGGTTTCCGTT
31268981 TAGCACTTCT
Statistics
Matches: 65, Mismatches: 33, Indels: 0
0.66 0.34 0.00
Matches are distributed among these distances:
21 65 1.00
ACGTcount: A:0.16, C:0.25, G:0.19, T:0.39
Consensus pattern (21 bp):
TATGGGTTTCCGTTCAACCCT
Found at i:31270627 original size:46 final size:46
Alignment explanation
Indices: 31270560--31270691 Score: 167
Period size: 46 Copynumber: 2.9 Consensus size: 46
31270550 TATAACTCAA
* * * *
31270560 TATGGTTTTCTTCACTGAAATATCATACCTACTTTTCACAAATCAG
1 TATGGTTTTCTTCACTAAAATACCATACCTACGTTCCACAAATCAG
*
31270606 TATGGTTTTCGTT-ACTAAAATACCATACCTACGTTCCACAACTCAG
1 TATGGTTTTC-TTCACTAAAATACCATACCTACGTTCCACAAATCAG
* * * *
31270652 TATGGTTTTCTTTATTGAATTACCATACCTACGTTCCACA
1 TATGGTTTTCTTCACTAAAATACCATACCTACGTTCCACA
31270692 CTTTGCCATG
Statistics
Matches: 76, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
45 2 0.03
46 72 0.95
47 2 0.03
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.38
Consensus pattern (46 bp):
TATGGTTTTCTTCACTAAAATACCATACCTACGTTCCACAAATCAG
Found at i:31276223 original size:19 final size:19
Alignment explanation
Indices: 31276199--31276237 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
31276189 GAACTGAAAG
31276199 TATGCTAATAAATGAATAA
1 TATGCTAATAAATGAATAA
31276218 TATGCTAATAAATGAATAA
1 TATGCTAATAAATGAATAA
31276237 T
1 T
31276238 CTTATATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.51, C:0.05, G:0.10, T:0.33
Consensus pattern (19 bp):
TATGCTAATAAATGAATAA
Found at i:31276743 original size:21 final size:21
Alignment explanation
Indices: 31276678--31276745 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
31276668 ATGGGTTTCA
* *
31276678 GTTCAGCTCTTTTGAGCTTCA
1 GTTCAGCTCTTATGAGCTTCC
* * * * *
31276699 GTTTATC-CTCTATGGGTTTTC
1 GTTCAGCTCT-TATGAGCTTCC
31276720 GTTCAGCTCTTATGAGCTTCC
1 GTTCAGCTCTTATGAGCTTCC
31276741 GTTCA
1 GTTCA
31276746 ATCCCTGTGG
Statistics
Matches: 33, Mismatches: 12, Indels: 4
0.67 0.24 0.08
Matches are distributed among these distances:
20 2 0.06
21 29 0.88
22 2 0.06
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (21 bp):
GTTCAGCTCTTATGAGCTTCC
Found at i:31276757 original size:42 final size:43
Alignment explanation
Indices: 31276668--31276759 Score: 118
Period size: 42 Copynumber: 2.2 Consensus size: 43
31276658 TTTAACCCTA
* *
31276668 ATGGG-TTTCAGTTCAGCTCTTTTGAGCTTCAGTTTATCCTCT
1 ATGGGTTTTCAGTTCAGCTCTTATGAGCTTCAGTTAATCCTCT
*
31276710 ATGGGTTTTC-GTTCAGCTCTTATGAGCTTCCGTTCAATCC-CT
1 ATGGGTTTTCAGTTCAGCTCTTATGAGCTTCAGTT-AATCCTCT
*
31276752 GTGGGTTT
1 ATGGGTTT
31276760 CCATTTAGCA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
42 36 0.82
43 8 0.18
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.43
Consensus pattern (43 bp):
ATGGGTTTTCAGTTCAGCTCTTATGAGCTTCAGTTAATCCTCT
Found at i:31281518 original size:66 final size:64
Alignment explanation
Indices: 31281386--31281519 Score: 214
Period size: 66 Copynumber: 2.1 Consensus size: 64
31281376 CATATCTTTG
* * *
31281386 ATTCCGGAGATAGTTTTGGGGCATAGAAACCTTAGTTAAATATTTTTTCATTTTGTTGTAATTT
1 ATTCCCGAGATAGTTTTGGGGCATAGAAACCTTAGGTAAATATTTTTTCATTTTATTGTAATTT
*
31281450 ATTCCCGAGATAGTTTTGGGGCATAAGAAAGCTTAGGTAAATATTTTTTTCATTTTATTGTAATT
1 ATTCCCGAGATAGTTTTGGGGCAT-AGAAACCTTAGGTAAATA-TTTTTTCATTTTATTGTAATT
31281515 T
64 T
31281516 ATTC
1 ATTC
31281520 TGATCCCTTT
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
64 23 0.36
65 16 0.25
66 25 0.39
ACGTcount: A:0.28, C:0.10, G:0.18, T:0.45
Consensus pattern (64 bp):
ATTCCCGAGATAGTTTTGGGGCATAGAAACCTTAGGTAAATATTTTTTCATTTTATTGTAATTT
Found at i:31282122 original size:14 final size:14
