Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 131 of 204
Found at i:40055530 original size:26 final size:26
Alignment explanation
Indices: 40055471--40055534 Score: 92
Period size: 26 Copynumber: 2.5 Consensus size: 26
40055461 CAATTGTACA
*
40055471 CCAATAAACTTTTGATGATTTTACCC
1 CCAATAAAATTTTGATGATTTTACCC
*
40055497 CCAATAAAATTTTGATGATTTTTCCC
1 CCAATAAAATTTTGATGATTTTACCC
* *
40055523 TCAGTAAAATTT
1 CCAATAAAATTT
40055535 CTAGAAAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.33, C:0.19, G:0.08, T:0.41
Consensus pattern (26 bp):
CCAATAAAATTTTGATGATTTTACCC
Found at i:40064000 original size:27 final size:30
Alignment explanation
Indices: 40063940--40064001 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
40063930 TTAATTAATA
* *
40063940 TTTTTATTTAATAAACTTGCTATTTTCAAG
1 TTTTTAGTTAATAAACATGCTATTTTCAAG
40063970 TTTTTAGTTAATAAACATG-T-TTTT-AAG
1 TTTTTAGTTAATAAACATGCTATTTTCAAG
40063997 TTTTT
1 TTTTT
40064002 TTATTTTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
27 8 0.27
28 4 0.13
29 1 0.03
30 17 0.57
ACGTcount: A:0.29, C:0.06, G:0.08, T:0.56
Consensus pattern (30 bp):
TTTTTAGTTAATAAACATGCTATTTTCAAG
Found at i:40064164 original size:14 final size:12
Alignment explanation
Indices: 40064131--40064155 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40064121 AAACATCAAC
40064131 TAATTTTTTATA
1 TAATTTTTTATA
40064143 TAATTTTTTATA
1 TAATTTTTTATA
40064155 T
1 T
40064156 GTAATTTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TAATTTTTTATA
Found at i:40064520 original size:95 final size:97
Alignment explanation
Indices: 40064371--40064567 Score: 263
Period size: 95 Copynumber: 2.1 Consensus size: 97
40064361 ATACATCAAT
** * * *
40064371 TATTTATTTTTTTCATGTACATTGTAGGTATGGTAAACTCTAATATAAAAAAATCAATTAATCAT
1 TATTTATTTTTTTCACCTACATTGTAGGGATGGTAAACTCTAATATAAAAAAATCAAATAATCAA
* *
40064436 TTCAAATATCATTATT-TTTTTATATGTGAAA
66 TTCAAATATCACTATTATTTTTATATGTAAAA
* * * * *
40064467 TATTTATTTTTTTCACCTACATTGT-GGGATGGTAGATTCTAATATTATAAAATCAAATAATTAA
1 TATTTATTTTTTTCACCTACATTGTAGGGATGGTAAACTCTAATATAAAAAAATCAAATAATCAA
*
40064531 TTCAATTATCACTATTATTTTTATATGTAAAA
66 TTCAAATATCACTATTATTTTTATATGTAAAA
40064563 TATTT
1 TATTT
40064568 CAAAAAAAAT
Statistics
Matches: 87, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
95 45 0.52
96 42 0.48
ACGTcount: A:0.37, C:0.09, G:0.08, T:0.47
Consensus pattern (97 bp):
TATTTATTTTTTTCACCTACATTGTAGGGATGGTAAACTCTAATATAAAAAAATCAAATAATCAA
TTCAAATATCACTATTATTTTTATATGTAAAA
Found at i:40064644 original size:47 final size:46
Alignment explanation
Indices: 40064519--40064645 Score: 132
Period size: 47 Copynumber: 2.7 Consensus size: 46
40064509 TATTATAAAA
* *
40064519 TCAAATAATTAATTCAATTATCACTATTATTTTTATATGTAAAATATT
1 TCAAATAATT-ATTCAAATATCAATA-TATTTTTATATGTAAAATATT
* * *
40064567 TCAAAAAAAATCATTTCAAATGTC-AT-TATTTTTATATGTAAAATATT
1 TC--AAATAATTA-TTCAAATATCAATATATTTTTATATGTAAAATATT
*
40064614 TCAAATAATTATTACAAATACCAATATATTTT
1 TCAAATAATTATT-CAAATATCAATATATTTT
40064646 CACCTACATT
Statistics
Matches: 64, Mismatches: 9, Indels: 13
0.74 0.10 0.15
Matches are distributed among these distances:
44 2 0.03
45 13 0.20
46 2 0.03
47 29 0.45
48 2 0.03
49 2 0.03
50 14 0.22
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.44
Consensus pattern (46 bp):
TCAAATAATTATTCAAATATCAATATATTTTTATATGTAAAATATT
Found at i:40072244 original size:25 final size:26
Alignment explanation
Indices: 40072194--40072250 Score: 89
Period size: 27 Copynumber: 2.2 Consensus size: 26
40072184 TATTTTTAAT
*
40072194 TTTTTTAAAAATAAAATAGAAAAAATA
1 TTTTCTAAAAATAAAATAG-AAAAATA
40072221 TTTTCTAAAAATAAAATAG-AAAATA
1 TTTTCTAAAAATAAAATAGAAAAATA
40072246 TTTTC
1 TTTTC
40072251 AGAAATCAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 11 0.38
27 18 0.62
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.37
Consensus pattern (26 bp):
TTTTCTAAAAATAAAATAGAAAAATA
Found at i:40076588 original size:10 final size:9
Alignment explanation
Indices: 40076529--40076636 Score: 73
Period size: 9 Copynumber: 11.9 Consensus size: 9
40076519 ATATTTTTCC
40076529 TATAAAAAT
1 TATAAAAAT
*
40076538 ATTTAAAAAT
1 -TATAAAAAT
*
40076548 TAT-TAAA-
1 TATAAAAAT
40076555 TATTAAAAA-
1 TA-TAAAAAT
*
40076564 TATTAAAATT
1 TA-TAAAAAT
*
40076574 TATAATAACT
1 TATAA-AAAT
40076584 TATAAAAAT
1 TATAAAAAT
40076593 TATAAAAA-
1 TATAAAAAT
*
40076601 -ATAAAAGCT
1 TATAAAA-AT
*
40076610 TATAAATAT
1 TATAAAAAT
40076619 TATAATAAAT
1 TATAA-AAAT
40076629 TATAAAAA
1 TATAAAAA
40076637 AATCTAAAAA
Statistics
Matches: 79, Mismatches: 11, Indels: 17
0.74 0.10 0.16
Matches are distributed among these distances:
7 8 0.10
8 4 0.05
9 36 0.46
10 31 0.39
ACGTcount: A:0.61, C:0.02, G:0.01, T:0.36
Consensus pattern (9 bp):
TATAAAAAT
Found at i:40076590 original size:45 final size:45
Alignment explanation
Indices: 40076541--40076636 Score: 115
Period size: 45 Copynumber: 2.1 Consensus size: 45
40076531 TAAAAATATT
* * * *
40076541 TAAAAATTATTAAATATTAAAAATATTA-AAAT-TTATAATAACTTA
1 TAAAAATTA-TAAAAAAT-AAAAGATTATAAATATTATAATAAATTA
*
40076586 TAAAAATTATAAAAAATAAAAGCTTATAAATATTATAATAAATTA
1 TAAAAATTATAAAAAATAAAAGATTATAAATATTATAATAAATTA
40076631 TAAAAA
1 TAAAAA
40076637 AATCTAAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
43 7 0.16
44 10 0.23
45 27 0.61
ACGTcount: A:0.61, C:0.02, G:0.01, T:0.35
Consensus pattern (45 bp):
TAAAAATTATAAAAAATAAAAGATTATAAATATTATAATAAATTA
Found at i:40076604 original size:26 final size:27
Alignment explanation
Indices: 40076575--40076633 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 27
40076565 ATTAAAATTT
40076575 ATAATAA-CTTATAAAAATTATAAAAA
1 ATAATAAGCTTATAAAAATTATAAAAA
* *
40076601 ATAA-AAGCTTATAAATATTATAATAA
1 ATAATAAGCTTATAAAAATTATAAAAA
*
40076627 ATTATAA
1 ATAATAA
40076634 AAAAATCTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 2 0.07
26 24 0.86
27 2 0.07
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (27 bp):
ATAATAAGCTTATAAAAATTATAAAAA
Found at i:40077053 original size:11 final size:10
Alignment explanation
Indices: 40077029--40077113 Score: 50
Period size: 10 Copynumber: 8.2 Consensus size: 10
40077019 GCTTTTTCAG
*
40077029 AATTTTTAAT
1 AATTTTTTAT
*
40077039 ATTTTTTTAT
1 AATTTTTTAT
* *
40077049 AATTTATTAG
1 AATTTTTTAT
*
40077059 AATTTATTAT
1 AATTTTTTAT
40077069 -A-TTTTTAT
1 AATTTTTTAT
40077077 AAGTTTTTTCTAT
1 AA--TTTTT-TAT
40077090 GAA-TTTTTAT
1 -AATTTTTTAT
40077100 AACTTTTTTTAT
1 AA--TTTTTTAT
40077112 AA
1 AA
40077114 AAATTTAAAT
Statistics
Matches: 59, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
8 6 0.10
9 4 0.07
10 27 0.46
11 4 0.07
12 13 0.22
13 3 0.05
14 2 0.03
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (10 bp):
AATTTTTTAT
Found at i:40077063 original size:21 final size:21
Alignment explanation
Indices: 40077040--40077113 Score: 73
