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 107 of 150
Found at i:33267296 original size:8 final size:8
Alignment explanation
Indices: 33267231--33267306 Score: 65
Period size: 8 Copynumber: 10.2 Consensus size: 8
33267221 ATGAATATAT
*
33267231 TATATATA
1 TATAAATA
*
33267239 TATATATA
1 TATAAATA
*
33267247 TATATATA
1 TATAAATA
33267255 TATAAA-A
1 TATAAATA
33267262 TA-AAATA
1 TATAAATA
33267269 TA-AAATA
1 TATAAATA
*
33267276 TA-AAAGA
1 TATAAATA
33267283 -AT-AATA
1 TATAAATA
33267289 TATAAATA
1 TATAAATA
*
33267297 TATATATA
1 TATAAATA
33267305 TA
1 TA
33267307 CAAACGTATA
Statistics
Matches: 60, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
6 7 0.12
7 19 0.32
8 34 0.57
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (8 bp):
TATAAATA
Found at i:33267327 original size:60 final size:53
Alignment explanation
Indices: 33267231--33267357 Score: 130
Period size: 56 Copynumber: 2.3 Consensus size: 53
33267221 ATGAATATAT
* * *
33267231 TATATATATATATATATATATATATATAAAATAAAATATAAAATATAAAAGAATAA
1 TATATAAATATATATATATACAAATATAAAATAAAATATAAAA-A-AAAA-AATAA
* *
33267287 TATATAAATATATATATATACAAACGTATAAAATGTAAAATGTAAAAAAAAAATTAA
1 TATATAAATATATATATATACAAA--TATAAAA--TAAAATATAAAAAAAAAAATAA
33267344 TAGTATAAA-ATATA
1 TA-TATAAATATATA
33267358 AATAGATATA
Statistics
Matches: 61, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
56 21 0.34
57 11 0.18
58 17 0.28
59 1 0.02
60 11 0.18
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (53 bp):
TATATAAATATATATATATACAAATATAAAATAAAATATAAAAAAAAAAATAA
Found at i:33269561 original size:13 final size:13
Alignment explanation
Indices: 33269543--33269572 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
33269533 TTTTACCTTT
*
33269543 TTAATTTTCTTAG
1 TTAATTTACTTAG
33269556 TTAATTTACTTAG
1 TTAATTTACTTAG
33269569 TTAA
1 TTAA
33269573 AATCTAGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.57
Consensus pattern (13 bp):
TTAATTTACTTAG
Found at i:33272450 original size:26 final size:25
Alignment explanation
Indices: 33272369--33272456 Score: 95
Period size: 26 Copynumber: 3.4 Consensus size: 25
33272359 TATTTTATTT
33272369 TTATTAAATTATATTTAATAATGATA
1 TTATTAAATTATATTTAATAAT-ATA
* * * * *
33272395 ATATTAAAATATGATTAAATTATGTA
1 TTATTAAATTAT-ATTTAATAATATA
*
33272421 TTATTAAATTATATTTAATAATAATC
1 TTATTAAATTATATTTAATAAT-ATA
33272447 TTATTAAATT
1 TTATTAAATT
33272457 TTAATAGCAA
Statistics
Matches: 49, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
25 8 0.16
26 33 0.67
27 8 0.16
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (25 bp):
TTATTAAATTATATTTAATAATATA
Found at i:33273087 original size:9 final size:9
Alignment explanation
Indices: 33273057--33273108 Score: 52
Period size: 10 Copynumber: 5.7 Consensus size: 9
33273047 ATTAATTTTT
33273057 AAAATT-TA
1 AAAATTATA
33273065 AAAATTCATA
1 AAAATT-ATA
*
33273075 AAAATTATT
1 AAAATTATA
*
33273084 AAAATTATTT
1 AAAATTA-TA
*
33273094 AAAAGTATA
1 AAAATTATA
33273103 AAAATT
1 AAAATT
33273109 TATTTTAGCA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
8 6 0.16
9 15 0.41
10 16 0.43
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (9 bp):
AAAATTATA
Found at i:33273111 original size:20 final size:19
Alignment explanation
Indices: 33273054--33273113 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
33273044 TTTATTAATT
* *
33273054 TTTAAAATTTAAAAATTCA
1 TTTAAAATATAAAAATTTA
* *
33273073 -TAAAAATTATTAAAA-TTA
1 TTTAAAA-TATAAAAATTTA
33273091 TTTAAAAGTATAAAAATTTA
1 TTTAAAA-TATAAAAATTTA
33273111 TTT
1 TTT
33273114 TAGCATTCCA
Statistics
Matches: 31, Mismatches: 7, Indels: 5
0.72 0.16 0.12
Matches are distributed among these distances:
18 7 0.23
19 18 0.58
20 6 0.19
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (19 bp):
TTTAAAATATAAAAATTTA
Found at i:33273865 original size:40 final size:40
Alignment explanation
Indices: 33273821--33273903 Score: 157
Period size: 40 Copynumber: 2.1 Consensus size: 40
33273811 TAAGATTTTA
33273821 AAATATATATAATTCAAAATTATTTAAACTTACAAAATAT
1 AAATATATATAATTCAAAATTATTTAAACTTACAAAATAT
*
33273861 AAATATATATAATTCAAAATTATTTAAACTTACTAAATAT
1 AAATATATATAATTCAAAATTATTTAAACTTACAAAATAT
33273901 AAA
1 AAA
33273904 AAAAAAACAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.37
Consensus pattern (40 bp):
AAATATATATAATTCAAAATTATTTAAACTTACAAAATAT
Found at i:33274325 original size:18 final size:21
Alignment explanation
Indices: 33274302--33274349 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 21
33274292 TAAATATTAA
33274302 TAATTTTTATGTAT-T-TT-T
1 TAATTTTTATGTATATGTTAT
* *
33274320 TAATTTTAATTTATATGTTAT
1 TAATTTTTATGTATATGTTAT
33274341 TAATTTTTA
1 TAATTTTTA
33274350 GAATCATGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 12 0.50
19 1 0.04
20 2 0.08
21 9 0.38
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (21 bp):
TAATTTTTATGTATATGTTAT
Found at i:33275173 original size:16 final size:16
Alignment explanation
Indices: 33275145--33275186 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
33275135 ATTTAAATTT
33275145 TTTTTAATTTTTA-TGAA
1 TTTTTAA-TTTTAGT-AA
33275162 TTTTTAATTTTAGTAA
1 TTTTTAATTTTAGTAA
*
33275178 TTTTAAATT
1 TTTTTAATT
33275187 ATTTTTATAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 15 0.65
17 8 0.35
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (16 bp):
TTTTTAATTTTAGTAA
Found at i:33277900 original size:17 final size:17
Alignment explanation
Indices: 33277864--33277898 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
33277854 TTTGTTCTCA
*
33277864 TATTTCTTTTTTATTTT
1 TATTTCTTTGTTATTTT
33277881 TATTTACTTTGTTATTTT
1 TATTT-CTTTGTTATTTT
33277899 ATGAGTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.14, C:0.06, G:0.03, T:0.77
Consensus pattern (17 bp):
TATTTCTTTGTTATTTT
Found at i:33281665 original size:43 final size:43
Alignment explanation
Indices: 33281617--33281702 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 43
33281607 TCATATTTCA
33281617 TTTCTCATCTCATAATCATTTCTCAACTTTGCCATTTCAATAT
1 TTTCTCATCTCATAATCATTTCTCAACTTTGCCATTTCAATAT
* * *
33281660 TTTCTCATCTCATATTCATTTCTCATCTTTGTCATTTCAATAT
1 TTTCTCATCTCATAATCATTTCTCAACTTTGCCATTTCAATAT
33281703 AAATCACATA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.23, C:0.24, G:0.02, T:0.50
Consensus pattern (43 bp):
TTTCTCATCTCATAATCATTTCTCAACTTTGCCATTTCAATAT
Found at i:33282926 original size:21 final size:22
Alignment explanation
Indices: 33282900--33282940 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
33282890 TTAACTATCA
33282900 TAACATATATATAAA-ATAAGT
1 TAACATATATATAAATATAAGT
33282921 TAACATATATATAAATATAA
1 TAACATATATATAAATATAA
33282941 ATGTATAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (22 bp):
TAACATATATATAAATATAAGT
Found at i:33283446 original size:29 final size:29
Alignment explanation
Indices: 33283413--33283528 Score: 110
Period size: 29 Copynumber: 4.0 Consensus size: 29
33283403 ATGCAGAGTT
*
33283413 GCACCAAAGTGCAATAACAGAACAAAGTG
1 GCACCGAAGTGCAATAACAGAACAAAGTG
* * *
33283442 GCACCGAAGTGCAATATCAAAACAGAA-TA
1 GCACCGAAGTGCAATAACAGAACA-AAGTG
** * * *
33283471 GCACCGAAGTGCTCTATCAGAATAGAGTG
1 GCACCGAAGTGCAATAACAGAACAAAGTG
*
33283500 GCATCGAAGTGC-ATAACAGAACAAGAGTG
1 GCACCGAAGTGCAATAACAGAACAA-AGTG
33283529 CTAGAATGTT
Statistics
Matches: 69, Mismatches: 15, Indels: 6
0.77 0.17 0.07
Matches are distributed among these distances:
28 9 0.13
29 58 0.84
30 2 0.03
ACGTcount: A:0.42, C:0.20, G:0.23, T:0.15
Consensus pattern (29 bp):
GCACCGAAGTGCAATAACAGAACAAAGTG
Found at i:33285278 original size:30 final size:32
Alignment explanation
Indices: 33285242--33285309 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 32
33285232 TTTTGTCCTC
*
33285242 CAACTTTTTTAAATA-T-ACACTTTAACCCCT
1 CAACTTTTTTAAATATTCACACTTTAACCCAT
*
33285272 CAAC--TTTTAAATATTCACACTTTGACCCAT
1 CAACTTTTTTAAATATTCACACTTTAACCCAT
33285302 C-ACTTTTT
1 CAACTTTTT
33285310 ATTTTTTACA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
28 9 0.28
29 3 0.09
30 17 0.53
31 3 0.09
ACGTcount: A:0.31, C:0.26, G:0.01, T:0.41
Consensus pattern (32 bp):
CAACTTTTTTAAATATTCACACTTTAACCCAT
Found at i:33285783 original size:26 final size:24
Alignment explanation
Indices: 33285747--33285796 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
33285737 TTATAAAATT
* *
33285747 TTAAAAAATTAATATTTTTTAAAA
1 TTAAAAAATTAAAATTATTTAAAA
33285771 TTAAAAATTATTAAAATTATTTAAAA
1 TTAAAAA--ATTAAAATTATTTAAAA
33285797 AGAATGAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 7 0.32
26 15 0.68
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
TTAAAAAATTAAAATTATTTAAAA
Found at i:33285784 original size:16 final size:16
Alignment explanation
Indices: 33285751--33285789 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
33285741 AAAATTTTAA
* * *
33285751 AAAATTAATATTTTTT
1 AAAATTAAAAATTATT
33285767 AAAATTAAAAATTATT
1 AAAATTAAAAATTATT
33285783 AAAATTA
1 AAAATTA
33285790 TTTAAAAAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AAAATTAAAAATTATT
Found at i:33288250 original size:24 final size:24
Alignment explanation
Indices: 33288215--33288261 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
33288205 CTGTGAATCG
*
33288215 GTATGCTCTCACGATCTATAAATA
1 GTATGCTCTCACGAGCTATAAATA
*
33288239 GTATGCTTTCACGAGCTATAAAT
1 GTATGCTCTCACGAGCTATAAAT
33288262 CGATAACCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (24 bp):
GTATGCTCTCACGAGCTATAAATA
Found at i:33293773 original size:14 final size:14
Alignment explanation
Indices: 33293748--33293782 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
33293738 AATTATCCAC
33293748 TTAAAT-AAAATTA
1 TTAAATAAAAATTA
33293761 TTAAATAAAAATTA
1 TTAAATAAAAATTA
33293775 TTAAATAA
1 TTAAATAA
33293783 TAATATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 6 0.29
14 15 0.71
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
TTAAATAAAAATTA
Found at i:33303851 original size:25 final size:25
Alignment explanation
Indices: 33303817--33303868 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
33303807 AACCCGATGT
*
33303817 GAATGATTCCACTTACTATCAGTGG
1 GAATGATTCCACTTACTATCAATGG
33303842 GAATGATTCCACTTACTATCAATGG
1 GAATGATTCCACTTACTATCAATGG
33303867 GA
1 GA
33303869 CTTTGATAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (25 bp):
GAATGATTCCACTTACTATCAATGG
Found at i:33308146 original size:23 final size:23
Alignment explanation
Indices: 33308116--33308188 Score: 85
Period size: 25 Copynumber: 3.0 Consensus size: 23
33308106 ATCTACCTTG