Alignment explanation
Indices: 31282103--31282129 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
31282093 TTTTCAGATC
31282103 TTATTATTTTATTA
1 TTATTATTTTATTA
31282117 TTATTATTTTATT
1 TTATTATTTTATT
31282130 CTCAATTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTATTATTTTATTA
Found at i:31282630 original size:18 final size:18
Alignment explanation
Indices: 31282590--31282630 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
31282580 TTAATCTTTG
31282590 ATTTA-TTATTTTATTTT
1 ATTTATTTATTTTATTTT
*
31282607 AGTTATTTATTTTAATTTT
1 ATTTATTTATTTT-ATTTT
31282626 -TTTAT
1 ATTTAT
31282631 CTGACTTGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 4 0.20
18 11 0.55
19 5 0.25
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (18 bp):
ATTTATTTATTTTATTTT
Found at i:31286966 original size:69 final size:69
Alignment explanation
Indices: 31286871--31287298 Score: 462
Period size: 69 Copynumber: 6.2 Consensus size: 69
31286861 TTTGTCTGTA
* * * * * *
31286871 AACCTTGATTGTATAGTTGAGAGCTTTGCTCTTGCTAACAATTTTGGAGGTTGCGGCTCTTCGCT
1 AACCTTGATTTTACAGTTGAGAGCTTTGCTCTCGCTAACTATTTTGGAGGTCGCGGCTCTTCGCC
**
31286936 TGTG
66 TACG
* * * * *
31286940 AACCTTAATTTTTCAGTTGGGAGCTTTGCTGTCGCTAACTATTTTGGAGGTCGCGGCTCTTCGCA
1 AACCTTGATTTTACAGTTGAGAGCTTTGCTCTCGCTAACTATTTTGGAGGTCGCGGCTCTTCGCC
*
31287005 TGCG
66 TACG
* *
31287009 AACCTTGATTTTACAGTTGAGAGCTTTGCTTTCGCTAACTGTTTTGGAGGTCGCGGCTCTTCGCC
1 AACCTTGATTTTACAGTTGAGAGCTTTGCTCTCGCTAACTATTTTGGAGGTCGCGGCTCTTCGCC
*
31287074 TACA
66 TACG
* * * * * *
31287078 AACCTTGATTTTACAGCTGGGAACTTTTCTCTCGCTAACTATTTTGGAGGTTGTGGCTCATT-GC
1 AACCTTGATTTTACAGTTGAGAGCTTTGCTCTCGCTAACTATTTTGGAGGTCGCGGCTC-TTCGC
31287142 CTACG
65 CTACG
* * * * * * * *
31287147 AACCTTGATTTTACAGCTAAGAGTTTTACTCTCACTAATTATTTTGGAGGTCACGACTCTTCGCC
1 AACCTTGATTTTACAGTTGAGAGCTTTGCTCTCGCTAACTATTTTGGAGGTCGCGGCTCTTCGCC
31287212 TACG
66 TACG
* * * * * * * * * *
31287216 AACCTTGATTTTACAGTTGGGAGCTTTACTCTAGCTAACTGTTTTGAAGGTTGTGGATTTTTGCC
1 AACCTTGATTTTACAGTTGAGAGCTTTGCTCTCGCTAACTATTTTGGAGGTCGCGGCTCTTCGCC
*
31287281 TGCG
66 TACG
31287285 AACCTTGATTTTAC
1 AACCTTGATTTTAC
31287299 CGGCTATAGT
Statistics
Matches: 301, Mismatches: 56, Indels: 4
0.83 0.16 0.01
Matches are distributed among these distances:
68 2 0.01
69 297 0.99
70 2 0.01
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.38
Consensus pattern (69 bp):
AACCTTGATTTTACAGTTGAGAGCTTTGCTCTCGCTAACTATTTTGGAGGTCGCGGCTCTTCGCC
TACG
Found at i:31292241 original size:39 final size:39
Alignment explanation
Indices: 31292187--31292261 Score: 116
Period size: 39 Copynumber: 1.9 Consensus size: 39
31292177 TGGACATAGC
*
31292187 TTGCGACCTCATTCCTGT-GAGGCTTACGCGAGCTCTTCT
1 TTGCGACCTCATTCCT-TCAAGGCTTACGCGAGCTCTTCT
*
31292226 TTGCGACCTCATTCCTTCAAGGCTTACTCGAGCTCT
1 TTGCGACCTCATTCCTTCAAGGCTTACGCGAGCTCT
31292262 CCTTGCGGGC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
38 1 0.03
39 32 0.97
ACGTcount: A:0.15, C:0.32, G:0.20, T:0.33
Consensus pattern (39 bp):
TTGCGACCTCATTCCTTCAAGGCTTACGCGAGCTCTTCT
Found at i:31294385 original size:24 final size:23
Alignment explanation
Indices: 31294358--31294420 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 23
31294348 TTTCTAAAAG
31294358 ATTTAGTTTTTATTAGTATAATAT
1 ATTTAGTTTTTATTAGTATAA-AT
**
31294382 ATTTAGCATTTATTAGTATAAAT
1 ATTTAGTTTTTATTAGTATAAAT
*
31294405 ATCTTTGTTATTTATT
1 AT-TTAGTT-TTTATT
31294421 TCCATATTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
23 4 0.12
24 22 0.69
25 6 0.19
ACGTcount: A:0.32, C:0.03, G:0.08, T:0.57
Consensus pattern (23 bp):
ATTTAGTTTTTATTAGTATAAAT
Found at i:31300516 original size:15 final size:15