Period size: 23 Copynumber: 3.5 Consensus size: 21
40077030 ATTTTTAATA
*
40077040 TTTTTTTATAATTTATTAGAA-
1 TTTTTTTATAATTT-TTATAAC
* *
40077061 -TTTATTAT-ATTTTTATAAG
1 TTTTTTTATAATTTTTATAAC
40077080 TTTTTTCTATGAATTTTTATAAC
1 TTTTTT-TAT-AATTTTTATAAC
40077103 TTTTTTTATAA
1 TTTTTTTATAA
40077114 AAATTTAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
18 5 0.11
19 4 0.09
20 11 0.25
21 5 0.11
22 3 0.07
23 16 0.36
ACGTcount: A:0.30, C:0.03, G:0.04, T:0.64
Consensus pattern (21 bp):
TTTTTTTATAATTTTTATAAC
Found at i:40077218 original size:9 final size:9
Alignment explanation
Indices: 40077042--40077509 Score: 109
Period size: 10 Copynumber: 48.8 Consensus size: 9
40077032 TTTTAATATT
40077042 TTTTTATAA
1 TTTTTATAA
*
40077051 TTTATTAGAA
1 TTT-TTATAA
40077061 TTTATTAT-A
1 TTT-TTATAA
40077070 TTTTTATAA
1 TTTTTATAA
40077079 GTTTTTTCTATGAA
1 ---TTTT-TAT-AA
40077093 TTTTTATAA
1 TTTTTATAA
40077102 CTTTTTTTATAAAAA
1 ---TTTTTAT---AA
*
40077117 TTTAAATATAA
1 TTT--TTATAA
*
40077128 TTTGT-TAA
1 TTTTTATAA
40077136 -TTTTATATA
1 TTTTTATA-A
40077145 TTTTTAATAA
1 TTTTT-ATAA
*
40077155 TTTATTAAAA
1 TTT-TTATAA
*
40077165 TTTATTA-GA
1 TTT-TTATAA
*
40077174 TATTTATAA
1 TTTTTATAA
* *
40077183 TATTTATAGG
1 TTTTTATA-A
* *
40077193 TTTCTATTA
1 TTTTTATAA
40077202 TATTTTATAA
1 T-TTTTATAA
40077212 TTTTTATACA
1 TTTTTATA-A
* *
40077222 TTTATATCAC
1 TTTTTAT-AA
* * *
40077232 TTTTGAGAT
1 TTTTTATAA
40077241 TTTTTA-AA
1 TTTTTATAA
*
40077249 TATTTATAA
1 TTTTTATAA
40077258 -TTTT-TAA
1 TTTTTATAA
40077265 TATTTTATAA
1 T-TTTTATAA
* *
40077275 GTTTTAAAGAA
1 -TTTT-TATAA
* *
40077286 TTTTTGTAGG
1 TTTTTATA-A
**
40077296 TTTCGATAAA
1 TTTTTAT-AA
*
40077306 ATTTTA-AA
1 TTTTTATAA
40077314 TATTTTA-AGCA
1 T-TTTTATA--A
40077325 TGTTTTATTAA
1 T-TTTTA-TAA
40077336 -TTTTATAAA
1 TTTTTAT-AA
*** *
40077345 AAATTAGAA
1 TTTTTATAA
*
40077354 TTTATTAGAA
1 TTT-TTATAA
40077364 TTTTTATAA
1 TTTTTATAA
*
40077373 TATTTATAATA
1 TTTTTAT-A-A
* *
40077384 TTTTTTTATT
1 TTTTTATA-A
40077394 TTTTTATAA
1 TTTTTATAA
40077403 TTTTTATAA
1 TTTTTATAA
40077412 TTTTATATAA
1 TTTT-TATAA
* *
40077422 ATTTTA-AT
1 TTTTTATAA
*
40077430 TTTTTTTAA
1 TTTTTATAA
*
40077439 -ATTTA-AA
1 TTTTTATAA
40077446 TTTTTAATAA
1 TTTTT-ATAA
40077456 TTTTTATAA
1 TTTTTATAA
40077465 -TTTTATAA
1 TTTTTATAA
*
40077473 TTGTTTCTAA
1 TT-TTTATAA
*
40077483 TTTTTTATTA
1 -TTTTTATAA
*
40077493 TTTTTAATAT
1 TTTTT-ATAA
40077503 TTTTTAT
1 TTTTTAT
40077510 TGAAAAATAT
Statistics
Matches: 340, Mismatches: 67, Indels: 104
0.67 0.13 0.20
Matches are distributed among these distances:
7 8 0.02
8 43 0.13
9 100 0.29
10 128 0.38
11 36 0.11
12 14 0.04
13 4 0.01
14 5 0.01
15 2 0.01
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (9 bp):
TTTTTATAA
Found at i:40077263 original size:17 final size:18
Alignment explanation
Indices: 40077241--40077505 Score: 64
Period size: 17 Copynumber: 14.8 Consensus size: 18
40077231 CTTTTGAGAT
40077241 TTTTTAAATA-TTTATAA
1 TTTTTAAATATTTTATAA
40077258 TTTTT-AATATTTTATAA
1 TTTTTAAATATTTTATAA
* * * *
40077275 GTTTTAAAGAATTTTTGTAGG
1 TTTTTAAA-TA-TTTTATA-A
*
40077296 TTTCGATAAA-ATTTTA-AA
1 TTT--TTAAATATTTTATAA
*
40077314 TATTTTAAGCATGTTTTATTAA
1 T-TTTTAA--ATATTTTA-TAA
** *
40077336 TTTTATAAA-AAATTAGAA
1 TTTT-TAAATATTTTATAA
40077354 TTTATTAGAAT-TTTTATAA
1 TTT-TTA-AATATTTTATAA
*
40077373 TATTTATAATATTTT-T--
1 TTTTTA-AATATTTTATAA
*
40077389 TTATT---T-TTTTATAA
1 TTTTTAAATATTTTATAA
40077403 TTTTTATAAT-TTTATATAA
1 TTTTTA-AATATTT-TATAA
* * *
40077422 ATTTT-AATTTTTTTTAA
1 TTTTTAAATATTTTATAA
*
40077439 -ATTTAAAT-TTTTAATAA
1 TTTTTAAATATTTT-ATAA
*
40077456 TTTTTATA-ATTTTATAA
1 TTTTTAAATATTTTATAA
* * *
40077473 TTGTTTCTAATTTTTTATTA
1 TT-TTT-AAATATTTTATAA
40077493 TTTTT-AATATTTT
1 TTTTTAAATATTTT
40077506 TTATTGAAAA
Statistics
Matches: 181, Mismatches: 33, Indels: 68
0.64 0.12 0.24
Matches are distributed among these distances:
11 4 0.02
12 2 0.01
14 4 0.02
16 14 0.08
17 45 0.25
18 36 0.20
19 35 0.19
20 25 0.14
21 6 0.03
22 6 0.03
23 4 0.02
ACGTcount: A:0.35, C:0.01, G:0.04, T:0.60
Consensus pattern (18 bp):
TTTTTAAATATTTTATAA
Found at i:40077424 original size:11 final size:10
Alignment explanation
Indices: 40077362--40077471 Score: 55
Period size: 9 Copynumber: 11.9 Consensus size: 10
40077352 AATTTATTAG
40077362 AATTTT-TAT
1 AATTTTATAT
40077371 AATATTTATA-
1 AAT-TTTATAT
*
40077381 ATATTTT-TTT
1 A-ATTTTATAT
* *
40077391 ATTTTTTTAT
1 AATTTTATAT
40077401 AATTTT-TAT
1 AATTTTATAT
40077410 AATTTTATAT
1 AATTTTATAT
40077420 AAATTTTA-AT
1 -AATTTTATAT
*
40077430 --TTTT-TTT
1 AATTTTATAT
*
40077437 AAATTTA-A-
1 AATTTTATAT
*
40077445 ATTTTTA-AT
1 AATTTTATAT
40077454 AATTTT-TAT
1 AATTTTATAT
40077463 AATTTTATA
1 AATTTTATA
40077472 ATTGTTTCTA
Statistics
Matches: 77, Mismatches: 10, Indels: 27
0.68 0.09 0.24
Matches are distributed among these distances:
7 5 0.06
8 6 0.08
9 33 0.43
10 22 0.29
11 11 0.14
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
AATTTTATAT
Found at i:40078054 original size:15 final size:15
Alignment explanation
Indices: 40078034--40078062 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
40078024 AATAAAATTA
40078034 TGTCTTTTATATTTC
1 TGTCTTTTATATTTC
40078049 TGTCTTTTATATTT
1 TGTCTTTTATATTT
40078063 TGCATGCATA
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:0.10, G:0.07, T:0.69
Consensus pattern (15 bp):
TGTCTTTTATATTTC
Found at i:40080676 original size:2 final size:2
Alignment explanation
Indices: 40080669--40080694 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40080659 TATAATTATG
40080669 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
40080695 GAGATGATCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40094260 original size:19 final size:17
Alignment explanation
Indices: 40094245--40094335 Score: 57
Period size: 17 Copynumber: 5.4 Consensus size: 17
40094235 ATTTTTATAG
40094245 TTTAATATTAAATTTAA
1 TTTAATATTAAATTTAA
40094262 TTTAATACTT--ATCTTAA
1 TTTAATA-TTAAAT-TTAA
* **
40094279 --TAGTATTTTA-TTAA
1 TTTAATATTAAATTTAA
* *
40094293 TTGAATATTAAAGTTATTA
1 TTTAATATTAAA-TT-TAA
40094312 TCTTAATATTAAATTTAA
1 T-TTAATATTAAATTTAA
40094330 TTTAAT
1 TTTAAT
40094336 GTTGATCTTG
Statistics
Matches: 56, Mismatches: 8, Indels: 20
0.67 0.10 0.24
Matches are distributed among these distances:
14 6 0.11
15 4 0.07
16 9 0.16
17 16 0.29
18 6 0.11
19 5 0.09
20 10 0.18
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTAATATTAAATTTAA
Found at i:40100279 original size:57 final size:55
Alignment explanation
Indices: 40100177--40100286 Score: 130
Period size: 57 Copynumber: 2.0 Consensus size: 55
40100167 TATTTCACAT
* * * *
40100177 TTTCATTCTCATTTTCATTTCTATTTTAGAGAACACCATATTCATTTCCAAATCA
1 TTTCATTCTCATTTTCATTTCTATCTTAGAAAAAACCATAATCATTTCCAAATCA
* * * *
40100232 TTTCATTTCTCCATTTTCATTTTTATCTTGGAAAAAACCTTAATCATTTTCAAAT