*
33308116 TTTGGACAGCTCTTATACATC-AA
1 TTTGGACAGCT-TTATACACCAAA
33308139 TTTGGACAGCATTTATACACCAAAA
1 TTTGGACAGC-TTTATACACC-AAA
*
33308164 TTTGGACAGCTTATATACAACAAA
1 TTTGGACAGCTT-TATACACCAAA
33308188 T
1 T
33308189 GGGCAGCATA
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
23 18 0.41
24 7 0.16
25 19 0.43
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.32
Consensus pattern (23 bp):
TTTGGACAGCTTTATACACCAAA
Found at i:33308239 original size:24 final size:22
Alignment explanation
Indices: 33308204--33308395 Score: 99
Period size: 24 Copynumber: 8.3 Consensus size: 22
33308194 GCATATACAT
*
33308204 ACCAAATTTAACAGCACTTTTAC
1 ACCAAATTTAACAGCA-TTATAC
33308227 ACCAAAATTTAACAGCATATATAC
1 ACC-AAATTTAACAGCAT-TATAC
* *
33308251 AGCAAA--TAGGCAGCA-TATAC
1 ACCAAATTTA-ACAGCATTATAC
33308271 ATACCAAATTTAACAGCACCTT-TAC
1 --ACCAAATTTAACAGCA--TTATAC
33308296 ACCAAAATTTAACAGCATATATAC
1 ACC-AAATTTAACAGCAT-TATAC
* ***
33308320 AACAAA-TGGGCAGCA-TATAC
1 ACCAAATTTAACAGCATTATAC
* * *
33308340 ATACCAAATTGAGCAGCATTTTTAC
1 --ACCAAATTTAACAGCA-TTATAC
*
33308365 ACCAAAATTTAACAACATATATAC
1 ACC-AAATTTAACAGCAT-TATAC
*
33308389 AACAAAT
1 ACCAAAT
33308396 AGGCAACATA
Statistics
Matches: 132, Mismatches: 17, Indels: 40
0.70 0.09 0.21
Matches are distributed among these distances:
20 10 0.08
21 2 0.02
22 22 0.17
23 35 0.27
24 55 0.42
25 7 0.05
26 1 0.01
ACGTcount: A:0.46, C:0.22, G:0.08, T:0.24
Consensus pattern (22 bp):
ACCAAATTTAACAGCATTATAC
Found at i:33308477 original size:20 final size:23
Alignment explanation
Indices: 33308314--33308508 Score: 105
Period size: 23 Copynumber: 8.6 Consensus size: 23
33308304 TTAACAGCAT
*
33308314 ATATACA-A-CAAAT-GGGCAGC
1 ATATACATACCAAATAGAGCAGC
*
33308334 ATATACATACCAAATTGAGCAGC
1 ATATACATACCAAATAGAGCAGC
* ** * ** * *
33308357 ATTTTTACACCAAAATTTAACAAC
1 ATATACATACC-AAATAGAGCAGC
* * * *
33308381 ATATATACAACAAATAG-GCAAC
1 ATATACATACCAAATAGAGCAGC
33308403 ATATACATACCAAA-ATGAGCAGC
1 ATATACATACCAAATA-GAGCAGC
* ** ** *
33308426 ATTTTTATACCAAAATTTAACAGC
1 ATATACATACC-AAATAGAGCAGC
* * *
33308450 ATATATACAACAAATAG-GCAGC
1 ATATACATACCAAATAGAGCAGC
*
33308472 ATATACATACCAAATTGAGCAGC
1 ATATACATACCAAATAGAGCAGC
33308495 ATATACATACCAAA
1 ATATACATACCAAA
33308509 ATTTAATAGG
Statistics
Matches: 131, Mismatches: 35, Indels: 15
0.72 0.19 0.08
Matches are distributed among these distances:
20 7 0.05
21 2 0.02
22 38 0.29
23 52 0.40
24 32 0.24
ACGTcount: A:0.47, C:0.20, G:0.10, T:0.23
Consensus pattern (23 bp):
ATATACATACCAAATAGAGCAGC
Found at i:33308496 original size:69 final size:69
Alignment explanation
Indices: 33308145--33308514 Score: 542
Period size: 69 Copynumber: 5.3 Consensus size: 69
33308135 TCAATTTGGA
* * * *
33308145 CAGCATTTATACACCAAAATTTGGACAGCTTATATACAACAAATGGGCAGCATATACATACCAAA
1 CAGCATTTTTACACCAAAATTT-AACAGCATATATACAACAAATAGGCAGCATATACATACCAAA
* *
33308210 TTTAA
65 TTGAG
* *
33308215 CAGCACTTTTACACCAAAATTTAACAGCATATATACAGCAAATAGGCAGCATATACATACCAAAT
1 CAGCATTTTTACACCAAAATTTAACAGCATATATACAACAAATAGGCAGCATATACATACCAAAT
* *
33308280 TTAA
66 TGAG
** *
33308284 CAGCACCTTTACACCAAAATTTAACAGCATATATACAACAAATGGGCAGCATATACATACCAAAT
1 CAGCATTTTTACACCAAAATTTAACAGCATATATACAACAAATAGGCAGCATATACATACCAAAT
33308349 TGAG
66 TGAG
* * *
33308353 CAGCATTTTTACACCAAAATTTAACAACATATATACAACAAATAGGCAACATATACATACCAAAA
1 CAGCATTTTTACACCAAAATTTAACAGCATATATACAACAAATAGGCAGCATATACATACCAAAT
33308418 TGAG
66 TGAG
*
33308422 CAGCATTTTTATACCAAAATTTAACAGCATATATACAACAAATAGGCAGCATATACATACCAAAT
1 CAGCATTTTTACACCAAAATTTAACAGCATATATACAACAAATAGGCAGCATATACATACCAAAT
33308487 TGAG
66 TGAG
* ** *
33308491 CAGCATATACATACCAAAATTTAA
1 CAGCATTTTTACACCAAAATTTAA
33308515 TAGGATACAA
Statistics
Matches: 276, Mismatches: 24, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
69 256 0.93
70 20 0.07
ACGTcount: A:0.45, C:0.21, G:0.09, T:0.24
Consensus pattern (69 bp):
CAGCATTTTTACACCAAAATTTAACAGCATATATACAACAAATAGGCAGCATATACATACCAAAT
TGAG
Found at i:33308571 original size:22 final size:22
Alignment explanation
Indices: 33308546--33308588 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
33308536 ACACCAAAAC
*
33308546 AGGCTTTTAGCGGCGCTTTTTT
1 AGGCCTTTAGCGGCGCTTTTTT
33308568 AGGCCTTTAGCGGCGCTTTTT
1 AGGCCTTTAGCGGCGCTTTTT
33308589 AGCGCCGCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.09, C:0.21, G:0.28, T:0.42
Consensus pattern (22 bp):
AGGCCTTTAGCGGCGCTTTTTT
Found at i:33308792 original size:43 final size:42
Alignment explanation
Indices: 33308690--33308900 Score: 148
Period size: 43 Copynumber: 5.0 Consensus size: 42
33308680 GCTTCTATCA
* * * *
33308690 TAAA-CGCCGCTGA-AGAGTAAGAGCTTTAGTGGCG-CTTTAG
1 TAAAGCGCCGCT-ATAGACTAAGACCTTTAGCGGCGTTTTTAG
*
33308730 TAGAAGCGCCGCTGA-AGACTAATACCTTTAGCGGCGTTTTTAG
1 TA-AAGCGCCGCT-ATAGACTAAGACCTTTAGCGGCGTTTTTAG
** **
33308773 TATAAGCGCCGCTATAGACTGGGGTCTTTAGCGGCGTTTTTAG
1 TA-AAGCGCCGCTATAGACTAAGACCTTTAGCGGCGTTTTTAG
* ** *
33308816 TAAAGTCGCCGCTATAGA-TCAGGGTCTTTAGTGGCGTTTTT-G
1 TAAAG-CGCCGCTATAGACT-AAGACCTTTAGCGGCGTTTTTAG
* **
33308858 CTCAAAGCGCCGCTATAGA-TCAGGTCTTTAGCGGCGTCTTTTA
1 -T-AAAGCGCCGCTATAGACTAAGACCTTTAGCGGCGT-TTTTA
33308901 CCAAAACGCC
Statistics
Matches: 145, Mismatches: 16, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
40 2 0.01
41 2 0.01
42 46 0.32
43 91 0.63
44 4 0.03
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.30
Consensus pattern (42 bp):
TAAAGCGCCGCTATAGACTAAGACCTTTAGCGGCGTTTTTAG
Found at i:33308918 original size:42 final size:41
Alignment explanation
Indices: 33308755--33308957 Score: 163
Period size: 43 Copynumber: 4.8 Consensus size: 41
33308745 AGACTAATAC
** * **
33308755 CTTTAGCGGCGTTTTTAGTATAAGCGCCGCTATAGACTGGGGT
1 CTTTAGCGGCGTTTTTACCA-AAACGCCGCTATAGA-TCAGGT
** *
33308798 CTTTAGCGGCGTTTTTAGTAAAGTCGCCGCTATAGATCAGGGT
1 CTTTAGCGGCGTTTTTACCAAA-ACGCCGCTATAGATCA-GGT
* * *
33308841 CTTTAGTGGCGTTTTTGCTCAAAGCGCCGCTATAGATCAGGT
1 CTTTAGCGGCGTTTTTAC-CAAAACGCCGCTATAGATCAGGT
* * * * *
33308883 CTTTAGCGGCGTCTTTTACCAAAACGCCACAATAGACCCTGAT
1 CTTTAGCGGCGT-TTTTACCAAAACGCCGCTATAGA-TCAGGT
* * *
33308926 CTATAGCGGCGCTTTTACCAAAAACGTCGCTA
1 CTTTAGCGGCGTTTTTACC-AAAACGCCGCTA
33308958 AAGACCAACA
Statistics
Matches: 133, Mismatches: 21, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
42 38 0.29
43 92 0.69
44 3 0.02
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.30
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTACCAAAACGCCGCTATAGATCAGGT
Found at i:33309341 original size:21 final size:21
Alignment explanation
Indices: 33309312--33309383 Score: 90
Period size: 21 Copynumber: 3.4 Consensus size: 21
33309302 TTTGACGCTG
*
33309312 CTCTGCTTCCCTCGCTGCAGC
1 CTCTACTTCCCTCGCTGCAGC
**
33309333 CTCTACTTCCCTCGCTTTAGC
1 CTCTACTTCCCTCGCTGCAGC
* *
33309354 CTCTGCTTCCCTCGTTGCAGC
1 CTCTACTTCCCTCGCTGCAGC
*
33309375 CTATACTTC
1 CTCTACTTC
33309384 TCTNNNNNNN
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.08, C:0.43, G:0.14, T:0.35
Consensus pattern (21 bp):
CTCTACTTCCCTCGCTGCAGC
Found at i:33320278 original size:41 final size:40
Alignment explanation
Indices: 33320214--33320495 Score: 208
Period size: 41 Copynumber: 6.9 Consensus size: 40
33320204 ATTTGTTACT
* ** *
33320214 ATTAGCGGCGCTTCGGCAAAAACGCCGCTAAAGGTCAATAC
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGTCAA-GC
* * * *
33320255 ATTAGCGGCGCTTAGATACAAACGCCGCTGAA-GACAAGAGA
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGTC-A-AGC
* * * * * *
33320296 ATTAGTGGCGCTCAGTTAGAAACGCCGCTAAAGATCCGAGC
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGT-CAAGC
* **
33320337 ATTGGCGGCGCTT-GTATAAAAACGCCGCTAAAGACCCCAAGC
1 ATTAGCGGCGCTTAG-ATAAAAACGCCGCTAAAG--GTCAAGC
* * * ** *
33320379 ATTAGCGGCGCATAGAAAAAAATGCCGCTAAATATCCGAGC
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGT-CAAGC
* * * * *
33320420 ATTAGCGGCGCATAGAAAAAAACACCGCTAAAGACTCGAGC
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAG-GTCAAGC
*
33320461 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGGT
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGT
33320496 TTAAAAAATC
Statistics
Matches: 190, Mismatches: 41, Indels: 21
0.75 0.16 0.08
Matches are distributed among these distances:
40 4 0.02
41 152 0.80
42 32 0.17
43 2 0.01
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.16
Consensus pattern (40 bp):
ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGTCAAGC
Found at i:33320416 original size:83 final size:82
Alignment explanation
Indices: 33320315--33320493 Score: 243
Period size: 83 Copynumber: 2.2 Consensus size: 82
33320305 GCTCAGTTAG
* * * *
33320315 AAACGCCGCTAAAGATCCGAGCATTGGCGGCGC-TTGTATAAAAACGCCGCTAAAGACCCCAAGC
1 AAACGCCGCTAAAGATCCGAGCATTAGCGGCGCATAG-AAAAAAACACCGCTAAAGA-CCCAAGC
33320379 ATTAGCGGCGCATAGAAAA
64 ATTAGCGGCGCATAGAAAA
* * * *
33320398 AAATGCCGCTAAATATCCGAGCATTAGCGGCGCATAGAAAAAAACACCGCTAAAGACTCGAGCAT
1 AAACGCCGCTAAAGATCCGAGCATTAGCGGCGCATAGAAAAAAACACCGCTAAAGACCCAAGCAT
* *
33320463 TAGCGGCGCTTAGACAA
66 TAGCGGCGCATAGAAAA
33320480 AAACGCCGCTAAAG
1 AAACGCCGCTAAAG
33320494 GTTTAAAAAA
Statistics
Matches: 83, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
82 34 0.41
83 47 0.57
84 2 0.02
ACGTcount: A:0.37, C:0.26, G:0.23, T:0.15
Consensus pattern (82 bp):
AAACGCCGCTAAAGATCCGAGCATTAGCGGCGCATAGAAAAAAACACCGCTAAAGACCCAAGCAT
TAGCGGCGCATAGAAAA
Found at i:33320491 original size:82 final size:81
Alignment explanation
Indices: 33320214--33320493 Score: 283
Period size: 82 Copynumber: 3.4 Consensus size: 81
33320204 ATTTGTTACT
* * * * * *
33320214 ATTAGCGGCGCTTCGGCAAAAACGCCGCTAAAGGT-CAATACATTAGCGGCGCTTAGATACAAAC
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGATCCGA-GCATTAGCGGCGC-TAGATAAAAAC
* * *
33320278 GCCGCTGAAGACAAGAGA
64 GCCGCTAAAGACACGAGC
* * ** * * *
33320296 ATTAGTGGCGCTCAGTTAGAAACGCCGCTAAAGATCCGAGCATTGGCGGCGCTTGTATAAAAACG
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGATCCGAGCATTAGCGGCGCTAG-ATAAAAACG
* *
33320361 CCGCTAAAGACCCCAAGC
65 CCGCTAAAGA-CACGAGC
* * * * * *
33320379 ATTAGCGGCGCATAGAAAAAAATGCCGCTAAATATCCGAGCATTAGCGGCGCATAGAAAAAAACA
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGATCCGAGCATTAGCGGCGC-TAGATAAAAACG
*
33320444 CCGCTAAAGACTCGAGC
65 CCGCTAAAGACACGAGC
33320461 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAG
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAG
33320494 GTTTAAAAAA
Statistics
Matches: 159, Mismatches: 35, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
81 2 0.01
82 90 0.57
83 65 0.41
84 2 0.01