Alignment explanation
Indices: 31300492--31300537 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 15
31300482 GAAGTTTAAG
31300492 AAAATAAAAATAAAA
1 AAAATAAAAATAAAA
* * *
31300507 CAACTAAAAACAAAA
1 AAAATAAAAATAAAA
31300522 AAAATAAAAATAAAA
1 AAAATAAAAATAAAA
31300537 A
1 A
31300538 GAAAACAGTA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.83, C:0.07, G:0.00, T:0.11
Consensus pattern (15 bp):
AAAATAAAAATAAAA
Found at i:31302147 original size:15 final size:15
Alignment explanation
Indices: 31302113--31302159 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
31302103 ATCAAAACAG
* *
31302113 TAAAACAAATAATAA
1 TAAAACTAATGATAA
31302128 T-AAACTAATGATAA
1 TAAAACTAATGATAA
31302142 TAAAACTAA-GAATAA
1 TAAAACTAATG-ATAA
31302157 TAA
1 TAA
31302160 GAGAAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 13 0.46
15 15 0.54
ACGTcount: A:0.66, C:0.06, G:0.04, T:0.23
Consensus pattern (15 bp):
TAAAACTAATGATAA
Found at i:31302187 original size:19 final size:18
Alignment explanation
Indices: 31302163--31302208 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
31302153 ATAATAAGAG
*
31302163 AAATAAAACAACAAATAAT
1 AAATAAAA-AACAAAAAAT
*
31302182 AAATAAATAAAGAAAAAAT
1 AAATAAA-AAACAAAAAAT
31302201 AAATAAAA
1 AAATAAAA
31302209 GTAAGGGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 1 0.04
19 22 0.92
20 1 0.04
ACGTcount: A:0.78, C:0.04, G:0.02, T:0.15
Consensus pattern (18 bp):
AAATAAAAAACAAAAAAT
Found at i:31319457 original size:22 final size:25
Alignment explanation
Indices: 31319431--31319482 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 25
31319421 TTATAATGAT
31319431 TTAATTTA-AAAATATA-TA-TAAA
1 TTAATTTATAAAATATATTATTAAA
*
31319453 TTAA-TTATAAAGTATATTATTAAA
1 TTAATTTATAAAATATATTATTAAA
31319477 TTAATT
1 TTAATT
31319483 ATATTATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 3 0.12
22 11 0.44
23 2 0.08
24 8 0.32
25 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (25 bp):
TTAATTTATAAAATATATTATTAAA
Found at i:31319471 original size:12 final size:11
Alignment explanation
Indices: 31319447--31319485 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
31319437 TAAAAATATA
31319447 TATAAATTAAT
1 TATAAATTAAT
*
31319458 TATAAAGTATAT
1 TATAAATTA-AT
31319470 TATTAAATTAAT
1 TA-TAAATTAAT
31319482 TATA
1 TATA
31319486 TTATAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 10 0.42
12 8 0.33
13 6 0.25
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (11 bp):
TATAAATTAAT
Found at i:31319497 original size:14 final size:17
Alignment explanation
Indices: 31319465--31319501 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 17
31319455 AATTATAAAG
31319465 TATATTATTAAATTAAT
1 TATATTATTAAATTAAT
31319482 TATATTA-TAAA-T-AT
1 TATATTATTAAATTAAT
31319496 TATATT
1 TATATT
31319502 GAGAAATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 8 0.40
15 1 0.05
16 4 0.20
17 7 0.35
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TATATTATTAAATTAAT
Found at i:31322483 original size:9 final size:9
Alignment explanation
Indices: 31322469--31322501 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
31322459 GTTAAACGAA
31322469 TCGAGTTAT
1 TCGAGTTAT
*
31322478 TCGAGTTAA
1 TCGAGTTAT
31322487 TCGAGTTAT
1 TCGAGTTAT
31322496 TCGAGT
1 TCGAGT
31322502 CAACTCGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.24, C:0.12, G:0.24, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:31322490 original size:18 final size:18
Alignment explanation
Indices: 31322467--31322501 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
31322457 GAGTTAAACG
31322467 AATCGAGTTATTCGAGTT