1 TTTCA-TTCT-CATTTTCATTTCTATCTTAGAAAAAACCATAATCATTTCCAAAT
40100287 GTTTCCTATT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
55 5 0.11
56 4 0.09
57 36 0.80
ACGTcount: A:0.29, C:0.20, G:0.04, T:0.47
Consensus pattern (55 bp):
TTTCATTCTCATTTTCATTTCTATCTTAGAAAAAACCATAATCATTTCCAAATCA
Found at i:40102201 original size:17 final size:17
Alignment explanation
Indices: 40102179--40102213 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
40102169 ATTACAAAAT
*
40102179 CAAATCTTATCAGATTA
1 CAAATCTTATAAGATTA
*
40102196 CAAATCTTCTAAGATTA
1 CAAATCTTATAAGATTA
40102213 C
1 C
40102214 TTTCCCTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.40, C:0.20, G:0.06, T:0.34
Consensus pattern (17 bp):
CAAATCTTATAAGATTA
Found at i:40104721 original size:30 final size:31
Alignment explanation
Indices: 40104687--40104747 Score: 88
Period size: 32 Copynumber: 2.0 Consensus size: 31
40104677 AACGTCCAAT
40104687 ATGAACTTAGACAA-ATTTATCCATATTCAA
1 ATGAACTTAGACAACATTTATCCATATTCAA
* *
40104717 ATGAACTTGGACAACTATTTGTCCATATTCA
1 ATGAACTTAGACAAC-ATTTATCCATATTCA
40104748 TTCTAAACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 13 0.48
32 14 0.52
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (31 bp):
ATGAACTTAGACAACATTTATCCATATTCAA
Found at i:40105308 original size:14 final size:14
Alignment explanation
Indices: 40105284--40105351 Score: 55
Period size: 15 Copynumber: 4.6 Consensus size: 14
40105274 AATTTTAAAC
* *
40105284 TTAAATTTTAAAAT
1 TTAAAATTTAAAAA
*
40105298 TTAAAAATTAAAAAAA
1 TT-AAAATT-TAAAAA
*
40105314 TTAAATTCTTAAAAA
1 TTAAAAT-TTAAAAA
* *
40105329 TAAAAATATAAAAA
1 TTAAAATTTAAAAA
40105343 TTAAAATTT
1 TTAAAATTT
40105352 CAAATTTATA
Statistics
Matches: 41, Mismatches: 10, Indels: 6
0.72 0.18 0.11
Matches are distributed among these distances:
14 15 0.37
15 19 0.46
16 7 0.17
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (14 bp):
TTAAAATTTAAAAA
Found at i:40108492 original size:44 final size:44
Alignment explanation
Indices: 40108444--40109068 Score: 264
Period size: 44 Copynumber: 14.2 Consensus size: 44
40108434 CTGTAACCTC
* * *
40108444 AGGGAGGTAAAATCTGCCATATTCGATCTACTCCACTACTGCCT
1 AGGGAGATAAAATCTGCCATCTTCAATCTACTCCACTACTGCCT
* ** * * * *
40108488 AGGGAGATAAGATCTGTAATCTTCAATTTATTCCACTGCTGCCC
1 AGGGAGATAAAATCTGCCATCTTCAATCTACTCCACTACTGCCT
* * *** * * *
40108532 AGGGAGATAGAAT-TACTGGCTTCAATGTACTCCACT-GTAACCT
1 AGGGAGATAAAATCTGCCATCTTCAATCTACTCCACTACT-GCCT
* * * ** *
40108575 CAGAGAGGTAAAATCTACCATCTTTGATCTACTCCACTACTGTCT
1 -AGGGAGATAAAATCTGCCATCTTCAATCTACTCCACTACTGCCT
* ** * * * * *
40108620 AGGGAGATAAGATCTGTAATATCCAATCTATTCCACTGCTGCCC
1 AGGGAGATAAAATCTGCCATCTTCAATCTACTCCACTACTGCCT
* * * * *
40108664 AGGGAGATAGAATTACTGGC-T-TT-AATGTACTCCACT-GTAACCT
1 AGGGAGATA-AAAT-CTGCCATCTTCAATCTACTCCACTACT-GCCT
* * *
40108707 CAGGGAGGTAAAATCCGCCATCTTCGATCTACTCCACTACTGCCT
1 -AGGGAGATAAAATCTGCCATCTTCAATCTACTCCACTACTGCCT
* ** * * * *
40108752 AGGGAGATAAGATCTGTAATCATCAATCTATTCCACTGCTGCCC
1 AGGGAGATAAAATCTGCCATCTTCAATCTACTCCACTACTGCCT
* * *** * ** *
40108796 AGGGAGATAGAAT-TACTGGCTTCAATGTACTCCA-TTGTAACCT
1 AGGGAGATAAAATCTGCCATCTTCAATCTACTCCACTACT-GCCT
* ** ** * * *
40108839 CAGGGAGGTAAAATCCACCATCTTTGATCTTCTCCACTACTACTT
1 -AGGGAGATAAAATCTGCCATCTTCAATCTACTCCACTACTGCCT
* ** * *
40108884 AGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTG-CT
1 AGGGAGATAAAATCTGCCATCTTCAATCTACTCCACTACTGCCT
* * *** * * *
40108927 CAGGGAGATAGAAT-TACTGGCTTCAATGTACTCCACT-GTAACCT
1 -AGGGAGATAAAATCTGCCATCTTCAATCTACTCCACTACT-GCCT
* * ** *
40108971 CAGGGAGGTAAAATCCGCCATCTTTGATCTACTCCACTACTGCTT
1 -AGGGAGATAAAATCTGCCATCTTCAATCTACTCCACTACTGCCT
* *** * * * *
40109016 AGGGAGATAAGATCTATAATCTTCAATCTATTCCACTGCTACCC
1 AGGGAGATAAAATCTGCCATCTTCAATCTACTCCACTACTGCCT
40109060 AGGGAGATA
1 AGGGAGATA
40109069 GAATTACTGG
Statistics
Matches: 407, Mismatches: 153, Indels: 42
0.68 0.25 0.07
Matches are distributed among these distances:
42 8 0.02
43 67 0.16
44 255 0.63
45 69 0.17
46 8 0.02
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (44 bp):
AGGGAGATAAAATCTGCCATCTTCAATCTACTCCACTACTGCCT
Found at i:40108525 original size:132 final size:132
Alignment explanation
Indices: 40108375--40109124 Score: 1212
Period size: 132 Copynumber: 5.7 Consensus size: 132
40108365 AGATCTGCTT
* * * * * *
40108375 TCTTCGATCGATTCCACTGCCGACCAGGGAGATAGAATTACTGGCTTCAATATATTCCACTGTAA
1 TCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAA
* * *
40108440 CCTCAGGGAGGTAAAATCTGCCATATTCGATCTACTCCACTACTGCCTAGGGAGATAAGATCTGT
66 CCTCAGGGAGGTAAAATCCGCCATCTTTGATCTACTCCACTACTGCCTAGGGAGATAAGATCTGT
40108505 AA
131 AA
*
40108507 TCTTCAATTTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAA
1 TCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAA
* ** *
40108572 CCTCAGAGAGGTAAAATCTACCATCTTTGATCTACTCCACTACTGTCTAGGGAGATAAGATCTGT
66 CCTCAGGGAGGTAAAATCCGCCATCTTTGATCTACTCCACTACTGCCTAGGGAGATAAGATCTGT
40108637 AA
131 AA
* * *
40108639 TATCCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTTAATGTACTCCACTGTAA
1 TCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAA
*
40108704 CCTCAGGGAGGTAAAATCCGCCATCTTCGATCTACTCCACTACTGCCTAGGGAGATAAGATCTGT
66 CCTCAGGGAGGTAAAATCCGCCATCTTTGATCTACTCCACTACTGCCTAGGGAGATAAGATCTGT
40108769 AA
131 AA
* *
40108771 TCATCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCATTGTAA
1 TCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAA
* * * *
40108836 CCTCAGGGAGGTAAAATCCACCATCTTTGATCTTCTCCACTACTACTTAGGGAGATAAGATCTGT
66 CCTCAGGGAGGTAAAATCCGCCATCTTTGATCTACTCCACTACTGCCTAGGGAGATAAGATCTGT
40108901 AA
131 AA
*
40108903 TCTTCAATCTATTCCACTGCTGCTCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAA
1 TCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAA
* *
40108968 CCTCAGGGAGGTAAAATCCGCCATCTTTGATCTACTCCACTACTGCTTAGGGAGATAAGATCTAT
66 CCTCAGGGAGGTAAAATCCGCCATCTTTGATCTACTCCACTACTGCCTAGGGAGATAAGATCTGT
40109033 AA
131 AA
* **
40109035 TCTTCAATCTATTCCACTGCTACCCAGGGAGATAGAATTACTGGCTTCAATGTACTCTTCTGTAA
1 TCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAA
* *
40109100 CCTTAGGGAGGTAAAATCCACCATC
66 CCTCAGGGAGGTAAAATCCGCCATC
40109125 AACCTGCTCC
Statistics
Matches: 574, Mismatches: 44, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
132 574 1.00
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (132 bp):
TCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAA
CCTCAGGGAGGTAAAATCCGCCATCTTTGATCTACTCCACTACTGCCTAGGGAGATAAGATCTGT
AA
Found at i:40109919 original size:13 final size:13
Alignment explanation
Indices: 40109903--40109927 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40109893 TAAATTGTCG
40109903 GGATAACAAAGAT
1 GGATAACAAAGAT
40109916 GGATAACAAAGA
1 GGATAACAAAGA
40109928 AATTGATTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.08, G:0.24, T:0.12
Consensus pattern (13 bp):
GGATAACAAAGAT