ACGTcount: A:0.35, C:0.25, G:0.24, T:0.16
Consensus pattern (81 bp):
ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGATCCGAGCATTAGCGGCGCTAGATAAAAACGC
CGCTAAAGACACGAGC
Found at i:33320625 original size:40 final size:40
Alignment explanation
Indices: 33320551--33320649 Score: 112
Period size: 40 Copynumber: 2.5 Consensus size: 40
33320541 GGCGCTTTAT
* * **
33320551 ATAAAACGCCGCTAATTC-CTATTTTTAGCGGCGCTTCGGG
1 ATAAATCGCCGCTAATGCTCTACCTTTAGCGGCGCTT-GGG
* *
33320591 AT-AATCGCCGCTGATGCTCTACCTTTAGCGGCGCTTTGG
1 ATAAATCGCCGCTAATGCTCTACCTTTAGCGGCGCTTGGG
*
33320630 CTAAATCGCCGCTAATGCTC
1 ATAAATCGCCGCTAATGCTC
33320650 GATTTGTTGT
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
39 15 0.31
40 34 0.69
ACGTcount: A:0.20, C:0.28, G:0.22, T:0.29
Consensus pattern (40 bp):
ATAAATCGCCGCTAATGCTCTACCTTTAGCGGCGCTTGGG
Found at i:33320750 original size:23 final size:23
Alignment explanation
Indices: 33320721--33320806 Score: 75
Period size: 23 Copynumber: 3.7 Consensus size: 23
33320711 TGTAGTGTAG
33320721 GCAGCATATACATACCAAATTGA
1 GCAGCATATACATACCAAATTGA
* ** *
33320744 GCAGCATTTTTATACCAAAATTTA
1 GCAGCATATACATACC-AAATTGA
* * * * *
33320768 ACAGCATATATACAACAAATAG-
1 GCAGCATATACATACCAAATTGA
33320790 GCAGCATATACATACCA
1 GCAGCATATACATACCA
33320807 CATCATATAC
Statistics
Matches: 47, Mismatches: 15, Indels: 3
0.72 0.23 0.05
Matches are distributed among these distances:
22 13 0.28
23 17 0.36
24 17 0.36
ACGTcount: A:0.44, C:0.21, G:0.10, T:0.24
Consensus pattern (23 bp):
GCAGCATATACATACCAAATTGA
Found at i:33321642 original size:41 final size:41
Alignment explanation
Indices: 33321615--33321766 Score: 207
Period size: 41 Copynumber: 3.7 Consensus size: 41
33321605 ATAAAACACT
* * * * *
33321615 GGCATAAAGCCTGCTAGGCACAAAGCCTGATACATTTCATC
1 GGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATTCACC
* *
33321656 GGCACAAAGCCTGCTA-GAATAAAGTCTGATATAATTCACC
1 GGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATTCACC
* *
33321696 GGCACAGATCCTGCTAGGCATAAAGCCTGATATAATTCACC
1 GGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATTCACC
*
33321737 GGCATAAAGCCTGCTAGGCATAAAGCCTGA
1 GGCACAAAGCCTGCTAGGCATAAAGCCTGA
33321767 ACTTACAGAA
Statistics
Matches: 96, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
40 32 0.33
41 64 0.67
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.21
Consensus pattern (41 bp):
GGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATTCACC
Found at i:33329471 original size:29 final size:29
Alignment explanation
Indices: 33329429--33329499 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
33329419 TCCACCATGA
* * *
33329429 CACGAACTCTCAATGATTAAGTTCTTTAC
1 CACGAACTATCAATGAATAAGCTCTTTAC
*
33329458 CACGAATTATCAATGAATAAGCTCTTTAC
1 CACGAACTATCAATGAATAAGCTCTTTAC
*
33329487 CACGAACTCTCAA
1 CACGAACTATCAA
33329500 CGAACAAGTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.35, C:0.25, G:0.10, T:0.30
Consensus pattern (29 bp):
CACGAACTATCAATGAATAAGCTCTTTAC
Found at i:33337167 original size:2 final size:2
Alignment explanation
Indices: 33337148--33337198 Score: 81
Period size: 2 Copynumber: 27.0 Consensus size: 2
33337138 ACCTAATTAT
33337148 TA TA T- TA T- TA TA -A 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
33337187 TA TA TA TA TA TA
1 TA TA TA TA TA TA
33337199 ACAAGTGCCT
Statistics
Matches: 46, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
1 3 0.07
2 43 0.93
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:33340558 original size:70 final size:70
Alignment explanation
Indices: 33340481--33340616 Score: 272
Period size: 70 Copynumber: 1.9 Consensus size: 70
33340471 CAACAAGCCA
33340481 ATGCAAGAAATGAAATAAATATTTTGAACTCAAAATGAAATAAGTAAAAACAAGAAGAAAGACAA
1 ATGCAAGAAATGAAATAAATATTTTGAACTCAAAATGAAATAAGTAAAAACAAGAAGAAAGACAA
33340546 CATTG
66 CATTG
33340551 ATGCAAGAAATGAAATAAATATTTTGAACTCAAAATGAAATAAGTAAAAACAAGAAGAAAGACAA
1 ATGCAAGAAATGAAATAAATATTTTGAACTCAAAATGAAATAAGTAAAAACAAGAAGAAAGACAA
33340616 C
66 C
33340617 GTTGGGCAAC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 66 1.00
ACGTcount: A:0.58, C:0.09, G:0.14, T:0.19
Consensus pattern (70 bp):
ATGCAAGAAATGAAATAAATATTTTGAACTCAAAATGAAATAAGTAAAAACAAGAAGAAAGACAA
CATTG
Found at i:33344543 original size:2 final size:2
Alignment explanation
Indices: 33344536--33344569 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
33344526 CTGCAACGTT
33344536 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
33344570 GTAAAACAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:33350748 original size:402 final size:402
Alignment explanation
Indices: 33350007--33350803 Score: 1339
Period size: 402 Copynumber: 2.0 Consensus size: 402
33349997 CAAAAAGAAA
33350007 TGCTTGCAAATAATTCCATCCAACCTGGCATGCTACAAAACTTGACCAGGAATTGGAGAAAGAGT
1 TGCTTGCAAATAATTCCATCCAACCTGGCATGCTACAAAACTTGACCAGGAATTGGAGAAAGAGT
33350072 TCGAAAACAATTCAGCAGTTAAGAGTAGGTAACAACACATGCCGCTTGGATGCAAATAAAGACCT
66 TCGAAAACAATTCAGCAGTTAAGAGTAGGTAACAACACATGCCGCTTGGATGCAAATAAAGACCT
33350137 TTGCATTTATTAGAAACACATTATATTTAAGAGATAAAGCTTGACACGCCTGGCATCAAGCAACT
131 TTGCATTTATTAGAAACACATTATATTTAAGAGATAAAGCTTGACACGCCTGGCATCAAGCAACT
*
33350202 AATCAGAATCGACAATAAGAATGTTAACAGCATGATTTTATCAAAATGCCTTCAGCATGTAATAC
196 AATC--AA-C-ACAATAAGAATGTTAACAGCATGATTTCATCAAAATGCCTTCAGCATGTAATAC
* * *
33350267 TTTCCAACTTATAACCAGAATTCATCATACAAAAAGAGAAATACAGGAAATGTACTTTGAAGGGA
257 TTTCCAACTTAAAAACAGAATTCATCATACAAAAAGAGAAATACAGGAAATGTACTTTAAAGGGA
* * *
33350332 TGGAAAGGATGTACGATAATTTGACTGGATAAGGTAAGAAGAGTAAGGTAAAGGTAAGGAAAATT
322 TGGAAAGGATGTACGATAATTTGACTGGACAAGGTAAGAAGAGTAAGGTAAAGGGAAGGAAAATG
33350397 ATGCTACAAAACTGTC
387 ATGCTACAAAACTGTC
*
33350413 TGCTTGCAAATAATTCCATCCAACCTGGCATGCTACAAAACTTGACCCGGAATTGGAGAAAGAGT
1 TGCTTGCAAATAATTCCATCCAACCTGGCATGCTACAAAACTTGACCAGGAATTGGAGAAAGAGT
* * *
33350478 TTGAAAACAATTCAGCAGTTAAGAGTAGGTAGCAACACATATGCTGCTTGGATGCAAATAAAGAC
66 TCGAAAACAATTCAGCAGTTAAGAGTAGGTAACAACAC--ATGCCGCTTGGATGCAAATAAAGAC
* *
33350543 CTTTGCATTTATTAGAAACACATTATATTTAAGAGATAAAGGTTGACACGCCTGGCGTCAAGCAA
129 CTTTGCATTTATTAGAAACACATTATATTTAAGAGATAAAGCTTGACACGCCTGGCATCAAGCAA
*
33350608 CTAATC-A-ACAATGAGAATGTTAACAGCATGATTTCATCAAAATGCCTTCAGCATGTAATACTT
194 CTAATCAACACAATAAGAATGTTAACAGCATGATTTCATCAAAATGCCTTCAGCATGTAATACTT
* * *
33350671 TCCAACTTAAAAACAGTATTCATCATACATAGAA-AGATATACAGGAAATGTACTTTAAAGGGAT
259 TCCAACTTAAAAACAGAATTCATCATACA-AAAAGAGAAATACAGGAAATGTACTTTAAAGGGAT
* *
33350735 GGAAAGGATGTACGTTAATTTGATTGGACAAGGTAAGAAGAGTAAGGTAAAGGGAAGGAAAATGA
323 GGAAAGGATGTACGATAATTTGACTGGACAAGGTAAGAAGAGTAAGGTAAAGGGAAGGAAAATGA
33350800 TGCT
388 TGCT
33350804 CTATTGTCTG
Statistics
Matches: 369, Mismatches: 19, Indels: 10
0.93 0.05 0.03
Matches are distributed among these distances:
402 172 0.47
403 3 0.01
405 1 0.00
406 100 0.27
408 93 0.25
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.25
Consensus pattern (402 bp):
TGCTTGCAAATAATTCCATCCAACCTGGCATGCTACAAAACTTGACCAGGAATTGGAGAAAGAGT
TCGAAAACAATTCAGCAGTTAAGAGTAGGTAACAACACATGCCGCTTGGATGCAAATAAAGACCT
TTGCATTTATTAGAAACACATTATATTTAAGAGATAAAGCTTGACACGCCTGGCATCAAGCAACT
AATCAACACAATAAGAATGTTAACAGCATGATTTCATCAAAATGCCTTCAGCATGTAATACTTTC
CAACTTAAAAACAGAATTCATCATACAAAAAGAGAAATACAGGAAATGTACTTTAAAGGGATGGA
AAGGATGTACGATAATTTGACTGGACAAGGTAAGAAGAGTAAGGTAAAGGGAAGGAAAATGATGC
TACAAAACTGTC
Found at i:33351256 original size:15 final size:16
Alignment explanation
Indices: 33351229--33351258 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
33351219 CTTTGAACCC
33351229 CTTTCCATCCACTTTT
1 CTTTCCATCCACTTTT
33351245 CTTTCC-TCCACTTT
1 CTTTCCATCCACTTT
33351259 GGGAAACAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.10, C:0.40, G:0.00, T:0.50
Consensus pattern (16 bp):
CTTTCCATCCACTTTT
Found at i:33354758 original size:1 final size:1
Alignment explanation
Indices: 33354752--33354781 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
33354742 AATGAACAAC
33354752 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
33354782 CAGAATATAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:33373226 original size:25 final size:26
Alignment explanation
Indices: 33373174--33373227 Score: 83
Period size: 27 Copynumber: 2.1 Consensus size: 26
33373164 AACCAGAAAA
*
33373174 ACAAAGAAACGTGCCAAAATACGGCAG
1 ACAAAGAAACGTGCC-AAATACGACAG
33373201 ACAAAGAAACGTGCC-AATACGACAG
1 ACAAAGAAACGTGCCAAATACGACAG
33373226 AC
1 AC
33373228 TTACATTGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 11 0.42
27 15 0.58
ACGTcount: A:0.48, C:0.24, G:0.20, T:0.07
Consensus pattern (26 bp):
ACAAAGAAACGTGCCAAATACGACAG
Found at i:33380575 original size:16 final size:15
Alignment explanation
Indices: 33380551--33380580 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
33380541 CAGTAATACA
33380551 AATTAAAGAAGTTAC
1 AATTAAAGAAGTTAC
33380566 AATTATAAGAAGTTA
1 AATTA-AAGAAGTTA
33380581 GACAAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.53, C:0.03, G:0.13, T:0.30
Consensus pattern (15 bp):
AATTAAAGAAGTTAC
Found at i:33385284 original size:138 final size:138
Alignment explanation
Indices: 33385023--33385295 Score: 361
Period size: 138 Copynumber: 2.0 Consensus size: 138
33385013 TGTCATTAGG
* * * *
33385023 GTTATCATTTTTCGGGTGCTGATCCTGAATATCCTACCAATGGCTGAGGTTCGATATTTGTTGGG
1 GTTACCATGTTTCGGGTGCTGATCCTGAATATCCTACCAATGGCTGAGGTTCGACATTTGTTGCG
* *
33385088 GATACTCATCAGCTTGTGTGAGCAGCATCGTGTAGCTTACATTCCGACCATCAACTTGTGTGAGC
66 GATACTCATCAGCTTGTGTGAGCAGCATCGTATAGCTTACATTCCGACCATCAACTTGTGTGAAC
33385153 AAACCCAA
131 AAACCCAA
* * *
33385161 GTTACCATGTTTCGGGTGCT-AGTCCTGAATGTCCTACCAATGGTTGAGTTTCGACATTTGTTGC
1 GTTACCATGTTTCGGGTGCTGA-TCCTGAATATCCTACCAATGGCTGAGGTTCGACATTTGTTGC
* * * * * * * *
33385225 GGATAGTCGTTCAGTTTGTGTGAGCGGTATCGTATAGTTTACATTCCG-CCGTCAGCTTGTGTGA
65 GGATACTC-ATCAGCTTGTGTGAGCAGCATCGTATAGCTTACATTCCGACCATCAACTTGTGTGA
33385289 ACAAACC
129 ACAAACC
33385296 TATTTTATGG
Statistics
Matches: 116, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
137 1 0.01
138 82 0.71
139 33 0.28
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (138 bp):
GTTACCATGTTTCGGGTGCTGATCCTGAATATCCTACCAATGGCTGAGGTTCGACATTTGTTGCG
GATACTCATCAGCTTGTGTGAGCAGCATCGTATAGCTTACATTCCGACCATCAACTTGTGTGAAC
AAACCCAA
Found at i:33386104 original size:20 final size:20
Alignment explanation
Indices: 33386079--33386154 Score: 116
Period size: 20 Copynumber: 3.8 Consensus size: 20
33386069 AAGCTTACGC
*
33386079 TAAGTAAATGGAATGGAAAG
1 TAAGTAAATGAAATGGAAAG
33386099 TAAGTAAATGAAATGGAAAG