1 AATCGAGTTATTCGAGTT
31322485 AATCGAGTTATTCGAGT
1 AATCGAGTTATTCGAGT
31322502 CAACTCGAAT
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:0.29, C:0.11, G:0.23, T:0.37
Consensus pattern (18 bp):
AATCGAGTTATTCGAGTT
Found at i:31322690 original size:30 final size:30
Alignment explanation
Indices: 31322628--31322687 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
31322618 AAACCTTTTT
* * *
31322628 ACTTTTCCCTCAAAACTTTTACTCCTTCCC
1 ACTTTCCCCCCAAAACTTTTACTCCCTCCC
31322658 ACTTTCCCCCCAAAACTTTTACTCTCCTCC
1 ACTTTCCCCCCAAAACTTTTACTC-CCTCC
31322688 ACTCCCAACC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.20, C:0.43, G:0.00, T:0.37
Consensus pattern (30 bp):
ACTTTCCCCCCAAAACTTTTACTCCCTCCC
Found at i:31323118 original size:26 final size:26
Alignment explanation
Indices: 31323089--31323141 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
31323079 CTATTAATAT
*
31323089 TATTAAATTAAATTTCATATTTTATA
1 TATTAAATTAAATTTCACATTTTATA
*
31323115 TATTAAATTAAATTTTACATTTTATA
1 TATTAAATTAAATTTCACATTTTATA
31323141 T
1 T
31323142 TGTTTATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.55
Consensus pattern (26 bp):
TATTAAATTAAATTTCACATTTTATA
Found at i:31323162 original size:17 final size:17
Alignment explanation
Indices: 31323140--31323186 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
31323130 TACATTTTAT
31323140 ATTGTTTATATTATTGA
1 ATTGTTTATATTATTGA
31323157 ATTGTTTAGTCA-TATTGA
1 ATTGTTTA-T-ATTATTGA
*
31323175 A-TATTTATATTA
1 ATTGTTTATATTA
31323187 AAATTGAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
15 1 0.04
16 3 0.12
17 13 0.50
18 8 0.31
19 1 0.04
ACGTcount: A:0.32, C:0.02, G:0.11, T:0.55
Consensus pattern (17 bp):
ATTGTTTATATTATTGA
Found at i:31323534 original size:5 final size:5
Alignment explanation
Indices: 31323524--31323549 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
31323514 GAACAAATAT
31323524 ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG A
31323550 ATTCCATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (5 bp):
ATTCG
Found at i:31330959 original size:133 final size:133
Alignment explanation
Indices: 31330721--31330984 Score: 510
Period size: 133 Copynumber: 2.0 Consensus size: 133
31330711 GGAACAAAGG
31330721 CGCTTTGATTTTGGCTAATGCATCTCAGCAAGGTATCTTTCAAGCGATTAGCAAACACCTTGGCC
1 CGCTTTGATTTTGGCTAATGCATCTCAGCAAGGTATCTTTCAAGCGATTAGCAAACACCTTGGCC
*
31330786 ACAATTTTGTACATCATCCTGCAAAGACTAATCGAACGTAAATTATTCATATCAATAGGTTCTTT
66 ACAATTTTGTACACCATCCTGCAAAGACTAATCGAACGTAAATTATTCATATCAATAGGTTCTTT
31330851 CCT
131 CCT
*
31330854 CGCTTTGATTTTGGCTAATGCATCTTAGCAAGGTATCTTTCAAGCGATTAGCAAACACCTTGGCC
1 CGCTTTGATTTTGGCTAATGCATCTCAGCAAGGTATCTTTCAAGCGATTAGCAAACACCTTGGCC
31330919 ACAATTTTGTACACCATCCTGCAAAGACTAATCGAACGTAAATTATTCATATCAATAGGTTCTTT
66 ACAATTTTGTACACCATCCTGCAAAGACTAATCGAACGTAAATTATTCATATCAATAGGTTCTTT
31330984 C
131 C
31330985 ATTTTAGGAA
Statistics
Matches: 129, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
133 129 1.00
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (133 bp):
CGCTTTGATTTTGGCTAATGCATCTCAGCAAGGTATCTTTCAAGCGATTAGCAAACACCTTGGCC
ACAATTTTGTACACCATCCTGCAAAGACTAATCGAACGTAAATTATTCATATCAATAGGTTCTTT
CCT
Found at i:31335668 original size:3 final size:3
Alignment explanation
Indices: 31335660--31335723 Score: 128
Period size: 3 Copynumber: 21.3 Consensus size: 3
31335650 GCTTCCTTTG
31335660 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
31335708 TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT T
31335724 TGCTTTCTTT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:31336144 original size:24 final size:24