Found at i:40115086 original size:20 final size:20
Alignment explanation
Indices: 40115049--40115090 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
40115039 AAATAAAAAC
* *
40115049 AAATAGAAATACATGTATTAA
1 AAATAGAAATAAAAGTA-TAA
40115070 AAATA-AAATAAAAGTATAA
1 AAATAGAAATAAAAGTATAA
40115089 AA
1 AA
40115091 GTATGCATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 5 0.26
20 9 0.47
21 5 0.26
ACGTcount: A:0.67, C:0.02, G:0.07, T:0.24
Consensus pattern (20 bp):
AAATAGAAATAAAAGTATAA
Found at i:40116896 original size:68 final size:69
Alignment explanation
Indices: 40116803--40116984 Score: 222
Period size: 68 Copynumber: 2.6 Consensus size: 69
40116793 TTTTATTTCG
* * * * *
40116803 AAATGTATAAACTTAATTTAATAAAATATTTCATTATTTCAAACTATTTATAAAAATTT-TTATT
1 AAATATATAAACTTAATTTAATAAAACATCTCATTATTTCAAACAACTTATAAAAATTTATTATT
40116867 CAAA
66 CAAA
* *
40116871 AAATATATAAACTTAATTTAATAAAACATCTCATTGTTTCAAACAACTTATTAAAATTTAAAACC
1 AAATATATAAACTTAATTTAATAAAACATCTCATTATTTCAAACAACTTATAAAAATTT---A--
40116936 CTTATTCAAA
61 -TTATTCAAA
* *
40116946 AAATATATAAACTTAATTTAATAACACATCTCCTTATTT
1 AAATATATAAACTTAATTTAATAAAACATCTCATTATTT
40116985 TTGTTTTTGT
Statistics
Matches: 97, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
68 52 0.54
75 45 0.46
ACGTcount: A:0.47, C:0.12, G:0.01, T:0.40
Consensus pattern (69 bp):
AAATATATAAACTTAATTTAATAAAACATCTCATTATTTCAAACAACTTATAAAAATTTATTATT
CAAA
Found at i:40117456 original size:67 final size:65
Alignment explanation
Indices: 40117348--40117605 Score: 320
Period size: 67 Copynumber: 3.9 Consensus size: 65
40117338 AGGATCCCGA
* * * * * *
40117348 ACTTACTAAAATCC-TTATTCGAAAATATATTAATTTAATTTAATAAAATATCTTATTGTTCTAA
1 ACTTACTAAAA-CCTTTATTCG-AAATGTATAAACTTAATTTAATAAAACATCTCATTATT-TAA
40117412 ACT
63 ACT
* *
40117415 ACTTACTAAAACCTTTATTCTAAACTGTATAAACTTAATTTAATAAAACATCACATTATTTTAAA
1 ACTTACTAAAACCTTTATTCGAAA-TGTATAAACTTAATTTAATAAAACATCTCATTA-TTTAAA
40117480 CT
64 CT
* * *
40117482 ACTTACGAAAACATTTATCCTGAAATGTATAAACTTAATTTAATAAAACATCTCATTATTTCAAA
1 ACTTACTAAAACCTTTATTC-GAAATGTATAAACTTAATTTAATAAAACATCTCATTATTT-AAA
40117547 CT
64 CT
* *
40117549 ACTTACTAAAATCTTTATTCGGAAATGTATAAACTTAATTTAATAACACATCTCATT
1 ACTTACTAAAACCTTTATTC-GAAATGTATAAACTTAATTTAATAAAACATCTCATT
40117606 GTTTTTGTTT
Statistics
Matches: 167, Mismatches: 19, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
66 8 0.05
67 154 0.92
68 5 0.03
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.39
Consensus pattern (65 bp):
ACTTACTAAAACCTTTATTCGAAATGTATAAACTTAATTTAATAAAACATCTCATTATTTAAACT
Found at i:40118054 original size:67 final size:67
Alignment explanation
Indices: 40117974--40118239 Score: 424
Period size: 67 Copynumber: 4.0 Consensus size: 67
40117964 GATCCCAAAG
** * * **
40117974 TCAAACTACTTACTAAAACCCATATTTGGAAATATATAAATTTAATTTAATAAAACATCTGGTTG
1 TCAAACTACTTACTAAAACCTTTATTTGGAAATGTATAAACTTAATTTAATAAAACATCTCATTG
40118039 TT
66 TT
* *
40118041 TCAAACTATTTACTAAAACCTTTATTTTGAAATGTATAAACTTAATTTAATAAAACATCTCATTG
1 TCAAACTACTTACTAAAACCTTTATTTGGAAATGTATAAACTTAATTTAATAAAACATCTCATTG
40118106 TT
66 TT
**
40118108 TCAAACTACTTACTAAAACCTTTATTCCGAAATGTATAAACTTAATTTAATAAAACATCTCATTG
1 TCAAACTACTTACTAAAACCTTTATTTGGAAATGTATAAACTTAATTTAATAAAACATCTCATTG
40118173 TT
66 TT
* *
40118175 TCAAACTACTTACTAAAACCTTTATTTGGAAATGTATAAATTTAATTTAATAACACATCTCATTG
1 TCAAACTACTTACTAAAACCTTTATTTGGAAATGTATAAACTTAATTTAATAAAACATCTCATTG
40118240 ATTTTGTTTT
Statistics
Matches: 184, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
67 184 1.00
ACGTcount: A:0.41, C:0.15, G:0.06, T:0.39
Consensus pattern (67 bp):
TCAAACTACTTACTAAAACCTTTATTTGGAAATGTATAAACTTAATTTAATAAAACATCTCATTG
TT
Found at i:40118114 original size:32 final size:32
Alignment explanation
Indices: 40118078--40118181 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 32
40118068 TGAAATGTAT
40118078 AAACTTAATTTAATAAAACATCTCATTGTTTC
1 AAACTTAATTTAATAAAACATCTCATTGTTTC
* * * *
40118110 AAAC-T-ACTTACTAAAACCTTTAT-TCCGAAATGTAT-
1 AAACTTAATTTAATAAAA-C---ATCT-C--ATTGTTTC
40118145 AAACTTAATTTAATAAAACATCTCATTGTTTC
1 AAACTTAATTTAATAAAACATCTCATTGTTTC
40118177 AAACT
1 AAACT
40118182 ACTTACTAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 22
0.64 0.10 0.27
Matches are distributed among these distances:
30 9 0.17
31 7 0.13
32 9 0.17
33 4 0.08
34 4 0.08
35 4 0.08
36 7 0.13
37 9 0.17
ACGTcount: A:0.41, C:0.17, G:0.04, T:0.38
Consensus pattern (32 bp):
AAACTTAATTTAATAAAACATCTCATTGTTTC
Found at i:40118125 original size:30 final size:30
Alignment explanation
Indices: 40118091--40118193 Score: 75
Period size: 30 Copynumber: 3.2 Consensus size: 30
40118081 CTTAATTTAA
40118091 TAAAACATCTCATTGTTTCAAACTACTTAC
1 TAAAACATCTCATTGTTTCAAACTACTTAC
* * * *
40118121 TAAAACCTTTAT-TCCGAAATGTAT-AAACTTAATTTAA
1 TAAAA-C---ATCT-C--ATTGTTTCAAAC-T-ACTTAC
40118158 TAAAACATCTCATTGTTTCAAACTACTTAC
1 TAAAACATCTCATTGTTTCAAACTACTTAC
40118188 TAAAAC
1 TAAAAC
40118194 CTTTATTTGG
Statistics
Matches: 54, Mismatches: 8, Indels: 22
0.64 0.10 0.26
Matches are distributed among these distances:
30 15 0.28
31 7 0.13
32 4 0.07
33 4 0.07
34 4 0.07
35 4 0.07
36 7 0.13
37 9 0.17
ACGTcount: A:0.41, C:0.19, G:0.04, T:0.36
Consensus pattern (30 bp):
TAAAACATCTCATTGTTTCAAACTACTTAC
Found at i:40118162 original size:37 final size:37
Alignment explanation
Indices: 40118048--40118163 Score: 88
Period size: 37 Copynumber: 3.3 Consensus size: 37
40118038 GTTTCAAACT
* **
40118048 ATTTACTAAAACCTTTATTTTGAAATGTATAAACTTA
1 ATTTAATAAAACCTTTATTCCGAAATGTATAAACTTA
* *
40118085 ATTTAATAAAA-C---A-TCTC--ATTGTTTCAAAC-T-
1 ATTTAATAAAACCTTTATTC-CGAAATGTAT-AAACTTA
* *
40118115 ACTTACTAAAACCTTTATTCCGAAATGTATAAACTTA
1 ATTTAATAAAACCTTTATTCCGAAATGTATAAACTTA
40118152 ATTTAATAAAAC
1 ATTTAATAAAAC
40118164 ATCTCATTGT
Statistics
Matches: 57, Mismatches: 11, Indels: 22
0.63 0.12 0.24
Matches are distributed among these distances:
30 9 0.16
31 7 0.12
32 5 0.09
33 1 0.02
34 2 0.04
35 6 0.11
36 7 0.12
37 20 0.35
ACGTcount: A:0.42, C:0.15, G:0.04, T:0.39
Consensus pattern (37 bp):
ATTTAATAAAACCTTTATTCCGAAATGTATAAACTTA
Found at i:40118224 original size:633 final size:630
Alignment explanation
Indices: 40116780--40118762 Score: 2645
Period size: 633 Copynumber: 3.1 Consensus size: 630
40116770 AAAGTTAAAT
** * *
40116780 TACTTACTAAAATTTTTATTTCGAAATGTATAAACTTAATTTAATAAAATATTTCATTATTTCAA
1 TACTTACTAAAACCTTTATTTCGAAATGTATAAACTTAATTTAATAAAACATCTCATTATTTCAA
* ** *
40116845 ACTATTTA-TAAAA-ATTTTTATTCAAAAAATATATAAACTTAATTTAATAAAACATCTCATTGT
66 ACTACTTACTAAAACA--TTTATTC-CGAAATGTATAAACTTAATTTAATAAAACATCTCATTGT
* * * ** *
40116908 TTCAAACAACTTATTAAAATTTAAAACCCTTATTCAAAAAATATATAAACTTAATTTAATAACAC
128 TTCAAACTAC---TT---A-CTAAAACCTTTATT-AGGAAATGTATAAACTTAATTTAATAACAC
* * *
40116973 ATCTCCTTATTTTTGTTTTTGTGTATATGCTCATTTAGTATTGACAGCAAATCTCTTTCCACATT