1 TAAGTAAATGAAATGGAAAG
* *
33386119 TGAGTAAATGAAATAGAAAG
1 TAAGTAAATGAAATGGAAAG
*
33386139 TAAGTAAATGGAATGG
1 TAAGTAAATGAAATGG
33386155 TTAGAAAATA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.51, C:0.00, G:0.28, T:0.21
Consensus pattern (20 bp):
TAAGTAAATGAAATGGAAAG
Found at i:33386167 original size:40 final size:40
Alignment explanation
Indices: 33386083--33386170 Score: 104
Period size: 40 Copynumber: 2.2 Consensus size: 40
33386073 TTACGCTAAG
* * ** *
33386083 TAAATGGAATGGAAAGTAAGTAAATGAAATGGAAAGTGAG
1 TAAATGAAATAGAAAGTAAGTAAATGAAATGGAAAGAAAA
* **
33386123 TAAATGAAATAGAAAGTAAGTAAATGGAATGGTTAGAAAA
1 TAAATGAAATAGAAAGTAAGTAAATGAAATGGAAAGAAAA
33386163 TAAATGAA
1 TAAATGAA
33386171 GTGGTTCATA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.53, C:0.00, G:0.25, T:0.22
Consensus pattern (40 bp):
TAAATGAAATAGAAAGTAAGTAAATGAAATGGAAAGAAAA
Found at i:33389086 original size:16 final size:16
Alignment explanation
Indices: 33389067--33389101 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
33389057 AATAATGAGT
33389067 AAAT-AAAATAACAATG
1 AAATAAAAATAA-AATG
33389083 AAATAAAAATAAAATG
1 AAATAAAAATAAAATG
33389099 AAA
1 AAA
33389102 ACAAATAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.74, C:0.03, G:0.06, T:0.17
Consensus pattern (16 bp):
AAATAAAAATAAAATG
Found at i:33389224 original size:68 final size:68
Alignment explanation
Indices: 33389135--33389274 Score: 210
Period size: 68 Copynumber: 2.1 Consensus size: 68
33389125 ACAACTTAAC
* *
33389135 ATTTTTCCATTTTTTTCCATGCCGAATGTGGGAGGAAGAACAAGAGAAAACCAACTTAGGGTCTT
1 ATTTTTCCATTTTCTTCCATGCCGAAGGTGGGAGGAAGAACAAGAGAAAACCAACTTAGGGTCTT
33389200 GAT
66 GAT
* * * * *
33389203 ATTTTTCCATTTTCTTGCATGCCGAAGGTGGGAGGAATAATAAGGGAAAACCGACTTAGGGTCTT
1 ATTTTTCCATTTTCTTCCATGCCGAAGGTGGGAGGAAGAACAAGAGAAAACCAACTTAGGGTCTT
33389268 GAT
66 GAT
33389271 -TTTT
1 ATTTT
33389275 CAAGGTTCAA
Statistics
Matches: 65, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
67 4 0.06
68 61 0.94
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.33
Consensus pattern (68 bp):
ATTTTTCCATTTTCTTCCATGCCGAAGGTGGGAGGAAGAACAAGAGAAAACCAACTTAGGGTCTT
GAT
Found at i:33392131 original size:6 final size:7
Alignment explanation
Indices: 33392090--33392142 Score: 56
Period size: 7 Copynumber: 7.6 Consensus size: 7
33392080 AACGTTTTCC
*
33392090 CAATTTC
1 CAATTTT
33392097 CAATTTT
1 CAATTTT
33392104 -ATATTTT
1 CA-ATTTT
*
33392111 CAATATT
1 CAATTTT
33392118 CAAATTTT
1 C-AATTTT
33392126 -AATTTT
1 CAATTTT
33392132 CAATTTT
1 CAATTTT
33392139 CAAT
1 CAAT
33392143 CCTCATTCCT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
6 7 0.18
7 26 0.67
8 6 0.15
ACGTcount: A:0.34, C:0.13, G:0.00, T:0.53
Consensus pattern (7 bp):
CAATTTT
Found at i:33393508 original size:15 final size:16
Alignment explanation
Indices: 33393488--33393528 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
33393478 TATTTTGTTT
33393488 TAAATTAATTTT-AAA
1 TAAATTAATTTTCAAA
*
33393503 TAAATTAAATTTTCAAT
1 TAAATT-AATTTTCAAA
33393520 TAAA-TAATT
1 TAAATTAATT
33393529 CTCTCAACCA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 10 0.43
16 7 0.30
17 6 0.26
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (16 bp):
TAAATTAATTTTCAAA
Found at i:33400698 original size:40 final size:40
Alignment explanation
Indices: 33400641--33400718 Score: 138
Period size: 40 Copynumber: 1.9 Consensus size: 40
33400631 AAATAGGAAT
* *
33400641 AAAATGAAAGATGTCGCACAGTTGTTAGTACCCTGTAGCA
1 AAAATAAAAGATATCGCACAGTTGTTAGTACCCTGTAGCA
33400681 AAAATAAAAGATATCGCACAGTTGTTAGTACCCTGTAG
1 AAAATAAAAGATATCGCACAGTTGTTAGTACCCTGTAG
33400719 TAGAATGGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.26
Consensus pattern (40 bp):
AAAATAAAAGATATCGCACAGTTGTTAGTACCCTGTAGCA
Found at i:33412734 original size:16 final size:17
Alignment explanation
Indices: 33412675--33412733 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
33412665 TAAAAGAAAT
33412675 AAAGAAAGACAAAAGCA-
1 AAAGAAAGACAAAAG-AG
*
33412692 AAACAAA-ACAAAA-AG
1 AAAGAAAGACAAAAGAG
33412707 AAAGAAAAAGA-AAAAGAG
1 AAAG--AAAGACAAAAGAG
33412725 AAAGAAAGA
1 AAAGAAAGA
33412734 AGAACCTACG
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
14 1 0.03
15 3 0.09
16 11 0.31
17 13 0.37
18 7 0.20
ACGTcount: A:0.76, C:0.07, G:0.17, T:0.00
Consensus pattern (17 bp):
AAAGAAAGACAAAAGAG
Found at i:33414625 original size:2 final size:2
Alignment explanation
Indices: 33414618--33414645 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
33414608 TTCTATCTAA
33414618 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
33414646 GAATCAAAAC
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:33418854 original size:10 final size:10
Alignment explanation
Indices: 33418824--33418854 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
33418814 TATTTTTCTC
33418824 TTTTTGTTTT
1 TTTTTGTTTT
*
33418834 GTTTTGTTTT
1 TTTTTGTTTT
33418844 TTTTTGTTTT
1 TTTTTGTTTT
33418854 T
1 T
33418855 ATAATGTATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (10 bp):
TTTTTGTTTT
Found at i:33421054 original size:155 final size:156
Alignment explanation
Indices: 33420878--33421180 Score: 446
Period size: 156 Copynumber: 1.9 Consensus size: 156
33420868 AGTTGGATGG
* * * * **
33420878 TTTTTTTGTACTATTGATTCTG-AAAAATAATTTTGAGAAGCGGGTTTTGAAAAATTATCCCGAG
1 TTTTTCTGTACTATTGATTCTGAAAAAATAATTTTGAGAAGAGGGTTCTCAAAAAAAATCCCGAG
* * * *
33420942 ATTCTTGGGAAATCTAATAGTTGGGGTTGAAAAATGCTTCAAGTAGGATGCACTGTTAGCAAAAG
66 ATTCATGGGAAATCTAATAGTTGGGGTTGAAAAACGCCTCAAGTAGGATGCACTGTCAGCAAAAG
33421007 TACTAAAAAAGCTCCCAGCTAGATAC
131 TACTAAAAAAGCTCCCAGCTAGATAC
* * * *
33421033 TTTTTCTGTACTATTGGTTCTGAAAAAATAATTTTTAGAAGATGGTTCTCAAAAAAAATCCCGGG
1 TTTTTCTGTACTATTGATTCTGAAAAAATAATTTTGAGAAGAGGGTTCTCAAAAAAAATCCCGAG
*
33421098 ATTCATGGGAAATCTGATAGTTGGGGTTGAAAAACGCCTCAAGTAGGATGCACTGTCAGCAAAAG
66 ATTCATGGGAAATCTAATAGTTGGGGTTGAAAAACGCCTCAAGTAGGATGCACTGTCAGCAAAAG
* *
33421163 TACTGAAAAAGTTCCCAG
131 TACTAAAAAAGCTCCCAG
33421181 TTGGACGCTC
Statistics
Matches: 130, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
155 20 0.15
156 110 0.85
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (156 bp):
TTTTTCTGTACTATTGATTCTGAAAAAATAATTTTGAGAAGAGGGTTCTCAAAAAAAATCCCGAG
ATTCATGGGAAATCTAATAGTTGGGGTTGAAAAACGCCTCAAGTAGGATGCACTGTCAGCAAAAG
TACTAAAAAAGCTCCCAGCTAGATAC
Found at i:33424260 original size:59 final size:59
Alignment explanation
Indices: 33424190--33424356 Score: 273
Period size: 59 Copynumber: 2.8 Consensus size: 59
33424180 TAATTCCTAA
* * *
33424190 TTTATTAAATGAAACAATGA-AAAAATAATTTGCACAAACATATTCTAAAGAACTTCTAT
1 TTTATTAAATGAAACAAT-ATAAAAATAATTTGTACAAAAATATTCAAAAGAACTTCTAT
*
33424249 TTTATTGAATGAAACAATATAAAAATAATTTGTACAAAAATATTCAAAAGAACTTCTAT
1 TTTATTAAATGAAACAATATAAAAATAATTTGTACAAAAATATTCAAAAGAACTTCTAT
*
33424308 TTTATTAAATGAAACAATATAAAAATAATTTGTACAAATATATTCAAAA
1 TTTATTAAATGAAACAATATAAAAATAATTTGTACAAAAATATTCAAAA
33424357 ATAAATCAAT
Statistics
Matches: 101, Mismatches: 6, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
58 1 0.01
59 100 0.99
ACGTcount: A:0.51, C:0.09, G:0.06, T:0.34
Consensus pattern (59 bp):
TTTATTAAATGAAACAATATAAAAATAATTTGTACAAAAATATTCAAAAGAACTTCTAT
Found at i:33426766 original size:40 final size:40
Alignment explanation
Indices: 33426651--33426766 Score: 142
Period size: 40 Copynumber: 2.9 Consensus size: 40
33426641 TTGGTGGAAA
**
33426651 ACACGGGGTAAAGCGCGTCCACGTCAGCGCGCTTTTGTTG
1 ACACGGGGTAAAGCGCGTCCACGTCAGCGCGCTTTTACTG
* * * * *
33426691 ACACAGGGTAAAGCACGCCCACATCAGCGCTCTTTTACTG
1 ACACGGGGTAAAGCGCGTCCACGTCAGCGCGCTTTTACTG
* * *
33426731 ACACGGGGTAAAGCGCGTCCTCGTCAACACGCTTTT
1 ACACGGGGTAAAGCGCGTCCACGTCAGCGCGCTTTT
33426767 CTACGTTTTC
Statistics
Matches: 61, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
40 61 1.00
ACGTcount: A:0.22, C:0.30, G:0.26, T:0.22
Consensus pattern (40 bp):
ACACGGGGTAAAGCGCGTCCACGTCAGCGCGCTTTTACTG
Found at i:33431233 original size:60 final size:60
Alignment explanation
Indices: 33431100--33431236 Score: 220
Period size: 60 Copynumber: 2.3 Consensus size: 60
33431090 GCCAGTTTCT
*
33431100 TGGGCAGAATAATAGGCAACATTTTGGGCCGAATACAGGCCAGTCTCTTGGGCCTGTTAG
1 TGGGCAGAATAATGGGCAACATTTTGGGCCGAATACAGGCCAGTCTCTTGGGCCTGTTAG
* * * **
33431160 TGGGCAGAATAATGGGCAGCATTTTGGGCCGAATGCAGGTCAGTCTCTTGGGTTTGTTAG
1 TGGGCAGAATAATGGGCAACATTTTGGGCCGAATACAGGCCAGTCTCTTGGGCCTGTTAG
33431220 TGGGCAGAATAATGGGC
1 TGGGCAGAATAATGGGC
33431237 CGAATAGTGG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 71 1.00
ACGTcount: A:0.23, C:0.17, G:0.34, T:0.26
Consensus pattern (60 bp):
TGGGCAGAATAATGGGCAACATTTTGGGCCGAATACAGGCCAGTCTCTTGGGCCTGTTAG
Found at i:33438547 original size:22 final size:20
Alignment explanation
Indices: 33438522--33438570 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
33438512 AAAACGTTCA
33438522 AAATATAGTTTTATTAAACAAT
1 AAATATA-TTTT-TTAAACAAT
* *
33438544 AAATGACATTTTTTAAACGAT
1 AAAT-ATATTTTTTAAACAAT
33438565 AAATAT
1 AAATAT
33438571 TGACTCTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 1 0.04
21 12 0.52
22 8 0.35
23 2 0.09
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.39
Consensus pattern (20 bp):
AAATATATTTTTTAAACAAT
Found at i:33446475 original size:29 final size:30
Alignment explanation
Indices: 33446414--33446469 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
33446404 TTTTTTACAA
33446414 AAAAATAATAAATTCAAATCTTTAAATAAT
1 AAAAATAATAAATTCAAATCTTTAAATAAT
*
33446444 AAAAATATTAAGATT-AAAT-TTTAAAT
1 AAAAATAATAA-ATTCAAATCTTTAAAT
33446470 TTTAAATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
29 7 0.29
30 14 0.58
31 3 0.12
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.36
Consensus pattern (30 bp):
AAAAATAATAAATTCAAATCTTTAAATAAT
Found at i:33446660 original size:18 final size:18
Alignment explanation
Indices: 33446619--33446684 Score: 62
Period size: 18 Copynumber: 3.6 Consensus size: 18
33446609 AAACAGTCAA
*
33446619 TTTTATAATTTTTTAGTA-
1 TTTTATAA-TTTTTAATAT
*
33446637 TGTTATAATTTTTAATAT
1 TTTTATAATTTTTAATAT
* *
33446655 TTTTATAATCATTTACTAT
1 TTTTATAAT-TTTTAATAT
33446674 TTTTAATAATT
1 TTTT-ATAATT
33446685 AATTTTACAA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
17 8 0.21
18 15 0.38
19 11 0.28
20 5 0.13
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (18 bp):
TTTTATAATTTTTAATAT
Found at i:33447036 original size:6 final size:6
Alignment explanation
Indices: 33447025--33447061 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