Alignment explanation
Indices: 31336116--31336177 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
31336106 ATTTTCATTT
*
31336116 AATTAATTATATTATTGTA-TAAAA
1 AATTAA-TATATAATTGTATTAAAA
*
31336140 AATTAATATATAATTTTATTAAAA
1 AATTAATATATAATTGTATTAAAA
*
31336164 TATT-ATATGATAAT
1 AATTAATAT-ATAAT
31336178 AAGTAAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 14 0.42
24 19 0.58
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (24 bp):
AATTAATATATAATTGTATTAAAA
Found at i:31336419 original size:54 final size:54
Alignment explanation
Indices: 31336346--31336484 Score: 149
Period size: 54 Copynumber: 2.6 Consensus size: 54
31336336 CCAATAGAAG
** *
31336346 CCTA-AAAGGCTTGGTTTCACTAAAAAGTGAGCTTGTGTGCTTGAAGAGGCAAAA
1 CCTATAAAGGCTTGAATTCACTAAAAAGTGAGC-TATGTGCTTGAAGAGGCAAAA
* * ** *
31336400 CCT-TAAAGGCTT-AACTTCACTAAAATGTGATCTATGTGCTTGAAGAGGTTAGA
1 CCTATAAAGGCTTGAA-TTCACTAAAAAGTGAGCTATGTGCTTGAAGAGGCAAAA
* *
31336453 CCTATAGAGGCTTGAATTCAGTAAAAAGTGAG
1 CCTATAAAGGCTTGAATTCACTAAAAAGTGAG
31336485 TCATCGTGCT
Statistics
Matches: 69, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
53 20 0.29
54 47 0.68
55 2 0.03
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (54 bp):
CCTATAAAGGCTTGAATTCACTAAAAAGTGAGCTATGTGCTTGAAGAGGCAAAA
Found at i:31338538 original size:7 final size:7
Alignment explanation
Indices: 31338526--31338551 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
31338516 AAATTGTATT
31338526 ATTTAAA
1 ATTTAAA
31338533 ATTTAAA
1 ATTTAAA
31338540 ATTTAAA
1 ATTTAAA
31338547 ATTTA
1 ATTTA
31338552 TATTCTCAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
ATTTAAA
Found at i:31338604 original size:7 final size:7
Alignment explanation
Indices: 31338592--31338617 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
31338582 CCCATTTCCC
31338592 CCCAAAG
1 CCCAAAG
31338599 CCCAAAG
1 CCCAAAG
31338606 CCCAAAG
1 CCCAAAG
31338613 CCCAA
1 CCCAA
31338618 TCCTTTTTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.46, G:0.12, T:0.00
Consensus pattern (7 bp):
CCCAAAG
Found at i:31346547 original size:18 final size:19
Alignment explanation
Indices: 31346490--31346545 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
31346480 AAATAAACAC
*
31346490 AAAAAAA-AATTTAGAAAATT
1 AAAAAAATATTTTA-AAAA-T
31346510 AAAAAAATATTTTAAAAAT
1 AAAAAAATATTTTAAAAAT
*
31346529 AAAAAAGTATTTTAAAA
1 AAAAAAATATTTTAAAA
31346546 TATTTTTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 17 0.52
20 11 0.33
21 5 0.15
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.29
Consensus pattern (19 bp):
AAAAAAATATTTTAAAAAT
Found at i:31349140 original size:20 final size:20
Alignment explanation
Indices: 31349115--31349163 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
31349105 CTACTGCCTC
* *
31349115 TGTCCCTTTCACCATGG-TGT
1 TGTCCCTTCCACCA-GGCTAT
31349135 TGTCCCTTCCACCAGGCTAT
1 TGTCCCTTCCACCAGGCTAT
31349155 TGTCCCTTC
1 TGTCCCTTC
31349164 AATGGGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 24 0.92
ACGTcount: A:0.10, C:0.37, G:0.16, T:0.37
Consensus pattern (20 bp):
TGTCCCTTCCACCAGGCTAT
Found at i:31349454 original size:60 final size:57
Alignment explanation
Indices: 31349384--31349519 Score: 130
Period size: 60 Copynumber: 2.2 Consensus size: 57
31349374 GTTTATAGTT
* * *
31349384 TTTGATTAGTATTTTG-TATGAATGTAAATTTTTTTACTTTTTATAATTATTTTAAAATTAA
1 TTTG-TTAGTATTTAGATATG-ATGTAAATTTTTGT--GTTTT-TAATTATTTTAAAATTAA
* *
31349445 TTTGTTAGTAATTTAGAATTATGTTTTAAATTTTTGTGTTTTTAATTATTTTAAAATTAA
1 TTTGTTAGT-ATTTAG-A-TATGATGTAAATTTTTGTGTTTTTAATTATTTTAAAATTAA
*
31349505 TTTATTAGTAATTTA