185 ATCTCATTGTTTTTGTTTTTGTGTATATGCCCATTTAGTATTGACAGCAAATCTCTTTCCACATT
* * **
40117038 GCACTCAATTTTCATATTTCAGGCGCTGGTTGAGTGAAAGAATCGAAAAAAAAT-TTATCTTTTT
250 GCACTCAATTTTCATATTTCAAGCACTGGTTGAGTGAAAGAATCGAAAAAAAATAACATCTTTTT
* * *
40117102 TACAGAAGTATACCAATTGTCACCATCAAATTTATCACCTAACTGAAAGTACCATGTTTGGCTTA
315 TAGAG-GGTATACCAATTGTCACCATCAAACTTATCACCTAACTGAAAGTACCATGTTTGGCTTA
* * ** *
40117167 TATATTACTTGGATACACAAAATAAAATATTTGCAAAGCTGCATCAAATTATACAAAAAAGGCTT
379 TATATTAC-TAGATACACAAAACAAAATATTTGCAAAGCCACATCAAATTATACAAAAAAAGCTT
* *
40117232 TTCTATTTCAAGATATCTTTCCATGCCAATATGGGTTATTCGAAAACAAATAGAGAATAGTTATT
443 TCCTATTTCAAGATATCTTTCCATGCCAATATGGGTTTTTCGAAAACAAATAGAGAATAGTTATT
*
40117297 ATTTAAAAAAACAACATATATTGAAAAGGAAGGTAAGGGAGAGGATCCC-G----A--ACTTACT
508 ACTT-AAAAAACAACATATATTGAAAAGGAAGGTAAGGGAGAGGATCCCAGTCAAACTACTTACT
* * * *
40117355 AAAATCCTTATTCGAAAATATATTAATTTAATTTAATAAAATATCTTATTG-TTCTAAAC
572 AAAACCCTTATTCGAAAATATATAAATTTAATTTAATAAAACATCTCATTGTTTC-AAAC
* * *
40117414 TACTTACTAAAACCTTTA-TTCTAAACTGTATAAACTTAATTTAATAAAACATCACATTATTTTA
1 TACTTACTAAAACCTTTATTTCGAAA-TGTATAAACTTAATTTAATAAAACATCTCATTATTTCA
* *
40117478 AACTACTTACGAAAACATTTA-TCCTGAAATGTATAAACTTAATTTAATAAAACATCTCATTATT
65 AACTACTTACTAAAACATTTATTCC-GAAATGTATAAACTTAATTTAATAAAACATCTCATTGTT
* *
40117542 TCAAACTACTTACTAAAATCTTTATTCGGAAATGTATAAACTTAATTTAATAACACATCTCATTG
129 TCAAACTACTTACTAAAACCTTTATTAGGAAATGTATAAACTTAATTTAATAACACATCTCATTG
* *
40117607 TTTTTGTTTCTGTGTATCTGCCCATTTAGTATTGACAGCAAATCTCTTTCCACATTGCACTCAAT
194 TTTTTGTTTTTGTGTATATGCCCATTTAGTATTGACAGCAAATCTCTTTCCACATTGCACTCAAT
* * * ** *
40117672 TTTCCTGTTTCAAGCACTGGTTTAGTGAAAGAAAGGAAAAAAAATAACATCCTTTTTAGACGGGT
259 TTTCATATTTCAAGCACTGGTTGAGTGAAAGAATCGAAAAAAAATAACATCTTTTTTAGA-GGGT
* *
40117737 ATACCAATTGTCGCCATCAAACTTATCACCTAACTGAAAGTACCATGTTTGGCTTATATATTTCG
323 ATACCAATTGTCACCATCAAACTTATCACCTAACTGAAAGTACCATGTTTGGCTTATATATTAC-
*
40117802 TAGATACACAAAACAAAATATTTGCAAAGCCCCATCAAATTATACAAAAAAAGCTTTCCTATTTC
387 TAGATACACAAAACAAAATATTTGCAAAGCCACATCAAATTATACAAAAAAAGCTTTCCTATTTC
* *
40117867 AAGATATCTTTCCATGCCAATATGGGTTTTTCAAAAACAAATAGAGAATATTTATTACTTAAAAA
452 AAGATATCTTTCCATGCCAATATGGGTTTTTCGAAAACAAATAGAGAATAGTTATTACTTAAAAA
* *
40117932 A-AACATATATTGAAAAGGAAGGTAAGTGAGAGGATCCCAAAGTCAAACTACTTACTAAAACCCA
517 ACAACATATATTGAAAAGGAAGGTAAGGGAGAGGATCCC--AGTCAAACTACTTACTAAAACCCT
* * **
40117996 TATTTGGAAATATATAAATTTAATTTAATAAAACATCTGGTTGTTTCAAAC
580 TATTCGAAAATATATAAATTTAATTTAATAAAACATCTCATTGTTTCAAAC
* * *
40118047 TATTTACTAAAACCTTTATTTTGAAATGTATAAACTTAATTTAATAAAACATCTCATTGTTTCAA
1 TACTTACTAAAACCTTTATTTCGAAATGTATAAACTTAATTTAATAAAACATCTCATTATTTCAA
*
40118112 ACTACTTACTAAAACCTTTATTCCGAAATGTATAAACTTAATTTAATAAAACATCTCATTGTTTC
66 ACTACTTACTAAAACATTTATTCCGAAATGTATAAACTTAATTTAATAAAACATCTCATTGTTTC
* * *
40118177 AAACTACTTACTAAAACCTTTATTTGGAAATGTATAAATTTAATTTAATAACACATCTCATTGAT
131 AAACTACTTACTAAAACCTTTATTAGGAAATGTATAAACTTAATTTAATAACACATCTCATTGTT
* * *
40118242 TTTGTTTTTGTGTAGATGCCCATTTAGTATTGACAGCAAATCTCTTTCCACATTGCATTCAATGT
196 TTTGTTTTTGTGTATATGCCCATTTAGTATTGACAGCAAATCTCTTTCCACATTGCACTCAATTT
* * * * * *
40118307 TCTTATTT-TAGACATTGGTTGAGTAAAAGAATCG--AAAAATTAACATCTTTTTTAGAGGGGTC
261 TCATATTTCAAG-CACTGGTTGAGTGAAAGAATCGAAAAAAAATAACATCTTTTTTAGA-GGGTA
* * *
40118369 TACCAATTGTCCCCATCAAACTTATCTCCTAACTGAAAGTACCATGTTTGGCTTATATATTACTT
324 TACCAATTGTCACCATCAAACTTATCACCTAACTGAAAGTACCATGTTTGGCTTATATATTACTA
*
40118434 GCATACACAAAACAAAATATTTGCAAAGCCATATCAAATTATACAAAAAAAAAAAAAAAAAAGCT
389 G-ATACACAAAACAAAATATTTGCAAAGCCACATCAAATTATAC-----------AAAAAAAGCT
* * *
40118499 TTCCTATTTCAAGATATCTTTCCATGCCAATATGGGTTATTT-GAAATCAAATAAAGAATAGCTA
442 TTCCTATTTCAAGATATCTTTCCATGCCAATATGGGTT-TTTCGAAAACAAATAGAGAATAGTTA
* *
40118563 TTACTTTAAGAAAACAATATATATTGAAAAGGAAGGTAAGGGAGAGGATCTCTAGGTCAAACTAC
506 TTAC-TTAA-AAAACAACATATATTGAAAAGGAAGGTAAGGGAGAGGATC-CCA-GTCAAACTAC
*
40118628 TTACTAAAACCCTTATTC-ATAAATGTATAAATTTAATTTAATAAAACATCTCATTGTTTCAAAC
567 TTACTAAAACCCTTATTCGA-AAATATATAAATTTAATTTAATAAAACATCTCATTGTTTCAAAC
* * *
40118692 TACTTACTAAAACCTTTGTTTCGAAATGTATAAACTTAATTTAATAAAACATATCATTGTTTCAA
1 TACTTACTAAAACCTTTATTTCGAAATGTATAAACTTAATTTAATAAAACATCTCATTATTTCAA
40118757 ACTACT
66 ACTACT
40118763 GATGTGGATG
Statistics
Matches: 1196, Mismatches: 115, Indels: 65
0.87 0.08 0.05
Matches are distributed among these distances:
624 36 0.03
625 139 0.12
626 199 0.17
627 3 0.00
630 4 0.00
631 125 0.10
632 2 0.00
633 361 0.30
634 73 0.06
635 4 0.00
636 1 0.00
642 69 0.06
643 7 0.01
644 5 0.00
645 167 0.14
646 1 0.00
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.36
Consensus pattern (630 bp):
TACTTACTAAAACCTTTATTTCGAAATGTATAAACTTAATTTAATAAAACATCTCATTATTTCAA
ACTACTTACTAAAACATTTATTCCGAAATGTATAAACTTAATTTAATAAAACATCTCATTGTTTC
AAACTACTTACTAAAACCTTTATTAGGAAATGTATAAACTTAATTTAATAACACATCTCATTGTT
TTTGTTTTTGTGTATATGCCCATTTAGTATTGACAGCAAATCTCTTTCCACATTGCACTCAATTT
TCATATTTCAAGCACTGGTTGAGTGAAAGAATCGAAAAAAAATAACATCTTTTTTAGAGGGTATA
CCAATTGTCACCATCAAACTTATCACCTAACTGAAAGTACCATGTTTGGCTTATATATTACTAGA
TACACAAAACAAAATATTTGCAAAGCCACATCAAATTATACAAAAAAAGCTTTCCTATTTCAAGA
TATCTTTCCATGCCAATATGGGTTTTTCGAAAACAAATAGAGAATAGTTATTACTTAAAAAACAA
CATATATTGAAAAGGAAGGTAAGGGAGAGGATCCCAGTCAAACTACTTACTAAAACCCTTATTCG
AAAATATATAAATTTAATTTAATAAAACATCTCATTGTTTCAAAC
Found at i:40118731 original size:67 final size:67
Alignment explanation
Indices: 40118619--40118762 Score: 227
Period size: 67 Copynumber: 2.1 Consensus size: 67
40118609 GATCTCTAGG
* * *
40118619 TCAAACTACTTACTAAAACCCTTATTCATAAATGTATAAATTTAATTTAATAAAACATCTCATTG
1 TCAAACTACTTACTAAAACCCTTATTCAGAAATGTATAAACTTAATTTAATAAAACATATCATTG
40118684 TT
66 TT
* *
40118686 TCAAACTACTTACTAAAACCTTTGTTTC-GAAATGTATAAACTTAATTTAATAAAACATATCATT
1 TCAAACTACTTACTAAAACCCTT-ATTCAGAAATGTATAAACTTAATTTAATAAAACATATCATT
40118750 GTT
65 GTT
40118753 TCAAACTACT
1 TCAAACTACT
40118763 GATGTGGATG
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
67 68 0.96
68 3 0.04
ACGTcount: A:0.41, C:0.17, G:0.04, T:0.38
Consensus pattern (67 bp):
TCAAACTACTTACTAAAACCCTTATTCAGAAATGTATAAACTTAATTTAATAAAACATATCATTG
TT
Found at i:40123243 original size:15 final size:15
Alignment explanation
Indices: 40123223--40123271 Score: 98
Period size: 15 Copynumber: 3.3 Consensus size: 15
40123213 GCTACTTGAT
40123223 AAGCCTGTCAGATTG
1 AAGCCTGTCAGATTG
40123238 AAGCCTGTCAGATTG
1 AAGCCTGTCAGATTG
40123253 AAGCCTGTCAGATTG
1 AAGCCTGTCAGATTG
40123268 AAGC
1 AAGC
40123272 TTGGTTGGCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (15 bp):
AAGCCTGTCAGATTG
Found at i:40129076 original size:14 final size:14
Alignment explanation
Indices: 40129045--40129086 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
40129035 TAATTGTATT
*
40129045 TTTTATA-TTTAGAG
1 TTTTATATTTTA-AA
40129059 TTTTATATTTTAAA
1 TTTTATATTTTAAA
*
40129073 TTTTAAATTTTAAA
1 TTTTATATTTTAAA