33447015 TTTATCACTA
33447025 AAAAAT AAAAAT AAAAAT AAAAAT --AAAT AAAAAT AAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAA
33447062 TAATTGAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 4 0.14
6 25 0.86
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:33447054 original size:10 final size:10
Alignment explanation
Indices: 33447027--33447064 Score: 58
Period size: 10 Copynumber: 3.6 Consensus size: 10
33447017 TATCACTAAA
33447027 AAATAAAAAT
1 AAATAAAAAT
33447037 AAAAATAAAAAT
1 --AAATAAAAAT
33447049 AAATAAAAAT
1 AAATAAAAAT
33447059 AAATAA
1 AAATAA
33447065 TTGAATTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 16 0.62
12 10 0.38
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:33447266 original size:19 final size:20
Alignment explanation
Indices: 33447242--33447285 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
33447232 GAGTTTAGGC
33447242 AAAATTTT-TTTTTATTTTT
1 AAAATTTTATTTTTATTTTT
33447261 AAAATTTTATTTTTATTTTT
1 AAAATTTTATTTTTATTTTT
33447281 AAAAT
1 AAAAT
33447286 AAATTTTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
AAAATTTTATTTTTATTTTT
Found at i:33447291 original size:19 final size:20
Alignment explanation
Indices: 33447250--33447294 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
33447240 GCAAAATTTT
**
33447250 TTTTTATTTTTAAAATTTTA
1 TTTTTATTTTTAAAATTAAA
33447270 TTTTTATTTTTAAAA-TAAA
1 TTTTTATTTTTAAAATTAAA
33447289 TTTTTA
1 TTTTTA
33447295 GTATTTATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTTATTTTTAAAATTAAA
Found at i:33447293 original size:20 final size:20
Alignment explanation
Indices: 33447249--33447311 Score: 58
Period size: 20 Copynumber: 3.0 Consensus size: 20
33447239 GGCAAAATTT
**
33447249 TTTTTTATTTTTAAAAT-TT
1 TTTTTTATTTTTAAAATAAA
33447268 TATTTTTATTTTTAAAATAAA
1 T-TTTTTATTTTTAAAATAAA
33447289 TTTTTAGTATTTATTAAAA-AAA
1 TTTTT--TATTT-TTAAAATAAA
33447311 T
1 T
33447312 AGGCCGGGCC
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
19 1 0.03
20 20 0.54
21 1 0.03
22 9 0.24
23 6 0.16
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
TTTTTTATTTTTAAAATAAA
Found at i:33448969 original size:61 final size:61
Alignment explanation
Indices: 33448874--33449002 Score: 249
Period size: 61 Copynumber: 2.1 Consensus size: 61
33448864 TTTAGAACTA
*
33448874 AATGATGTTATCAATTAAAGAGGTAATAATTTTTTGTCAATGATGAATGCTTTAATATAAG
1 AATGATGTTATCAATTAAAGAGGTAATAATTTTTTGTCAACGATGAATGCTTTAATATAAG
33448935 AATGATGTTATCAATTAAAGAGGTAATAATTTTTTGTCAACGATGAATGCTTTAATATAAG
1 AATGATGTTATCAATTAAAGAGGTAATAATTTTTTGTCAACGATGAATGCTTTAATATAAG
33448996 AATGATG
1 AATGATG
33449003 GAATGACATT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
61 67 1.00
ACGTcount: A:0.40, C:0.05, G:0.17, T:0.38
Consensus pattern (61 bp):
AATGATGTTATCAATTAAAGAGGTAATAATTTTTTGTCAACGATGAATGCTTTAATATAAG
Found at i:33452322 original size:17 final size:16
Alignment explanation
Indices: 33452289--33452334 Score: 60
Period size: 15 Copynumber: 2.9 Consensus size: 16
33452279 AAAAAATAGA
33452289 ATTTTTATTTT-TGAATT
1 ATTTTTATTTTAT-AA-T
33452306 ATTTTTATTTTATAAT
1 ATTTTTATTTTATAAT
33452322 -TTTTTATTTTATA
1 ATTTTTATTTTATA
33452335 TAATTGATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
15 13 0.46
16 1 0.04
17 13 0.46
18 1 0.04
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (16 bp):
ATTTTTATTTTATAAT
Found at i:33452514 original size:27 final size:27
Alignment explanation
Indices: 33452487--33452566 Score: 72
Period size: 28 Copynumber: 2.8 Consensus size: 27
33452477 TTGATTGATA
33452487 TATATTTG-AATATTTATATTTTATATAT
1 TATATTTGTAAT-TTT-TATTTTATATAT
* *
33452515 TGTTTTTGTAATTTTTATTTTATATAAT
1 TATATTTGTAATTTTTATTTTATAT-AT
*
33452543 GTATATATTATAATTTTTTATTTT
1 -TATAT-TTGTAA-TTTTTATTTT
33452567 TGAATTATGT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
27 10 0.24
28 11 0.26
29 6 0.14
30 5 0.12
31 10 0.24
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (27 bp):
TATATTTGTAATTTTTATTTTATATAT
Found at i:33455768 original size:20 final size:20
Alignment explanation
Indices: 33455743--33455782 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
33455733 GCCTGTTACC
33455743 CAAAAGCTATTCCCGTTTCT
1 CAAAAGCTATTCCCGTTTCT
33455763 CAAAAGCTATTCCCGTTTCT
1 CAAAAGCTATTCCCGTTTCT
33455783 TTCTTTCATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.30, G:0.10, T:0.35
Consensus pattern (20 bp):
CAAAAGCTATTCCCGTTTCT
Found at i:33462075 original size:26 final size:26
Alignment explanation
Indices: 33462039--33462088 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
33462029 AACCAAATAG
33462039 CACGATATGTATTCGTATAGCACTAT
1 CACGATATGTATTCGTATAGCACTAT
33462065 CACGATATGTATTCGTATAGCACT
1 CACGATATGTATTCGTATAGCACT
33462089 TAATGTCCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (26 bp):
CACGATATGTATTCGTATAGCACTAT
Found at i:33463150 original size:21 final size:21
Alignment explanation
Indices: 33463095--33463150 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
33463085 TTCTCACATC
*
33463095 AATTTAATATTAAAGAATAAT
1 AATTTAATATAAAAGAATAAT
**
33463116 -ATTTTCTATCAAAAGAATAAT
1 AATTTAATAT-AAAAGAATAAT
*
33463137 AATTTGATATAAAA
1 AATTTAATATAAAA
33463151 TATTTAAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
20 7 0.25
21 14 0.50
22 7 0.25
ACGTcount: A:0.54, C:0.04, G:0.05, T:0.38
Consensus pattern (21 bp):
AATTTAATATAAAAGAATAAT
Found at i:33463865 original size:69 final size:68
Alignment explanation
Indices: 33463738--33463912 Score: 192
Period size: 69 Copynumber: 2.5 Consensus size: 68
33463728 ATCATCCTGA
* * * *
33463738 AATTGCATACAAAAAGTTATAATACTCCACCACCACACCCATTTAAACATTCAAAAAGT-AGCAA
1 AATTACATACAAAAAGTTATATTA-TCCACCACCACACACATTTAAACATACAAAAAGTGA-CAA
33463802 -CCTAC
64 CCCT-C
* * * * *
33463807 AATTACATACAAAAAGTTATATTAGTTCACCACCACATACATTTACACATAGACAAAGTGACAAC
1 AATTACATACAAAAAGTTATATTA-TCCACCACCACACACATTTAAACATACAAAAAGTGACAAC
33463872 CCTC
65 CCTC
* *
33463876 TATGACATACAAAAAGTTATATTCATCCACCACCACA
1 AATTACATACAAAAAGTTATATT-ATCCACCACCACA
33463913 ATCACATCTT
Statistics
Matches: 90, Mismatches: 13, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
69 85 0.94
70 5 0.06
ACGTcount: A:0.44, C:0.26, G:0.06, T:0.23
Consensus pattern (68 bp):
AATTACATACAAAAAGTTATATTATCCACCACCACACACATTTAAACATACAAAAAGTGACAACC
CTC
Found at i:33469474 original size:25 final size:25
Alignment explanation
Indices: 33469365--33469474 Score: 70
Period size: 25 Copynumber: 4.5 Consensus size: 25
33469355 AGCTTTGGAT
* *
33469365 AGCCATATATCGGGAAG-TTCAAGCG
1 AGCCATATATCGGGAAGCTCCAA-AG
* **
33469390 AGCC--ATATCAGGAAGCTCCGGAG
1 AGCCATATATCGGGAAGCTCCAAAG
**
33469413 AG-CAT-TAATCAAGAAGCTCACAAAG
1 AGCCATAT-ATCGGGAAGCTC-CAAAG
*
33469438 AGCC-TTTAATCGGGAAGCTCCAAAG
1 AGCCATAT-ATCGGGAAGCTCCAAAG
33469463 AGCCATATATCG
1 AGCCATATATCG
33469475 AGACGCTCAT
Statistics
Matches: 66, Mismatches: 11, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
22 1 0.02
23 14 0.21
24 13 0.20
25 23 0.35
26 15 0.23
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (25 bp):
AGCCATATATCGGGAAGCTCCAAAG
Found at i:33469482 original size:25 final size:26
Alignment explanation
Indices: 33469418--33469483 Score: 73
Period size: 25 Copynumber: 2.6 Consensus size: 26
33469408 CGGAGAGCAT
* *
33469418 TAATCAAGAAGCTCACAAAGAGCCTT
1 TAATCGAGAAGCTCACAAAGAGCCTA
*
33469444 TAATCGGGAAGCTC-CAAAGAGCC-A
1 TAATCGAGAAGCTCACAAAGAGCCTA
*
33469468 TATATCGAGACGCTCA
1 TA-ATCGAGAAGCTCA
33469484 TAAGAGTTGC
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
24 2 0.06
25 19 0.58
26 12 0.36
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.18
Consensus pattern (26 bp):
TAATCGAGAAGCTCACAAAGAGCCTA
Found at i:33469947 original size:5 final size:5
Alignment explanation
Indices: 33469928--33469961 Score: 59
Period size: 5 Copynumber: 6.6 Consensus size: 5
33469918 GAATATAACA
33469928 TCAAT TCATAT TCAAT TCAAT TCAAT TCAAT TCA
1 TCAAT TCA-AT TCAAT TCAAT TCAAT TCAAT TCA
33469962 CATATTTGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 23 0.82
6 5 0.18
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.41
Consensus pattern (5 bp):
TCAAT
Found at i:33470534 original size:31 final size:30
Alignment explanation
Indices: 33470484--33470543 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
33470474 TATTTAATCC
*
33470484 ATTTATCATATTTATTTATTTTATCTTTCCA
1 ATTTATCATATTTATTTATTTAAT-TTTCCA
*
33470515 ATTTCATCAT-TTTCTTTATTTAATTTTCC
1 ATTT-ATCATATTTATTTATTTAATTTTCC
33470544 GTGGATGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 5 0.19
31 16 0.62
32 5 0.19
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (30 bp):
ATTTATCATATTTATTTATTTAATTTTCCA
Found at i:33472086 original size:24 final size:23
Alignment explanation
Indices: 33472008--33472094 Score: 104
Period size: 23 Copynumber: 3.7 Consensus size: 23
33471998 TTAGTGTTCA
**
33472008 TGAACATGTTCATTTAAC-TTAAT
1 TGAACATGTTCA-CGAACATTAAT
*
33472031 TGAACATGTTCACGAACATTAAA
1 TGAACATGTTCACGAACATTAAT
* *
33472054 TGAACATGTTCATGGACATATAAT
1 TGAACATGTTCACGAACAT-TAAT
33472078 TGAACATGTTCACGAAC
1 TGAACATGTTCACGAAC
33472095 CATGTTAATA
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
22 3 0.06
23 33 0.61
24 18 0.33
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (23 bp):
TGAACATGTTCACGAACATTAAT
Found at i:33478136 original size:25 final size:25
Alignment explanation
Indices: 33478099--33478148 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
33478089 ACAGTAAACA
* * *
33478099 CGAATTATGTAGAAAGCCTTTGTGG
1 CGAATTATCTAGAAAACCCTTGTGG
*
33478124 CGAATTCTCTAGAAAACCCTTGTGG
1 CGAATTATCTAGAAAACCCTTGTGG
33478149 TACATTCACT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (25 bp):
CGAATTATCTAGAAAACCCTTGTGG
Found at i:33479655 original size:26 final size:26
Alignment explanation
Indices: 33479626--33479678 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
33479616 TACAGTACAT
33479626 ACTTTCTTCTAAAACTAAAATCTTTG
1 ACTTTCTTCTAAAACTAAAATCTTTG
*
33479652 ACTTTCTTCTAGAACTAAAATCTTTG
1 ACTTTCTTCTAAAACTAAAATCTTTG
33479678 A
1 A
33479679 AACTTCTGCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.34, C:0.19, G:0.06, T:0.42
Consensus pattern (26 bp):
ACTTTCTTCTAAAACTAAAATCTTTG
Found at i:33480262 original size:21 final size:21
Alignment explanation
Indices: 33480219--33480264 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
33480209 TGACCCCAGA
*
33480219 TCTTGCAAATCATCAATCTTC
1 TCTTGCAAATCATCAATCATC
* * *
33480240 TCTTGCAACTCATTATTCATC