1 TTTGTTAGT-ATTTA
31349520 AATTTGTAAG
Statistics
Matches: 65, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
60 37 0.57
61 13 0.20
63 11 0.17
64 4 0.06
ACGTcount: A:0.32, C:0.01, G:0.09, T:0.58
Consensus pattern (57 bp):
TTTGTTAGTATTTAGATATGATGTAAATTTTTGTGTTTTTAATTATTTTAAAATTAA
Found at i:31350743 original size:2 final size:2
Alignment explanation
Indices: 31350736--31350786 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
31350726 TACGCATGTT
*
31350736 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31350778 TA TA TA TA T
1 TA TA TA TA T
31350787 NNNNNNNNNN
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:31350900 original size:2 final size:2
Alignment explanation
Indices: 31350887--31350935 Score: 80
Period size: 2 Copynumber: 24.0 Consensus size: 2
31350877 NNNNNNNNNN
31350887 AT AT ACT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
31350930 AC AT AT
1 AT AT AT
31350936 GCATTTCTAT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 42 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:31353173 original size:55 final size:55
Alignment explanation
Indices: 31353025--31353192 Score: 204
Period size: 55 Copynumber: 3.1 Consensus size: 55
31353015 ATGGTATGTT
* * *
31353025 TTTTGTAATCGTGCCTATCTGACAGGCGCCAATCAAATTTTTATATTAAAAA-A--A
1 TTTT-TAATCGCGCCTATCTGACAGGAGCGAATC-AATTTTTATATTAAAAATATTA
*
31353079 ATTTTAATCGCGCCTATCTGACA-GACGCGAATCAATTTTTATATTAAAAATATTA
1 TTTTTAATCGCGCCTATCTGACAGGA-GCGAATCAATTTTTATATTAAAAATATTA
*
31353134 TTTTTAATCGCGCCTAT-TGATAGGAGCGAATCAATTTTTTATATTAAAAAATATT-
1 TTTTTAATCGCGCCTATCTGACAGGAGCGAATCAA-TTTTTATATT-AAAAATATTA
31353189 TTTT
1 TTTT
31353193 GTTTAAATAA
Statistics
Matches: 101, Mismatches: 6, Indels: 13
0.84 0.05 0.11
Matches are distributed among these distances:
52 18 0.18
53 25 0.25
54 16 0.16
55 33 0.33
56 9 0.09
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (55 bp):
TTTTTAATCGCGCCTATCTGACAGGAGCGAATCAATTTTTATATTAAAAATATTA
Found at i:31353595 original size:18 final size:18
Alignment explanation
Indices: 31353549--31353595 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
31353539 AGCTCTCAGG
31353549 CATTCTTCTCCCTTCATC
1 CATTCTTCTCCCTTCATC
* ***
31353567 CAGTAAGCTCCCTTCATC
1 CATTCTTCTCCCTTCATC
31353585 CATTCTTCTCC
1 CATTCTTCTCC
31353596 ATTCCTTCAT
Statistics
Matches: 21, Mismatches: 8, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.15, C:0.43, G:0.04, T:0.38
Consensus pattern (18 bp):
CATTCTTCTCCCTTCATC
Found at i:31357486 original size:11 final size:11
Alignment explanation
Indices: 31357470--31357502 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
31357460 TGATCATTCT
31357470 AAAAAAATGAC
1 AAAAAAATGAC
*
31357481 AAAAAAA-GAG
1 AAAAAAATGAC
31357491 AAAAAAATGAC
1 AAAAAAATGAC
31357502 A
1 A
31357503 TTTTGTATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.76, C:0.06, G:0.12, T:0.06
Consensus pattern (11 bp):
AAAAAAATGAC
Found at i:31357870 original size:132 final size:132
Alignment explanation
Indices: 31357629--31358325 Score: 885
Period size: 132 Copynumber: 5.4 Consensus size: 132
31357619 GAATAGACCA
* * * * *
31357629 TTGAAGATTGCAGATCCTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCGAATCATATC
1 TTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGCGGAGCAGATCAAAGACAGCAAATCTTATC
* * * *
31357694 TTCCCAAAATAGTGAAGAAGCAGATTTAAGCCATTAATCTTATCTCCCTGAGCAGCAGTGGAGTA
66 TTCCCAAGATAGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCTCCCTGAGCAGCAGTGGAGTA
31357759 GG
131 GG
* * *
31357761 TTGAAGATTGTAGATCCTGTCTCTCTAAGCAGTAGCGGAGCAGATCAAAAACAGAAAATCTTATC