40129087 ATTCAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 21 0.84
15 4 0.16
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (14 bp):
TTTTATATTTTAAA
Found at i:40130215 original size:30 final size:29
Alignment explanation
Indices: 40130145--40130221 Score: 73
Period size: 30 Copynumber: 2.6 Consensus size: 29
40130135 AGAATATTTA
* **
40130145 AAGATCAAATTGATAGAATTTGTAATGTG
1 AAGATCAAATTAATAGAATTTGTAAAATG
* * * *
40130174 AAGAGCTAAATTTATAGAATTATTTAAAATT
1 AAGATC-AAATTAATAGAATT-TGTAAAATG
40130205 AAGATCAAATTAATAGA
1 AAGATCAAATTAATAGA
40130222 TCATGCAAGT
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
29 5 0.13
30 23 0.61
31 10 0.26
ACGTcount: A:0.48, C:0.04, G:0.14, T:0.34
Consensus pattern (29 bp):
AAGATCAAATTAATAGAATTTGTAAAATG
Found at i:40131437 original size:17 final size:17
Alignment explanation
Indices: 40131415--40131448 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
40131405 CATCTAAAGG
40131415 TGGTATTGAGAATTCAA
1 TGGTATTGAGAATTCAA
40131432 TGGTATTGAGAATTCAA
1 TGGTATTGAGAATTCAA
40131449 CATCTAAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.35
Consensus pattern (17 bp):
TGGTATTGAGAATTCAA
Found at i:40138462 original size:12 final size:12
Alignment explanation
Indices: 40138424--40138463 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
40138414 AATTTTAGAT
40138424 TTATTATTATGG
1 TTATTATTATGG
* * *
40138436 TTATTGTTCTTG
1 TTATTATTATGG
40138448 TTATTATTATGG
1 TTATTATTATGG
40138460 TTAT
1 TTAT
40138464 ATTGTCATTG
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.20, C:0.03, G:0.15, T:0.62
Consensus pattern (12 bp):
TTATTATTATGG
Found at i:40138884 original size:107 final size:107
Alignment explanation
Indices: 40138698--40138901 Score: 345
Period size: 107 Copynumber: 1.9 Consensus size: 107
40138688 TTCAAAAAAA
*
40138698 TTCAAAGTAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTTC
1 TTCAAAGTAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTAGGTTTC
*
40138763 AATTTCTCGCTCGACCAAATAGCCAATTATCCCTTTGAAACT
66 AATTTCTCGCTCGACCAAATAGCCAAATATCCCTTTGAAACT
* *
40138805 TTCAAAGTAAGGTAATATTTTGCGTTTGGAAATTCGAGAGAACGTGCCCTAACGTGCTAGGTTTC
1 TTCAAAGTAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTAGGTTTC
* * *
40138870 GATTTCTCGTTCGACCAAATAGCTAAATATCC
66 AATTTCTCGCTCGACCAAATAGCCAAATATCC
40138902 TATTAAATCT
Statistics
Matches: 90, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
107 90 1.00
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (107 bp):
TTCAAAGTAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTAGGTTTC
AATTTCTCGCTCGACCAAATAGCCAAATATCCCTTTGAAACT
Found at i:40141206 original size:1 final size:1
Alignment explanation
Indices: 40141200--40141247 Score: 51
Period size: 1 Copynumber: 48.0 Consensus size: 1
40141190 GAATTCAATT
* * * * *
40141200 AAAAAAAACAAAAAAAAAAGAAAAAAAGAAAAAGAAAAGAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
40141248 GGAGAGGCTA
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.90, C:0.02, G:0.08, T:0.00
Consensus pattern (1 bp):
A
Found at i:40141225 original size:19 final size:19
Alignment explanation
Indices: 40141201--40141245 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
40141191 AATTCAATTA
40141201 AAAAAAACAAAAAAAAAAG
1 AAAAAAACAAAAAAAAAAG
* *
40141220 AAAAAAAGAAAAAGAAAAG
1 AAAAAAACAAAAAAAAAAG
40141239 AAAAAAA
1 AAAAAAA
40141246 AAGGAGAGGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.89, C:0.02, G:0.09, T:0.00
Consensus pattern (19 bp):
AAAAAAACAAAAAAAAAAG
Found at i:40148406 original size:15 final size:15
Alignment explanation
Indices: 40148386--40148426 Score: 64
Period size: 16 Copynumber: 2.7 Consensus size: 15
40148376 TGACATTCTG
40148386 CATTCATACAAATAT
1 CATTCATACAAATAT
*
40148401 CATTCAATGCAAATAT
1 CATTC-ATACAAATAT
40148417 CATTCATACA
1 CATTCATACA
40148427 CATCTAGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.44, C:0.22, G:0.02, T:0.32
Consensus pattern (15 bp):
CATTCATACAAATAT
Found at i:40148781 original size:131 final size:131
Alignment explanation
Indices: 40148545--40149262 Score: 1071
Period size: 131 Copynumber: 5.5 Consensus size: 131
40148535 CGGTGAAGAA
*
40148545 ACCAGCCTTATCTTCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGC
1 ACCAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGC
*
40148610 AGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGGAGCAGATTTAGGC
66 AGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGGAGCAGATTTAAGC
40148675 C
131 C
* *
40148676 ACCAGCCTTATCTCCCTGAGCAGTAGTGGAATAGGTTGAAGATTGTAGATCTTATCTCCCTAAGC
1 ACCAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGC
* * * * * *
40148741 AGTAGTGGAGCAGATTGAAGATGGTAAATCTTTTCATTCCAAGATAGTGGGGAGCTGATTTAAGC
66 AGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGGAGCAGATTTAAGC
40148806 C
131 C
* *
40148807 ACCAGCCTTGTCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGC
1 ACCAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGC
* *
40148872 AGTAATGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAATGGGGAGCAGATTTAAGC
66 AGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGGAGCAGATTTAAGC
40148937 C
131 C
* * *
40148938 ACCAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTAAAGATTATAGATCTTATCTCCCTAAGC
1 ACCAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGC
* *
40149003 AGTAGTGGAGCAGATCGAAGACGGCAAATATTATCTTTCCAAGATAATGGGGAGCAGATTTAAGC
66 AGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGGAGCAGATTTAAGC
40149068 C
131 C
* * * * * *
40149069 ACCAACCTTGTCTCTCTAAGCAACAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAAC
1 ACCAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGC
* * * *
40149134 AGTAGTGGAGCAGATCGAAGACGAG-GAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAA
66 AGTAGTGGAGCAGATCGAAGACG-GCAAATCTTATCTTTCCAAGATAGT-GGGGAGCAGATTTAA
40149198 GCC
129 GCC
** * * * * *
40149201 ACTGGTCC-TATCTCCTTGAGCAGCAGTGGAGTACGTTGAAGAATGTAGATCTTGTCTTCCTA
1 ACCAG-CCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTA
40149263 TACTAGCAGT
Statistics
Matches: 532, Mismatches: 52, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
131 465 0.87
132 65 0.12
133 2 0.00
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.27
Consensus pattern (131 bp):
ACCAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGC
AGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGGAGCAGATTTAAGC
C
Found at i:40149923 original size:19 final size:19
Alignment explanation
Indices: 40149901--40149939 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
40149891 GACAGTAAAC
*
40149901 AAAAAACGA-AAAATAAATG
1 AAAAAA-GACAAAAGAAATG
40149920 AAAAAAGACAAAAGAAATG
1 AAAAAAGACAAAAGAAATG
40149939 A
1 A
40149940 TGAAAATAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.74, C:0.05, G:0.13, T:0.08
Consensus pattern (19 bp):