1 TCTTGCAAATCATCAATCATC
33480261 TCTT
1 TCTT
33480265 CTATCTTCTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.28, G:0.04, T:0.43
Consensus pattern (21 bp):
TCTTGCAAATCATCAATCATC
Found at i:33484301 original size:20 final size:20
Alignment explanation
Indices: 33484276--33484314 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
33484266 TGGAGCATGA
*
33484276 ATATTGAAACCTTAGGAAAT
1 ATATTGAAACCTTAAGAAAT
*
33484296 ATATTGATACCTTAAGAAA
1 ATATTGAAACCTTAAGAAA
33484315 AGTATCGGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.10, G:0.13, T:0.31
Consensus pattern (20 bp):
ATATTGAAACCTTAAGAAAT
Found at i:33485673 original size:21 final size:20
Alignment explanation
Indices: 33485648--33485698 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
33485638 TTTTTCCTAA
* *
33485648 GATGTGAATTGGATTGAATT
1 GATGTAAATTGGATTAAATT
*
33485668 GAATGTAAATTGTATTAAATT
1 G-ATGTAAATTGGATTAAATT
*
33485689 GATGTTAATT
1 GATGTAAATT
33485699 CATTCGTATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.35, C:0.00, G:0.22, T:0.43
Consensus pattern (20 bp):
GATGTAAATTGGATTAAATT
Found at i:33486363 original size:25 final size:25
Alignment explanation
Indices: 33486299--33486368 Score: 65
Period size: 25 Copynumber: 2.8 Consensus size: 25
33486289 TTCCCGTTAC
*
33486299 ATGGCTCACATGAACTTTCCATTAT
1 ATGGCTCACATGAGCTTTCCATTAT
*
33486324 ATGGCTCGA-AAGAGC-TTCTCATT-T
1 ATGGCTC-ACATGAGCTTTC-CATTAT
*
33486348 ATGTGCTCACATGAGCATTCC
1 ATG-GCTCACATGAGCTTTCC
33486369 TGAATATGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
24 8 0.22
25 25 0.68
26 4 0.11
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (25 bp):
ATGGCTCACATGAGCTTTCCATTAT
Found at i:33488782 original size:17 final size:18
Alignment explanation
Indices: 33488748--33488782 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
33488738 AAATAAAATA
*
33488748 TTTAGAAATTTAATTATT
1 TTTACAAATTTAATTATT
33488766 TTTACAAATTT-ATTATT
1 TTTACAAATTTAATTATT
33488783 GAAGATGGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.57
Consensus pattern (18 bp):
TTTACAAATTTAATTATT
Found at i:33489909 original size:28 final size:27
Alignment explanation
Indices: 33489877--33489952 Score: 71
Period size: 28 Copynumber: 2.7 Consensus size: 27
33489867 ATCCAGATGA
*
33489877 AACACACCACTAATAACATGGAGGTAGT
1 AACACACCA-AAATAACATGGAGGTAGT
** *
33489905 AACACGATTAAAATAATATGGAGGTAGT
1 AACAC-ACCAAAATAACATGGAGGTAGT
**
33489933 AACACAATTAAAATAACATG
1 AACAC-ACCAAAATAACATG
33489953 TATTGAATAT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
28 39 0.95
29 2 0.05
ACGTcount: A:0.49, C:0.14, G:0.16, T:0.21
Consensus pattern (27 bp):
AACACACCAAAATAACATGGAGGTAGT
Found at i:33491949 original size:2 final size:2
Alignment explanation
Indices: 33491942--33491969 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
33491932 ACATGCACTC
33491942 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
33491970 GAATGCATAA
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:33492805 original size:97 final size:98
Alignment explanation
Indices: 33492629--33492824 Score: 317
Period size: 97 Copynumber: 2.0 Consensus size: 98
33492619 GTGTAATAAA
**
33492629 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGGTT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
* *
33492694 CCTCTAAAATCCCAAACT-TGAAATATTTCCTTT
66 CCTCTAAAACCCCAAACTCAG-AATATTTCCTTT
33492727 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAA-CACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
33492791 CCT-TCAAAACCCCAAACTCAGAATATTTCCTTT
66 CCTCT-AAAACCCCAAACTCAGAATATTTCCTTT
33492824 A
1 A
33492825 TTTTTTTAAA
Statistics
Matches: 92, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
96 1 0.01
97 52 0.57
98 39 0.42
ACGTcount: A:0.38, C:0.26, G:0.09, T:0.27
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
CCTCTAAAACCCCAAACTCAGAATATTTCCTTT
Found at i:33493653 original size:12 final size:12
Alignment explanation
Indices: 33493632--33493662 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
33493622 AATTGAAATG
*
33493632 AAAAATAAATTT
1 AAAAACAAATTT
33493644 AAAAACAAATTT
1 AAAAACAAATTT
33493656 AAAAACA
1 AAAAACA
33493663 TAAAAAAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (12 bp):
AAAAACAAATTT
Found at i:33495127 original size:44 final size:42
Alignment explanation
Indices: 33494825--33495480 Score: 330
Period size: 44 Copynumber: 15.2 Consensus size: 42
33494815 CGCGACGTTG
* * * *
33494825 GGGAGATAAGATTGGTATGTTTAGTCTGCCCCCACTGCAATTTCAA
1 GGGAGATAAGACT-GT-TGCTTAGTCTG-CTCCACTGCAACTTC-A
33494871 GGG-GATAAGACTTGCGTT-CTTCAGTCTGCTCCACTGCAACTTCA
1 GGGAGATAAGAC-T--GTTGCTT-AGTCTGCTCCACTGCAACTTCA
** * *
33494915 GGGAGATAAGACTAGACGC-GA-TCTGC-CCTCTGCAACTTCA
1 GGGAGATAAGACT-GTTGCTTAGTCTGCTCCACTGCAACTTCA
* ** * * ** * *
33494955 GAGAGATAAGATCTGAGGTTTTAATCCACTCCATTGCAACTTTA
1 GGGAGATAAGA-CTGTTG-CTTAGTCTGCTCCACTGCAACTTCA
* * * * *
33494999 GGGAGATAGGATTGTCGGCTTTAATCTGCTCAACTGCAACTTCA
1 GGGAGATAAGACTGT-TGC-TTAGTCTGCTCCACTGCAACTTCA
* *
33495043 GGGAGATAAGA-TTTTCCATCTTTAGTCTGC-CTCACTGCAACTTCA
1 GGGAGATAAGACTGTT---GC-TTAGTCTGCTC-CACTGCAACTTCA
33495088 -GGAGGATAAGACCTGCTTGCTTAGTCTGCTCCACTGCAACTTCA
1 GGGA-GATAAGA-CTG-TTGCTTAGTCTGCTCCACTGCAACTTCA
* * *
33495132 GGGAGATAAGACTAGATGC-GA-TCTGCT-CTCTGCAACTTCA
1 GGGAGATAAGACT-GTTGCTTAGTCTGCTCCACTGCAACTTCA
* * * *
33495172 GAGAGATAAGACTAGATGC-GA-TCTGCT-CTCTGCAACTTCA
1 GGGAGATAAGACT-GTTGCTTAGTCTGCTCCACTGCAACTTCA
* * * *
33495212 GAGAGATAAGATCTGTGGTTTAAATCTGCTCCACTGCAACTTCA
1 GGGAGATAAGA-CTGTTGCTT-AGTCTGCTCCACTGCAACTTCA
* * * * * *
33495256 GGGAGATAGGATTATCGGCTTTAATCTGCTCCACTACAACTTCA
1 GGGAGATAAGACTGT-TGC-TTAGTCTGCTCCACTGCAACTTCA
* *
33495300 GGGAGATAAGACTTGCCAT-CTTCAGTCTGCCCCCACTGCAACTTCA
1 GGGAGATAAGAC-TG--TTGCTT-AGTCTG-CTCCACTGCAACTTCA
*
33495346 -GGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCA
1 GGGA-GATAAGAC-TG-TTGCTTAGTCTGCTCCACTGCAACTTCA
* * **
33495390 GGGAGATAAG-CTAGATGC-GA-TCTGCT-TTCTGCAACTTCA
1 GGGAGATAAGACT-GTTGCTTAGTCTGCTCCACTGCAACTTCA
* * * *
33495429 GAGAGATAAGATCCAAGGTT--TTAATCCGCTCCACTGCAACTTCA
1 GGGAGATAAGA--C--TGTTGCTTAGTCTGCTCCACTGCAACTTCA
33495473 GGGAGATA
1 GGGAGATA
33495481 GGATTATCGG
Statistics
Matches: 488, Mismatches: 75, Indels: 96
0.74 0.11 0.15
Matches are distributed among these distances:
39 20 0.04
40 96 0.20
41 16 0.03
42 9 0.02
43 30 0.06
44 186 0.38
45 87 0.18
46 39 0.08
47 3 0.01
48 2 0.00
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (42 bp):
GGGAGATAAGACTGTTGCTTAGTCTGCTCCACTGCAACTTCA
Found at i:33495178 original size:40 final size:40
Alignment explanation
Indices: 33495112--33495222 Score: 195
Period size: 40 Copynumber: 2.8 Consensus size: 40
33495102 GCTTGCTTAG
* *
33495112 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGA
1 TCTGCT-CTCTGCAACTTCAGAGAGATAAGACTAGATGCGA
33495153 TCTGCTCTCTGCAACTTCAGAGAGATAAGACTAGATGCGA
1 TCTGCTCTCTGCAACTTCAGAGAGATAAGACTAGATGCGA
33495193 TCTGCTCTCTGCAACTTCAGAGAGATAAGA
1 TCTGCTCTCTGCAACTTCAGAGAGATAAGA
33495223 TCTGTGGTTT
Statistics
Matches: 68, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
40 62 0.91
41 6 0.09
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.24
Consensus pattern (40 bp):
TCTGCTCTCTGCAACTTCAGAGAGATAAGACTAGATGCGA
Found at i:33495406 original size:257 final size:257
Alignment explanation
Indices: 33494895--33495439 Score: 885
Period size: 257 Copynumber: 2.1 Consensus size: 257
33494885 CGTTCTTCAG
* *
33494895 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGACGCGATCTGCCCTCTGCAACTTCAGAGAG
1 TCTGCT-CTCTGCAACTTCAGAGAGATAAGACTAGACGCGATCTGCCCTCTGCAACTTCAGAGAG
* * * *
33494960 ATAAGATCTGAGGTTTTAATCCACTCCATTGCAACTTTAGGGAGATAGGATTGTCGGCTTTAATC
65 ATAAGATCTGAGGTTTAAATCCACTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAATC
* * * * *
33495025 TGCTCAACTGCAACTTCAGGGAGATAAGATTTTCCATCTTTAGTCTGCCTCACTGCAACTTCAGG
130 TGCTCAACTACAACTTCAGGGAGATAAGACTTGCCATCTTCAGTCTGCCCCACTGCAACTTCAGG
*
33495090 AGGATAAGACCTGCTTGCTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGA
195 AGGATAAGACCTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGA
* *
33495153 TCTGCTCTCTGCAACTTCAGAGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGA
1 TCTGCTCTCTGCAACTTCAGAGAGATAAGACTAGACGCGATCTGCCCTCTGCAACTTCAGAGAGA
* **
33495218 TAAGATCTGTGGTTTAAATCTGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAATCT
66 TAAGATCTGAGGTTTAAATCCACTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAATCT
*
33495283 GCTCCACTACAACTTCAGGGAGATAAGACTTGCCATCTTCAGTCTGCCCCCACTGCAACTTCAGG
131 GCTCAACTACAACTTCAGGGAGATAAGACTTGCCATCTTCAGTCTG-CCCCACTGCAACTTCAGG
*
33495348 AGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAG-CTAGATGCGA
195 AGGATAAGACCTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGA
*
33495410 TCTGCTTTCTGCAACTTCAGAGAGATAAGA
1 TCTGCTCTCTGCAACTTCAGAGAGATAAGA
33495440 TCCAAGGTTT
Statistics
Matches: 266, Mismatches: 20, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
257 193 0.73
258 73 0.27
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.28
Consensus pattern (257 bp):
TCTGCTCTCTGCAACTTCAGAGAGATAAGACTAGACGCGATCTGCCCTCTGCAACTTCAGAGAGA
TAAGATCTGAGGTTTAAATCCACTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAATCT
GCTCAACTACAACTTCAGGGAGATAAGACTTGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGA
GGATAAGACCTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGA
Found at i:33495429 original size:217 final size:211
Alignment explanation
Indices: 33494873--33495494 Score: 664
Period size: 217 Copynumber: 2.9 Consensus size: 211
33494863 AATTTCAAGG
* * * * **
33494873 GGATAAGACTTGCGTTCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGACGCGATC
1 GGATAAGACCTGCATGCTT-AGTCTGCCCCACTGCAACTTCAGGGAGATAAGACTAGATACGATC
* * * *** ** * *
33494938 TGCCCTCTGCAACTTCAGAGAGATAAGATCTGAGGTTTTAATCCACTC-CATTGCAACTTTAGGG
65 TGCTCACTGCAACTTCAGAGAGATAAGA-CT-A-GATGCGATCTGCTCTC--TGCAACTTCAGAG
* * * * **
33495002 AGATAGGAT-TGTCGGCTTTAATCTGCTCAACTGCAACTTCAGGGAGATAAGATTTTCCATCTTT
125 AGATAAGATCTGT-GG-TTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGATTAT-CGGCTTT
* *
33495066 AGTCTGCCTCACTGCAACTTCAGGA
187 AATCTGCCTCACTACAACTTCAGGA
* * *
33495091 GGATAAGACCTGCTTGCTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCT
1 GGATAAGACCTGCATGCTTAGTCTGCCCCACTGCAACTTCAGGGAGATAAGACTAGATACGATCT
*
33495156 GCTCTCTGCAACTTCAGAGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAA
66 GCTCACTGCAACTTCAGAGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAA
33495221 GATCTGTGGTTTAAATCTGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAATCTG-C
131 GATCTGTGGTTT-AATCTGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAATCTGCC
33495285 TCCACTACAACTTCAGG-
195 T-CACTACAACTTCAGGA
* * *
33495302 GAGATAAGACTTGCCAT-CTTCAGTCTGCCCCCACTGCAACTTCA-GGAGGATAAGACTTGCTTA
1 G-GATAAGACCTG-CATGCTT-AGTCTG-CCCCACTGCAACTTCAGGGA-GATAAGACTAG-ATA
* * *
33495365 CTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAG-CTAGATGCGATCTGCTTTCTGCAACTTCA
60 C-GA-TCTGCT-CACTGCAACTTCAGAGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCA
*** *
33495429 GAGAGATAAGATCCAAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTT
122 GAGAGATAAGATCTGTGG-TTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTT
33495494 T
186 T
33495495 CTTCTGTTTG
Statistics
Matches: 355, Mismatches: 35, Indels: 29
0.85 0.08 0.07
Matches are distributed among these distances:
211 3 0.01
212 40 0.11
213 66 0.19
214 36 0.10
215 4 0.01
216 3 0.01
217 163 0.46
218 40 0.11
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.28
Consensus pattern (211 bp):
GGATAAGACCTGCATGCTTAGTCTGCCCCACTGCAACTTCAGGGAGATAAGACTAGATACGATCT
GCTCACTGCAACTTCAGAGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAA
GATCTGTGGTTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAATCTGCCT
CACTACAACTTCAGGA
Found at i:33507717 original size:12 final size:12
Alignment explanation
Indices: 33507696--33507726 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
33507686 AATTGAAATG
*
33507696 AAAAATAAATTT
1 AAAAACAAATTT
33507708 AAAAACAAATTT
1 AAAAACAAATTT
33507720 AAAAACA
1 AAAAACA
33507727 TAAAAAAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (12 bp):
AAAAACAAATTT
Found at i:33508475 original size:15 final size:15
Alignment explanation
Indices: 33508455--33508483 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
33508445 CAATAAATCT
33508455 GTTTGATTTGATTTC
1 GTTTGATTTGATTTC
33508470 GTTTGATTTGATTT
1 GTTTGATTTGATTT
33508484 TCTTTCCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.03, G:0.21, T:0.62
Consensus pattern (15 bp):
GTTTGATTTGATTTC
Found at i:33510086 original size:3 final size:3
Alignment explanation
Indices: 33510080--33510107 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
33510070 CCCTTAACAG
33510080 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
33510108 TAGACTATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:33510191 original size:3 final size:3
Alignment explanation
Indices: 33510183--33510216 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
33510173 ATGTCTTTGC
33510183 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
33510217 GGCTCTCTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:33516612 original size:3 final size:3
Alignment explanation
Indices: 33516602--33516651 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
33516592 TTTTTTTCAG
* * * *
33516602 TCT T-T TCT TCT TCT TCT TCT TCT TCT CCT GCT TCT TCT TAT TCT TTT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
33516649 TCT
1 TCT
33516652 CTGTTAAGGG
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.02, C:0.30, G:0.02, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:33516758 original size:20 final size:20
Alignment explanation
Indices: 33516733--33516772 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
33516723 CAACGTGGCA
*
33516733 AGTTAACTGGCTACATCAGC
1 AGTTAACTGGCCACATCAGC
*
33516753 AGTTAACTTGCCACATCAGC
1 AGTTAACTGGCCACATCAGC
33516773 GGTCTCGTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (20 bp):
AGTTAACTGGCCACATCAGC
Found at i:33516872 original size:30 final size:31
Alignment explanation
Indices: 33516805--33516875 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
33516795 AAATTGTTAA
* *
33516805 TTAGTGACTGTTTTGTCACTTTTTTATAACG
1 TTAGTGACTGTTTTGTCACTTTTTCATAAAG
* *
33516836 TTAGTGATTGTTTTGTTA-TTTTTCA-AAAG
1 TTAGTGACTGTTTTGTCACTTTTTCATAAAG
33516865 TTGAGTGACTG
1 TT-AGTGACTG
33516876 AAATGAAACC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
29 5 0.15
30 13 0.38
31 16 0.47
ACGTcount: A:0.21, C:0.08, G:0.20, T:0.51
Consensus pattern (31 bp):
TTAGTGACTGTTTTGTCACTTTTTCATAAAG
Found at i:33518732 original size:4 final size:4
Alignment explanation
Indices: 33518723--33518751 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
33518713 ACTAATGGTA
33518723 TAAT TAAT TAAT TAAT TAAT TAAT TAAT T
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT T
33518752 TTAAATCATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TAAT
Found at i:33518868 original size:17 final size:16
Alignment explanation
Indices: 33518823--33518868 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 16
33518813 CATTATAAAA
33518823 ATTAAAATACAAAT-T
1 ATTAAAATACAAATAT
*
33518838 -TTCAAATA-AAATAT
1 ATTAAAATACAAATAT
33518852 ATTAACAATACAAATAT
1 ATTAA-AATACAAATAT
33518869 TAGACTCTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 3 0.12
16 4 0.16
17 6 0.24
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTAAAATACAAATAT
Found at i:33518870 original size:15 final size:14
Alignment explanation
Indices: 33518823--33518870 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
33518813 CATTATAAAA
33518823 ATTAAAATACAAAT
1 ATTAAAATACAAAT
* * *
33518837 TTTCAAATAAAATAT
1 ATTAAAATACAA-AT
33518852 ATTAACAATACAAAT
1 ATTAA-AATACAAAT
33518867 ATTA
1 ATTA
33518871 GACTCTTAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
14 9 0.35
15 11 0.42
16 6 0.23
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.33
Consensus pattern (14 bp):
ATTAAAATACAAAT
Found at i:33526282 original size:27 final size:28
Alignment explanation
Indices: 33526208--33526284 Score: 84
Period size: 27 Copynumber: 2.7 Consensus size: 28
33526198 TATGAAGTTT
* *
33526208 GCCACAAAGGCTTCCCTTTTTAATAGATC
1 GCCACAAAGGCTT-ACTTTTTAATAAATC
*
33526237 GCCACAAAAGGCTTTCTTTTT-ATAAATC
1 GCCAC-AAAGGCTTACTTTTTAATAAATC
**
33526265 GTTACAAAGGCTTACTTTTT
1 GCCACAAAGGCTTACTTTTT
33526285 TGGCGTGTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
27 14 0.33
28 9 0.21
29 11 0.26
30 8 0.19
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (28 bp):
GCCACAAAGGCTTACTTTTTAATAAATC
Found at i:33526285 original size:28 final size:28
Alignment explanation
Indices: 33526208--33526285 Score: 77
Period size: 28 Copynumber: 2.8 Consensus size: 28
33526198 TATGAAGTTT
* * *
33526208 GCCACAAAGGCTTCCCTTTTTAATAGATC
1 GCCACAAAGGCTT-ACTTTTTTATAAATC
*
33526237 GCCACAAAAGGCTTTC-TTTTTATAAATC
1 GCCAC-AAAGGCTTACTTTTTTATAAATC
**
33526265 GTTACAAAGGCTTACTTTTTT
1 GCCACAAAGGCTTACTTTTTT
33526286 GGCGTGTTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
27 9 0.22
28 18 0.44
29 6 0.15
30 8 0.20
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.37
Consensus pattern (28 bp):
GCCACAAAGGCTTACTTTTTTATAAATC
Found at i:33530039 original size:41 final size:41
Alignment explanation
Indices: 33529960--33530150 Score: 217
Period size: 42 Copynumber: 4.6 Consensus size: 41
33529950 ATGCCATATC
* * *
33529960 CCAGATATGGTCTTACATGCTATCAT-ATATCGATGCCAATAG-
1 CCAGACATGGTCTTACACG-AATC-TCATATCGATGCCAAT-GT
*
33530002 CCAG-CTATGGGCTTACACGAATCTCATATCGATGCCAATGT
1 CCAGAC-ATGGTCTTACACGAATCTCATATCGATGCCAATGT
*
33530043 CCAGACATGGTCTTACACGAATCTCATATTGATGCCAATGT
1 CCAGACATGGTCTTACACGAATCTCATATCGATGCCAATGT
* * *
33530084 CCCAGACATAGTCTTACACGAATCACATAACGATGCCAATGTT
1 -CCAGACATGGTCTTACACGAATCTCATATCGATGCCAATG-T
*
33530127 CCTGACATGGTCTTACACGTAATC
1 CCAGACATGGTCTTACACG-AATC
33530151 ATATCACAGT
Statistics
Matches: 130, Mismatches: 12, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
40 2 0.02
41 54 0.42
42 69 0.53
43 5 0.04
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.28
Consensus pattern (41 bp):
CCAGACATGGTCTTACACGAATCTCATATCGATGCCAATGT
Found at i:33533109 original size:82 final size:76
Alignment explanation
Indices: 33532972--33533191 Score: 250
Period size: 82 Copynumber: 2.8 Consensus size: 76
33532962 GAAACAATTT
* * * *
33532972 TTTTTCATTTTTGGGTAAATTGTAAATAAGTATATTATTGATTTAAAAATGCAATATGATACAAT
1 TTTTTCATTTTT-TGTAAATTGTAAATAAGTATATTATTAATGTAAAAATACAATA--ATACAAT
33533037 AAAAATAAAAATAAA
63 AAAAATAAAAA-AAA
*
33533052 TTTTTTTATTTTTTTCGTAAATTGTAAATAAGTATATTATTAATGTAAAAATAC---AATACAA-
1 -TTTTTCA-TTTTTT-GTAAATTGTAAATAAGTATATTATTAATGTAAAAATACAATAATACAAT
* * * *
33533113 CACAATACAAACAA
63 AAAAATAAAAAAAA
33533127 TTTTTCATTTTTTGTAAATTGTAAATAAGTATATTATTAATGTAAAAATACAATACAATACAATA
1 TTTTTCATTTTTTGTAAATTGTAAATAAGTATATTATTAATGTAAAAATACAAT--AATACAATA
33533192 CAATACAATA
Statistics
Matches: 120, Mismatches: 11, Indels: 19
0.80 0.07 0.13
Matches are distributed among these distances:
72 38 0.32
73 6 0.05
74 6 0.05
75 2 0.02
76 8 0.07
77 13 0.11
79 1 0.01
81 6 0.05
82 40 0.33
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.40
Consensus pattern (76 bp):
TTTTTCATTTTTTGTAAATTGTAAATAAGTATATTATTAATGTAAAAATACAATAATACAATAAA
AATAAAAAAAA
Found at i:33533138 original size:72 final size:72
Alignment explanation
Indices: 33532972--33533200 Score: 251
Period size: 72 Copynumber: 3.0 Consensus size: 72
33532962 GAAACAATTT
* * * *
33532972 TTTTTCATTTTTGGGTAAATTGTAAATAAGTATATTATTGATTTAAAAATGCAATATGATACAAT
1 TTTTTCATTTTT-CGTAAATTGTAAATAAGTATATTATTAATGTAAAAAT---ACA--ATACAA-
* * *
33533037 AAAAATAAAAATAAA
59 AACAATACAAA-CAA
* *
33533052 TTTTTTTATTTTTTTCGTAAATTGTAAATAAGTATATTATTAATGTAAAAATACAATACAACACA
1 -TTTTTCA--TTTTTCGTAAATTGTAAATAAGTATATTATTAATGTAAAAATACAATACAAAACA
33533117 ATACAAACAA
63 ATACAAACAA
* *
33533127 TTTTTCATTTTTTGTAAATTGTAAATAAGTATATTATTAATGTAAAAATACAATACAATACAATA
1 TTTTTCATTTTTCGTAAATTGTAAATAAGTATATTATTAATGTAAAAATACAATACAAAACAATA
33533192 CAATACAA
66 CAA-ACAA
33533200 T
1 T
33533201 ACAATACAAT
Statistics
Matches: 133, Mismatches: 12, Indels: 14
0.84 0.08 0.09
Matches are distributed among these distances:
72 59 0.44
73 5 0.04
74 6 0.05
75 2 0.02
76 8 0.06
77 6 0.05
79 2 0.02
81 6 0.05
82 34 0.26
83 5 0.04
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.40
Consensus pattern (72 bp):
TTTTTCATTTTTCGTAAATTGTAAATAAGTATATTATTAATGTAAAAATACAATACAAAACAATA
CAAACAA
Found at i:33533183 original size:5 final size:5
Alignment explanation
Indices: 33533173--33533515 Score: 578
Period size: 5 Copynumber: 68.6 Consensus size: 5
33533163 TTAATGTAAA
33533173 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
* *
33533223 AATAC AATAC AATAC AATAC AATGC AATAC AATAC AATAC GATAC AATAC
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