1 TTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGCGGAGCAGATCAAAGACAGCAAATCTTATC
31357826 TTCCCAAGATAGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCTCCCTGAGCAGCAGTGGAGTA
66 TTCCCAAGATAGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCTCCCTGAGCAGCAGTGGAGTA
31357891 GG
131 GG
* * *
31357893 TTGAAGATTGCAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCAAAGACAGCGAATCTTATC
1 TTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGCGGAGCAGATCAAAGACAGCAAATCTTATC
* * * *
31357958 TTCCCAAGATAGTGGAGAAGCAAATTTAAGCCATTGGTCCTATCTCCCTGAGTAGAAGTGGAGTA
66 TTCCCAAGATAGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCTCCCTGAGCAGCAGTGGAGTA
31358023 GG
131 GG
* * * * * *
31358025 ATGAAGAATGTAGATACTGTCTCCCTAAGTAGTAGTGGAGCAGATC-ATG---G---ATCTTATC
1 TTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGCGGAGCAGATCAAAGACAGCAAATCTTATC
* * ** * *
31358083 TTCCCAAGGTAGTAGG-GAAGCAAATTTAAGCC---CCTCCTATTTCCCTGAGCAACAGTGGAGT
66 TTCCCAAGATAGT-GGAGAAGCAGATTTAAGCCATTAGTCCTATCTCCCTGAGCAGCAGTGGAGT
31358144 AGG
130 AGG
* * * * *
31358147 TTGAAGATTGTAGATTCTGTCTCCCTAAGCAGTAGCGGAGCAGGTCGAGGACGGCAAATCTTATC
1 TTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGCGGAGCAGATCAAAGACAGCAAATCTTATC
* * * * ***
31358212 TTCCTAAGATAGTAGTGAAGCAGATGTAAGCCACCGGTCCTATCTCCCTGAGCAGCAGTGGAGTA
66 TTCCCAAGATAGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCTCCCTGAGCAGCAGTGGAGTA
*
31358277 AG
131 GG
* * *
31358279 TTGAAGAATGTAGATACTGTCTCCCTAAGCAGTAGTGGAGCAGATCA
1 TTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGCGGAGCAGATCA
31358326 TGGATCTTAT
Statistics
Matches: 494, Mismatches: 59, Indels: 24
0.86 0.10 0.04
Matches are distributed among these distances:
122 66 0.13
123 2 0.00
125 36 0.07
126 3 0.01
128 2 0.00
129 33 0.07
131 2 0.00
132 350 0.71
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (132 bp):
TTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGCGGAGCAGATCAAAGACAGCAAATCTTATC
TTCCCAAGATAGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCTCCCTGAGCAGCAGTGGAGTA
GG
Found at i:31358223 original size:254 final size:255
Alignment explanation
Indices: 31357629--31358344 Score: 979
Period size: 254 Copynumber: 2.8 Consensus size: 255
31357619 GAATAGACCA
* *
31357629 TTGAAGATTGCAGATCCTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCGAATCATATC
1 TTGAAGATTGCAGATTCTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATC
* * ** *
31357694 TTCCCAAAATAGTGAAGAAGCAGATTTAAGCCATTAATCTTATCTCCCTGAGCAGCAGTGGAGTA
66 TTCCCAAGATAGTGGAGAAGCAGATTTAAGCCATTGGTCCTATCTCCCTGAGCAGCAGTGGAGTA
* * * * * *
31357759 GGTTGAAGATTGTAGATCCTGTCTCTCTAAGCAGTAGCGGAGCAGATCAAAAACAGAAAATCTTA
131 GGTTGAAGAATGTAGATACTGTCTCCCTAAGCAGTAGTGGAGCAGATC----A-TG--GATCTTA
* * *
31357824 TCTTCCCAAGATAGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCTCCCTGAGCAGCAGTGGAG
189 TCTTCCCAAGATAGTGGAGAAGCAAATTTAAGCC--TACTCCTATCTCCCTGAGCAACAGTGGAG
31357889 TAGG
252 TAGG
* *
31357893 TTGAAGATTGCAGA-TCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCAAAGACAGCGAATCTTAT
1 TTGAAGATTGCAGATTC-TGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTAT
* * *
31357957 CTTCCCAAGATAGTGGAGAAGCAAATTTAAGCCATTGGTCCTATCTCCCTGAGTAGAAGTGGAGT
65 CTTCCCAAGATAGTGGAGAAGCAGATTTAAGCCATTGGTCCTATCTCCCTGAGCAGCAGTGGAGT
* *
31358022 AGGATGAAGAATGTAGATACTGTCTCCCTAAGTAGTAGTGGAGCAGATCATGGATCTTATCTTCC
130 AGGTTGAAGAATGTAGATACTGTCTCCCTAAGCAGTAGTGGAGCAGATCATGGATCTTATCTTCC
* * *
31358087 CAAGGTAGTAGG-GAAGCAAATTTAAGCC-CCTCCTATTTCCCTGAGCAACAGTGGAGTAGG
195 CAAGATAGT-GGAGAAGCAAATTTAAGCCTACTCCTATCTCCCTGAGCAACAGTGGAGTAGG
* * * *
31358147 TTGAAGATTGTAGATTCTGTCTCCCTAAGCAGTAGCGGAGCAGGTCGAGGACGGCAAATCTTATC
1 TTGAAGATTGCAGATTCTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATC
* * * * **
31358212 TTCCTAAGATAGTAGTGAAGCAGATGTAAGCCACCGGTCCTATCTCCCTGAGCAGCAGTGGAGTA
66 TTCCCAAGATAGTGGAGAAGCAGATTTAAGCCATTGGTCCTATCTCCCTGAGCAGCAGTGGAGTA
*
31358277 AGTTGAAGAATGTAGATACTGTCTCCCTAAGCAGTAGTGGAGCAGATCATGGATCTTATCTTCCC
131 GGTTGAAGAATGTAGATACTGTCTCCCTAAGCAGTAGTGGAGCAGATCATGGATCTTATCTTCCC
31358342 AAG
196 AAG
31358345 TGGAGTGGAT
Statistics
Matches: 405, Mismatches: 44, Indels: 16
0.87 0.09 0.03
Matches are distributed among these distances:
254 205 0.51
255 2 0.00
257 35 0.09
258 2 0.00
259 1 0.00
260 1 0.00
263 1 0.00
264 158 0.39
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (255 bp):
TTGAAGATTGCAGATTCTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATC
TTCCCAAGATAGTGGAGAAGCAGATTTAAGCCATTGGTCCTATCTCCCTGAGCAGCAGTGGAGTA
GGTTGAAGAATGTAGATACTGTCTCCCTAAGCAGTAGTGGAGCAGATCATGGATCTTATCTTCCC
AAGATAGTGGAGAAGCAAATTTAAGCCTACTCCTATCTCCCTGAGCAACAGTGGAGTAGG
Found at i:31367531 original size:16 final size:16
Alignment explanation
Indices: 31367510--31367548 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
31367500 TTAACTCATT
*
31367510 TAATTTTTATATAATG
1 TAATTTTTATATAATA
31367526 TAATTTTTATATAATA
1 TAATTTTTATATAATA
31367542 TAATTTT
1 TAATTTT
31367549 ATTTGATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (16 bp):
TAATTTTTATATAATA
Found at i:31368635 original size:53 final size:53
Alignment explanation
Indices: 31368555--31368690 Score: 200
Period size: 53 Copynumber: 2.6 Consensus size: 53
31368545 ACTCGTTCAT
* *
31368555 ACAGTTGGGGTTCCGCAGTTTTAGCCATGCTGTATCGCGAACTTTGTCGGACG
1 ACAGTTGGGGGTCCGCAGTTTTAGCCATGCTGTATCGCAAACTTTGTCGGACG
* * * *
31368608 ACAGTTGGGGGTCTGCAGTTTTAGCCATACTGTATCGCAAACTTTGTTGGATG
1 ACAGTTGGGGGTCCGCAGTTTTAGCCATGCTGTATCGCAAACTTTGTCGGACG
* *
31368661 ACAGTTAGGGGTCCACAGTTTTAGCCATGC
1 ACAGTTGGGGGTCCGCAGTTTTAGCCATGC
31368691 AGTTTTAGCA
Statistics
Matches: 73, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 73 1.00
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.31
Consensus pattern (53 bp):
ACAGTTGGGGGTCCGCAGTTTTAGCCATGCTGTATCGCAAACTTTGTCGGACG
Found at i:31369739 original size:28 final size:28
Alignment explanation
Indices: 31369699--31369757 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
31369689 TCGCAAGAAG
31369699 AGGATCTGTGTGTATTTTCCATAAAGCC
1 AGGATCTGTGTGTATTTTCCATAAAGCC
31369727 AGGATCTGTGTGTATTTTCCATAAAGCC
1 AGGATCTGTGTGTATTTTCCATAAAGCC
31369755 AGG
1 AGG
31369758 TTCCATCTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (28 bp):
AGGATCTGTGTGTATTTTCCATAAAGCC
Found at i:31371210 original size:20 final size:20
Alignment explanation
Indices: 31371185--31371222 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
31371175 ACTAGATCTA
31371185 TTAAAAAAATTTCAAAATTC
1 TTAAAAAAATTTCAAAATTC
* *
31371205 TTAAAATAGTTTCAAAAT
1 TTAAAAAAATTTCAAAAT
31371223 GAAAAAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.08, G:0.03, T:0.37
Consensus pattern (20 bp):
TTAAAAAAATTTCAAAATTC
Found at i:31376057 original size:42 final size:42
Alignment explanation
Indices: 31375998--31376086 Score: 178
Period size: 42 Copynumber: 2.1 Consensus size: 42
31375988 CGTTGCAAAC
31375998 AGAAATGTTGATAATTTTGTTCATCAAAACATTTTTAATTCG
1 AGAAATGTTGATAATTTTGTTCATCAAAACATTTTTAATTCG
31376040 AGAAATGTTGATAATTTTGTTCATCAAAACATTTTTAATTCG
1 AGAAATGTTGATAATTTTGTTCATCAAAACATTTTTAATTCG
31376082 AGAAA
1 AGAAA
31376087 CATAATCAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.40
Consensus pattern (42 bp):
AGAAATGTTGATAATTTTGTTCATCAAAACATTTTTAATTCG
Done.