AAAAAAGACAAAAGAAATG
Found at i:40151111 original size:12 final size:12
Alignment explanation
Indices: 40151090--40151129 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
40151080 AAATTTAGAT
40151090 TTATTATTATGG
1 TTATTATTATGG
* *
40151102 TTATTGTTATTG
1 TTATTATTATGG
*
40151114 TTATTATTATGC
1 TTATTATTATGG
40151126 TTAT
1 TTAT
40151130 ATTGTCATTG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.23, C:0.03, G:0.12, T:0.62
Consensus pattern (12 bp):
TTATTATTATGG
Found at i:40155696 original size:7 final size:7
Alignment explanation
Indices: 40155684--40155714 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
40155674 TTTGCTGTCT
40155684 ATAAATA
1 ATAAATA
40155691 ATAAATA
1 ATAAATA
40155698 ATAAATA
1 ATAAATA
40155705 ATAAATA
1 ATAAATA
40155712 ATA
1 ATA
40155715 TAAAAATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
ATAAATA
Found at i:40155742 original size:7 final size:8
Alignment explanation
Indices: 40155720--40155746 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
40155710 TAATATAAAA
40155720 ATATTTTT
1 ATATTTTT
40155728 ATATTTTT
1 ATATTTTT
40155736 ATATTTTT
1 ATATTTTT
40155744 ATA
1 ATA
40155747 ATTTAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (8 bp):
ATATTTTT
Found at i:40156260 original size:31 final size:31
Alignment explanation
Indices: 40156222--40156300 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
40156212 AAATTACACC
40156222 AACAATCACTCAACTTTGATCTCAATGACAA
1 AACAATCACTCAACTTTGATCTCAATGACAA
*
40156253 AACAATCACTCAAATTTGATCTCAATGACAA
1 AACAATCACTCAACTTTGATCTCAATGACAA
**
40156284 AACTGTCACTCAACTTT
1 AACAATCACTCAACTTT
40156301 CAAAACAGCC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.41, C:0.25, G:0.06, T:0.28
Consensus pattern (31 bp):
AACAATCACTCAACTTTGATCTCAATGACAA
Found at i:40156627 original size:74 final size:74
Alignment explanation
Indices: 40156511--40156654 Score: 261
Period size: 74 Copynumber: 1.9 Consensus size: 74
40156501 TATCTCCGTC
*
40156511 GCTCTTCTTCTAATCTATCTCTCATCCTCCTTTGCTACAATACCTAGTCCAATTTTGACTTTGGG
1 GCTCTTCTTCTAATCTATCTCTCATCCTCCTTTGCTACAATACCTAGTCCAATTTTGACTTTAGG
40156576 ATCTTCGCT
66 ATCTTCGCT
* *
40156585 GCTCTTCTTCTAATCTATCTCTCATCCTTCTTTGCTATAATACCTAGTCCAATTTTGACTTTAGG
1 GCTCTTCTTCTAATCTATCTCTCATCCTCCTTTGCTACAATACCTAGTCCAATTTTGACTTTAGG
40156650 ATCTT
66 ATCTT
40156655 GTTAATCACT
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 67 1.00
ACGTcount: A:0.19, C:0.28, G:0.10, T:0.44
Consensus pattern (74 bp):
GCTCTTCTTCTAATCTATCTCTCATCCTCCTTTGCTACAATACCTAGTCCAATTTTGACTTTAGG
ATCTTCGCT
Found at i:40157520 original size:175 final size:174
Alignment explanation
Indices: 40157230--40157563 Score: 454
Period size: 175 Copynumber: 1.9 Consensus size: 174
40157220 CCTTGTCTAG
* *
40157230 CGTGGTAAGTTAACTACCCACATCAACTAGTTTACTGGCCAAGTCACCTTTCCCATTAGACCTAT
1 CGTGGTAAGTTAACTACCCACATCAACTAGTTAACTGGCCAAGTCACCTGTCCCATTAGACCTAT
* * * *
40157295 AATGGAAAATGTTAATGAGTGACTGATATATAATTTTTCGATAACGTTAGTGACTGATTTTTTAT
66 AACGAAAAATGTTAATGAGTGACTGATATATAATTTTTCGATAACGTTAGTGACTAATTTGTTAT
40157360 TTTTTGAAAGTTGAGTAACTAAATTGAAACTTTGTCTCGTCCAA
131 TTTTTGAAAGTTGAGTAACTAAATTGAAACTTTGTCTCGTCCAA
* ** * * * * * *
40157404 CGTGGTAAGTTAAATTGGCCACGTCAGCTAGTTAACTGGCCACGTCACCTGTCCCGTTAGGCCTG
1 CGTGGTAAGTT-AACTACCCACATCAACTAGTTAACTGGCCAAGTCACCTGTCCCATTAGACCTA
* * * *
40157469 TAACGAAAAATGTTAATGAGTGACTGATTTGTCACTTTTT-GATAGCGTTAGTGACTAATTTGTT
65 TAACGAAAAATGTTAATGAGTGACTGATATAT-AATTTTTCGATAACGTTAGTGACTAATTTGTT
* *
40157533 ATTTTTTGAAAGTTGAGTGACTGAATTGAAA
129 ATTTTTTGAAAGTTGAGTAACTAAATTGAAA
40157564 TCAGAGTGAC
Statistics
Matches: 137, Mismatches: 21, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
174 11 0.08
175 120 0.88
176 6 0.04
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.35
Consensus pattern (174 bp):
CGTGGTAAGTTAACTACCCACATCAACTAGTTAACTGGCCAAGTCACCTGTCCCATTAGACCTAT
AACGAAAAATGTTAATGAGTGACTGATATATAATTTTTCGATAACGTTAGTGACTAATTTGTTAT
TTTTTGAAAGTTGAGTAACTAAATTGAAACTTTGTCTCGTCCAA
Found at i:40157552 original size:30 final size:32
Alignment explanation
Indices: 40157485--40157559 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 32
40157475 AAAATGTTAA
* *
40157485 TGAGTGACTGATTTGTCACTTTTTGATAGCGT
1 TGAGTGACTAATTTGTCACTTTTTGATAGAGT
* *
40157517 T-AGTGACTAATTTGTTATTTTTTGA-A-AGT
1 TGAGTGACTAATTTGTCACTTTTTGATAGAGT
40157546 TGAGTGACTGAATT
1 TGAGTGACT-AATT
40157560 GAAATCAGAG
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
29 3 0.08
30 8 0.22
31 25 0.68
32 1 0.03
ACGTcount: A:0.24, C:0.08, G:0.23, T:0.45
Consensus pattern (32 bp):
TGAGTGACTAATTTGTCACTTTTTGATAGAGT
Found at i:40158524 original size:5 final size:5
Alignment explanation
Indices: 40158516--40158545 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
40158506 AAGAGAATGA
40158516 AAAAG AAAAG AAAAG AAAAG AAAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG -AAAAG AAAA
40158546 TAACATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:40158529 original size:10 final size:11
Alignment explanation
Indices: 40158514--40158545 Score: 57
Period size: 10 Copynumber: 3.0 Consensus size: 11
40158504 AGAAGAGAAT
40158514 GAAAAAGAAAA
1 GAAAAAGAAAA
40158525 G-AAAAGAAAA
1 GAAAAAGAAAA
40158535 GAAAAAGAAAA
1 GAAAAAGAAAA
40158546 TAACATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (11 bp):
GAAAAAGAAAA
Found at i:40158555 original size:16 final size:16
Alignment explanation
Indices: 40158516--40158545 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40158506 AAGAGAATGA
40158516 AAAAG-AAAAGAAAAG
1 AAAAGAAAAAGAAAAG
40158531 AAAAGAAAAAGAAAA
1 AAAAGAAAAAGAAAA
40158546 TAACATAAAA
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:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAAGAAAAG
Found at i:40158555 original size:21 final size:22
Alignment explanation
Indices: 40158514--40158562 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
40158504 AGAAGAGAAT
40158514 GAAAAAGAAAAGAAAAGAAAA-
1 GAAAAAGAAAAGAAAAGAAAAG
* * *
40158535 GAAAAAGAAAATAACATAAAAG
1 GAAAAAGAAAAGAAAAGAAAAG
40158557 GAAAAA
1 GAAAAA
40158563 AATTAAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.78, C:0.02, G:0.16, T:0.04
Consensus pattern (22 bp):
GAAAAAGAAAAGAAAAGAAAAG
Found at i:40161927 original size:18 final size:18
Alignment explanation
Indices: 40161906--40161945 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
40161896 TGCGGCTGCT
40161906 GCTGAGGCTGAGACTGTG
1 GCTGAGGCTGAGACTGTG
* * *
40161924 GCTGTGGCTGTGGCTGTG
1 GCTGAGGCTGAGACTGTG
40161942 GCTG
1 GCTG
40161946 CTGCGAAGAC
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:0.07, C:0.17, G:0.47, T:0.28
Consensus pattern (18 bp):
GCTGAGGCTGAGACTGTG
Found at i:40161928 original size:6 final size:6
Alignment explanation
Indices: 40161919--40161945 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