* * * * *
33533273 GATAC AATAC GATAC AATAC GATAC AATAT GATAC AATAC AATAC AATAC
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
*
33533323 AATAC AATAC AATAT AATAC AATAC AATAC AATAC AATAC AATAC AATAC
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
*
33533373 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC ATTAC
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
* *
33533423 AATAC AATTC AATAC AATTC AATAC AATAC AATAC AATAC AATAC AATAC
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
*
33533473 AATAC AATAC ACTAC AATAC AATAC AATAC AATAC AATAC AAT
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AAT
33533516 TTTTTCATTT
Statistics
Matches: 314, Mismatches: 24, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 314 1.00
ACGTcount: A:0.57, C:0.20, G:0.02, T:0.22
Consensus pattern (5 bp):
AATAC
Found at i:33534287 original size:166 final size:166
Alignment explanation
Indices: 33534012--33534344 Score: 594
Period size: 166 Copynumber: 2.0 Consensus size: 166
33534002 TAGTAAAAGC
**
33534012 ACGAGAAAAATATGAAACATATTGATTGGGAAGTGGTGCACCCATCAATATAGTATTTGGGGTTG
1 ACGAGAAAAATATGAAACATATTGATCAGGAAGTGGTGCACCCATCAATATAGTATTTGGGGTTG
33534077 GAGTTAATGATGATGAACTTGACGTATGTACTCCCGACCGCGACCTCATCTGAGGTCATGTTGGG
66 GAGTTAATGATGATGAACTTGACGTATGTACTCCCGACCGCGACCTCATCTGAGGTCATGTTGGG
*
33534142 CTTCTACAATGAATTTTTGTACTCCTTTCCTCCTCT
131 CTTCTACAATGAATTTTTCTACTCCTTTCCTCCTCT
**
33534178 ACGAGAAAAATATGAAACATATTGATCAGGAAGTGGTGCACCCATCGGTATAGTATTTGGGGTTG
1 ACGAGAAAAATATGAAACATATTGATCAGGAAGTGGTGCACCCATCAATATAGTATTTGGGGTTG
* * *
33534243 GAGTTAATGATGATGAACTTGACGTATGTACTCCTGATCGCGACCTCATCTGGGGTCATGTTGGG
66 GAGTTAATGATGATGAACTTGACGTATGTACTCCCGACCGCGACCTCATCTGAGGTCATGTTGGG
33534308 CTTCTACAATGAATTTTTCTACTCCTTTCCTCCTCT
131 CTTCTACAATGAATTTTTCTACTCCTTTCCTCCTCT
33534344 A
1 A
33534345 GCAGTAGATA
Statistics
Matches: 159, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
166 159 1.00
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (166 bp):
ACGAGAAAAATATGAAACATATTGATCAGGAAGTGGTGCACCCATCAATATAGTATTTGGGGTTG
GAGTTAATGATGATGAACTTGACGTATGTACTCCCGACCGCGACCTCATCTGAGGTCATGTTGGG
CTTCTACAATGAATTTTTCTACTCCTTTCCTCCTCT
Found at i:33544801 original size:35 final size:36
Alignment explanation
Indices: 33544762--33544832 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 36
33544752 TCTAGGATCA
*
33544762 CATATATTT-GAAGATCACCT-TCCATATTTGCCAAG
1 CATATATTTGGAAGATCA-CTGTCCATATTTACCAAG
*
33544797 CATATCTTTGGAAGATCACTGTCCATATTTACCAAG
1 CATATATTTGGAAGATCACTGTCCATATTTACCAAG
33544833 TTTCGGAGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
35 10 0.31
36 22 0.69
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.34
Consensus pattern (36 bp):
CATATATTTGGAAGATCACTGTCCATATTTACCAAG
Found at i:33548483 original size:27 final size:26
Alignment explanation
Indices: 33548453--33548524 Score: 63
Period size: 27 Copynumber: 2.7 Consensus size: 26
33548443 ATTTTCATCA
33548453 TCCTAGTAGACTACCCCACATTTAGTG
1 TCCT-GTAGACTACCCCACATTTAGTG
* * ** *
33548480 TCCTGGAAGGCTACCCCATTTTTATTG
1 TCCT-GTAGACTACCCCACATTTAGTG
*
33548507 TCCCTGTGGACTACCCCA
1 T-CCTGTAGACTACCCCA
33548525 TTTTTATCGT
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
27 32 0.91
28 3 0.09
ACGTcount: A:0.21, C:0.32, G:0.17, T:0.31
Consensus pattern (26 bp):
TCCTGTAGACTACCCCACATTTAGTG
Found at i:33548525 original size:27 final size:27
Alignment explanation
Indices: 33548490--33548565 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 27
33548480 TCCTGGAAGG
* *
33548490 CTACCCCATTTTTATTGTCCCTGTGGA
1 CTACCCCATTTTTATTGTCCCGGTCGA
*
33548517 CTACCCCATTTTTATCGTCCCGGTCGA
1 CTACCCCATTTTTATTGTCCCGGTCGA
* *
33548544 CTACCCCACTTTTAATGTCCCG
1 CTACCCCATTTTTATTGTCCCG
33548566 ACGGGCTCTC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.16, C:0.36, G:0.13, T:0.36
Consensus pattern (27 bp):
CTACCCCATTTTTATTGTCCCGGTCGA
Found at i:33551458 original size:50 final size:50
Alignment explanation
Indices: 33551303--33551465 Score: 174
Period size: 50 Copynumber: 3.3 Consensus size: 50
33551293 AAATGCATGG
* * ** * *
33551303 TTTAAGATGCAAACTAAAGGAACA-AACGAGTTACTTAATGCATGACTTAA
1 TTTATGATGCAAACTTAACTAACATAA-GAGTTACATAATGCATGAATTAA
*
33551353 TTTAATGATGCAAACTTCAACTAACATGAGAGTTACATAAAT-CATGTAA-TAA
1 TTT-ATGATGCAAACTT-AACTAACATAAGAGTTACAT-AATGCATG-AATTAA
*
33551405 TTTATGATGCAAACTTAACTAACATAAGAGTTACATAATGCATGAATTTA
1 TTTATGATGCAAACTTAACTAACATAAGAGTTACATAATGCATGAATTAA
33551455 TTTA--ATGCAAA
1 TTTATGATGCAAA
33551466 ACACATAATT
Statistics
Matches: 97, Mismatches: 9, Indels: 16
0.80 0.07 0.13
Matches are distributed among these distances:
48 7 0.07
49 5 0.05
50 32 0.33
51 24 0.25
52 24 0.25
53 5 0.05
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.31
Consensus pattern (50 bp):
TTTATGATGCAAACTTAACTAACATAAGAGTTACATAATGCATGAATTAA
Found at i:33554355 original size:46 final size:45
Alignment explanation
Indices: 33554288--33554468 Score: 182
Period size: 46 Copynumber: 4.0 Consensus size: 45
33554278 CGTGATTTTA
* ** *
33554288 CATGATGCTATAGCGCCTTTCAACTATGGTCTTACTCATATTCTAC
1 CATGATGCCATAGCATCTTTCAACTATGGTCTTACTCAT-TTCTAT
* **
33554334 CATGATGCCATAGCATCTTTCAACTACGGTAGTACTCATTTTCTAT
1 CATGATGCCATAGCATCTTTCAACTATGGTCTTACTCA-TTTCTAT
* * * * * * * *
33554380 TATTATGCTATAGAATCTTTCAGCTATGGTCTTACCCATCTATAT
1 CATGATGCCATAGCATCTTTCAACTATGGTCTTACTCATTTCTAT
* * *
33554425 CATGATGTCATAGCATCTTTTAGCTATGGTCTTACTCATTTCTA
1 CATGATGCCATAGCATCTTTCAACTATGGTCTTACTCATTTCTA
33554469 GGCGTATAGC
Statistics
Matches: 107, Mismatches: 27, Indels: 3
0.78 0.20 0.02
Matches are distributed among these distances:
45 40 0.37
46 66 0.62
47 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.13, T:0.40
Consensus pattern (45 bp):
CATGATGCCATAGCATCTTTCAACTATGGTCTTACTCATTTCTAT
Found at i:33559780 original size:112 final size:112
Alignment explanation
Indices: 33559652--33559880 Score: 458
Period size: 112 Copynumber: 2.0 Consensus size: 112
33559642 TTACGAATTG
33559652 ACCCTCGGGCTAGCTAAATTAAGGTAAAACGAACTCAAAAACATAAAAAATACTAAAAACGCGGC
1 ACCCTCGGGCTAGCTAAATTAAGGTAAAACGAACTCAAAAACATAAAAAATACTAAAAACGCGGC
33559717 AACATTACGTACCATGCATACAAGACAAAGCGTTGCCGAAACTTCAC
66 AACATTACGTACCATGCATACAAGACAAAGCGTTGCCGAAACTTCAC
33559764 ACCCTCGGGCTAGCTAAATTAAGGTAAAACGAACTCAAAAACATAAAAAATACTAAAAACGCGGC
1 ACCCTCGGGCTAGCTAAATTAAGGTAAAACGAACTCAAAAACATAAAAAATACTAAAAACGCGGC
33559829 AACATTACGTACCATGCATACAAGACAAAGCGTTGCCGAAACTTCAC
66 AACATTACGTACCATGCATACAAGACAAAGCGTTGCCGAAACTTCAC
33559876 ACCCT
1 ACCCT
33559881 TAGCTATGGA
Statistics
Matches: 117, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
112 117 1.00
ACGTcount: A:0.43, C:0.25, G:0.15, T:0.17
Consensus pattern (112 bp):
ACCCTCGGGCTAGCTAAATTAAGGTAAAACGAACTCAAAAACATAAAAAATACTAAAAACGCGGC
AACATTACGTACCATGCATACAAGACAAAGCGTTGCCGAAACTTCAC
Found at i:33564912 original size:46 final size:46
Alignment explanation
Indices: 33564874--33564993 Score: 172
Period size: 45 Copynumber: 2.7 Consensus size: 46
33564864 TGCCATGGTG
33564874 TCTTTCAGCTATGGTCTAACTCATCTTCTATCATGATGCCATAACA
1 TCTTTCAGCTATGGTCTAACTCATCTTCTATCATGATGCCATAACA
* * * * * *
33564920 TCTTTTAGCTATGGTATTATTCATCTT-TATTATGATGCCATACCA
1 TCTTTCAGCTATGGTCTAACTCATCTTCTATCATGATGCCATAACA
33564965 TCTTTCAGCTATGGTCTAACTCAT-TTCTA
1 TCTTTCAGCTATGGTCTAACTCATCTTCTA
33564994 GGCGTATAGC
Statistics
Matches: 63, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
44 2 0.03
45 38 0.60
46 23 0.37
ACGTcount: A:0.24, C:0.23, G:0.11, T:0.42
Consensus pattern (46 bp):
TCTTTCAGCTATGGTCTAACTCATCTTCTATCATGATGCCATAACA
Found at i:33568646 original size:27 final size:27
Alignment explanation
Indices: 33568616--33568684 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 27
33568606 ACATGTTACT
* *
33568616 GTCCCAATTGTCTA-CCGCGTGTTTAGC
1 GTCCCAATGGACTATCC-CGTGTTTAGC
* *
33568643 GTCCCAGTGGACTATCCCGTGTTTAGT
1 GTCCCAATGGACTATCCCGTGTTTAGC
*
33568670 GTCCCAGTGGACTAT
1 GTCCCAATGGACTAT
33568685 TCCATCTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
27 35 0.95
28 2 0.05
ACGTcount: A:0.16, C:0.28, G:0.25, T:0.32
Consensus pattern (27 bp):
GTCCCAATGGACTATCCCGTGTTTAGC
Found at i:33568694 original size:27 final size:27
Alignment explanation
Indices: 33568637--33568701 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
33568627 CTACCGCGTG
* * *
33568637 TTTAGCGTCCCAGTGGACTATCCCGTG
1 TTTAGTGTCCCAGTGGACTATCCCATC
*
33568664 TTTAGTGTCCCAGTGGACTATTCCATC
1 TTTAGTGTCCCAGTGGACTATCCCATC
33568691 TTTAGTGTCCC
1 TTTAGTGTCCC
33568702 GATGAACTAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.15, C:0.28, G:0.22, T:0.35
Consensus pattern (27 bp):
TTTAGTGTCCCAGTGGACTATCCCATC
Found at i:33568942 original size:45 final size:46
Alignment explanation
Indices: 33568785--33568958 Score: 217
Period size: 46 Copynumber: 3.8 Consensus size: 46
33568775 TTCACGGATA
* * *
33568785 CCATAACGTCTTTCAACAATGGTCTTACTCATCTTCTACCATGATG
1 CCATAACATCTTTCAACTATGGTCTTACTCATCTTCTATCATGATG
* * * * *
33568831 TCATAACATCTTTCAGCTATGGTATTACTCATTTTCTATTATGATG
1 CCATAACATCTTTCAACTATGGTCTTACTCATCTTCTATCATGATG
* * *
33568877 CAATAACATCTTTTAACTATGTTCTTACTCATCTT-TATCATGATG
1 CCATAACATCTTTCAACTATGGTCTTACTCATCTTCTATCATGATG
* *
33568922 CCATAGCATCTTTCAGCTATGGTCTTACTCAT-TTCTA
1 CCATAACATCTTTCAACTATGGTCTTACTCATCTTCTA
33568959 GGCGTATAGC
Statistics
Matches: 106, Mismatches: 21, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
44 2 0.02
45 38 0.36
46 66 0.62
ACGTcount: A:0.26, C:0.23, G:0.10, T:0.41
Consensus pattern (46 bp):
CCATAACATCTTTCAACTATGGTCTTACTCATCTTCTATCATGATG
Found at i:33568943 original size:91 final size:92
Alignment explanation
Indices: 33568787--33568955 Score: 259
Period size: 91 Copynumber: 1.8 Consensus size: 92
33568777 CACGGATACC
* *
33568787 ATAACGTCTTTCAACAATGGTCTTACTCATCTTCTACCATGATGTCATAACATCTTTCAGCTATG
1 ATAACATCTTTCAACAATGGTCTTACTCATCTTCTACCATGATGCCATAACATCTTTCAGCTATG
33568852 GTATTACTCATTTTCTATTATGATGCA
66 GTATTACTCATTTTCTATTATGATGCA
* * * * *
33568879 ATAACATCTTTTAACTATGTTCTTACTCATCTT-TATCATGATGCCATAGCATCTTTCAGCTATG
1 ATAACATCTTTCAACAATGGTCTTACTCATCTTCTACCATGATGCCATAACATCTTTCAGCTATG
*
33568943 GTCTTACTCATTT
66 GTATTACTCATTT
33568956 CTAGGCGTAT
Statistics
Matches: 69, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
91 40 0.58
92 29 0.42
ACGTcount: A:0.26, C:0.22, G:0.10, T:0.42
Consensus pattern (92 bp):
ATAACATCTTTCAACAATGGTCTTACTCATCTTCTACCATGATGCCATAACATCTTTCAGCTATG
GTATTACTCATTTTCTATTATGATGCA
Done.