40161909 GAGGCTGAGA
40161919 CTGTGG CTGTGG CTGTGG CTGTGG CTG
1 CTGTGG CTGTGG CTGTGG CTGTGG CTG
40161946 CTGCGAAGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.48, T:0.33
Consensus pattern (6 bp):
CTGTGG
Found at i:40161933 original size:24 final size:24
Alignment explanation
Indices: 40161876--40161927 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
40161866 GTGGCTGGCT
* *
40161876 GCTGCTGCTGAGGCTGGGATTGCG
1 GCTGCTGCTGAGGCTGAGACTGCG
*
40161900 GCTGCTGCTGAGGCTGAGACTGTG
1 GCTGCTGCTGAGGCTGAGACTGCG
40161924 GCTG
1 GCTG
40161928 TGGCTGTGGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.10, C:0.21, G:0.44, T:0.25
Consensus pattern (24 bp):
GCTGCTGCTGAGGCTGAGACTGCG
Found at i:40165101 original size:29 final size:29
Alignment explanation
Indices: 40165044--40165103 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
40165034 ATAAAATATG
* * *
40165044 GAACTCGTCGAAGGAAGCTCCTAAACTTA
1 GAACTCGTCAAAGGAAGCACCGAAACTTA
* *
40165073 GAACTCGTCAAAGGGAGCACCGAACCTTA
1 GAACTCGTCAAAGGAAGCACCGAAACTTA
40165102 GA
1 GA
40165104 CTTGAAAGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.35, C:0.25, G:0.23, T:0.17
Consensus pattern (29 bp):
GAACTCGTCAAAGGAAGCACCGAAACTTA
Found at i:40171300 original size:119 final size:119
Alignment explanation
Indices: 40171164--40171511 Score: 517
Period size: 116 Copynumber: 2.9 Consensus size: 119
40171154 ACTTCCAGCA
* * *
40171164 CTAACCACCACAATACCTAAGTAGGGAAAATTTCGACTGTTCTTCCATTGAATATTTTAATGTGT
1 CTAACCACCACAATACCTAAGTAGGCAAAACTTCCACTGTTCTTCCATTGAATATTTTAATGTGT
*
40171229 CCCAACTCCCAACACAATTGATTTTCAGAAACACAATACACCAAGACTCCAGTC
66 CCCAACTCCCAACACAATTGATTTTCTGAAACACAATACACCAAGACTCCAGTC
* * * *
40171283 CTAACCACCACAATACCTAGGTAGGCAAAACTTCCACAGTTCTCCCATTGAATATCTTAATGTGT
1 CTAACCACCACAATACCTAAGTAGGCAAAACTTCCACTGTTCTTCCATTGAATATTTTAATGTGT
*
40171348 CCCAACT---AACACAATTGATTTTCTGAAACACAGTACACCAAGACTCCAGTC
66 CCCAACTCCCAACACAATTGATTTTCTGAAACACAATACACCAAGACTCCAGTC
*
40171399 CTAACCACCACAATACCTCAGTAGGCAAAACTTCCACAT-TTCTTCCATTGAAT-TCTTTAATGT
1 CTAACCACCACAATACCTAAGTAGGCAAAACTTCCAC-TGTTCTTCCATTGAATAT-TTTAATGT
** * *
40171462 GTCTGAACTCCCAACAAAATTGATTTTCTGAAACACAATACACCGAGACT
64 GTCCCAACTCCCAACACAATTGATTTTCTGAAACACAATACACCAAGACT
40171512 TTCTATAGGA
Statistics
Matches: 205, Mismatches: 19, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
115 1 0.00
116 104 0.51
119 100 0.49
ACGTcount: A:0.35, C:0.28, G:0.11, T:0.27
Consensus pattern (119 bp):
CTAACCACCACAATACCTAAGTAGGCAAAACTTCCACTGTTCTTCCATTGAATATTTTAATGTGT
CCCAACTCCCAACACAATTGATTTTCTGAAACACAATACACCAAGACTCCAGTC
Found at i:40172057 original size:21 final size:21
Alignment explanation
Indices: 40172033--40172072 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
40172023 TTCAATTCCA
40172033 CTTCTACTTATTTTCTTAGAG
1 CTTCTACTTATTTTCTTAGAG
40172054 CTTCTACTTATTTTCTTAG
1 CTTCTACTTATTTTCTTAG
40172073 CAGCCAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.17, C:0.20, G:0.07, T:0.55
Consensus pattern (21 bp):
CTTCTACTTATTTTCTTAGAG
Found at i:40172984 original size:18 final size:19
Alignment explanation
Indices: 40172947--40172984 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
40172937 TTGTTTTAAA
* *
40172947 TATGTTTGTTAAAAAGTTT
1 TATGTTTGTAAAAAAATTT
40172966 TATGTTT-TAAAAAAATTT
1 TATGTTTGTAAAAAAATTT
40172984 T
1 T
40172985 GTTAGAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.53
Consensus pattern (19 bp):
TATGTTTGTAAAAAAATTT
Found at i:40182249 original size:15 final size:14
Alignment explanation
Indices: 40182214--40182252 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
40182204 TGCAAAGTTG
40182214 ATAATTA-ATTAAT
1 ATAATTATATTAAT
40182227 ATATATTATATTAAAT
1 ATA-ATTATATT-AAT
40182243 ATAATTATAT
1 ATAATTATAT
40182253 ATAAGTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 3 0.13
14 4 0.17
15 10 0.43
16 6 0.26
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
ATAATTATATTAAT
Found at i:40182375 original size:29 final size:29
Alignment explanation
Indices: 40182320--40182376 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
40182310 ACCTTTTAAA
*
40182320 AATATTTACAAAAAGAGATAACTAATGTC
1 AATATTTACAAAAAGAGATAACAAATGTC
40182349 AATATTTACAAAAAGAG-TAACCAAATGT
1 AATATTTACAAAAAGAGATAA-CAAATGT
40182377 TGCAATTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 3 0.12
29 23 0.88
ACGTcount: A:0.53, C:0.11, G:0.11, T:0.26
Consensus pattern (29 bp):
AATATTTACAAAAAGAGATAACAAATGTC
Found at i:40189869 original size:48 final size:48
Alignment explanation
Indices: 40189793--40189896 Score: 199
Period size: 48 Copynumber: 2.2 Consensus size: 48
40189783 TTACCCTCAA
40189793 TTTATTTAGCTGGCGGTAATCCACACACATCCTCATTGTACTATCTTT
1 TTTATTTAGCTGGCGGTAATCCACACACATCCTCATTGTACTATCTTT
*
40189841 TTTATTTAGCTGGCGGTAATCCATACACATCCTCATTGTACTATCTTT
1 TTTATTTAGCTGGCGGTAATCCACACACATCCTCATTGTACTATCTTT
40189889 TTTATTTA
1 TTTATTTA
40189897 CAAACAGAAT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 55 1.00
ACGTcount: A:0.23, C:0.22, G:0.12, T:0.43
Consensus pattern (48 bp):
TTTATTTAGCTGGCGGTAATCCACACACATCCTCATTGTACTATCTTT
Found at i:40197316 original size:19 final size:20
Alignment explanation
Indices: 40197279--40197316 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
40197269 GTAGGGGTCA
40197279 ACACGCCCATGTGGAAAGGC
1 ACACGCCCATGTGGAAAGGC
*
40197299 ACACGCCCGTGT-GAAAGG
1 ACACGCCCATGTGGAAAGG
40197317 AGGCACATGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.29, C:0.29, G:0.32, T:0.11
Consensus pattern (20 bp):
ACACGCCCATGTGGAAAGGC
Found at i:40198162 original size:6 final size:6
Alignment explanation
Indices: 40198151--40198193 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
40198141 TTTTCATATC
* *
40198151 AAAAAT AAAAAT ATAAAT AAAAAT AAGAAAA AACAAAT AAAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AA-AAAT AA-AAAT AAAAA
40198194 AATCTAACCT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
6 21 0.68
7 10 0.32
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:40199658 original size:32 final size:32
Alignment explanation
Indices: 40199622--40199687 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
40199612 CAAATTTGGT
40199622 AATTAAAAAATTATGCAAACTTTACAGAAAAC
1 AATTAAAAAATTATGCAAACTTTACAGAAAAC
* *
40199654 AATTAAAATATTATGCAAACTTTACATAAAAC
1 AATTAAAAAATTATGCAAACTTTACAGAAAAC
40199686 AA
1 AA
40199688 ATTTTTCTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.56, C:0.12, G:0.05, T:0.27
Consensus pattern (32 bp):
AATTAAAAAATTATGCAAACTTTACAGAAAAC
Found at i:40199918 original size:11 final size:12
Alignment explanation
Indices: 40199888--40199921 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
40199878 AAACAAAATT
40199888 TTAAAAATATAA
1 TTAAAAATATAA
40199900 TTAAAAATATAA
1 TTAAAAATATAA
*
40199912 -TAGAAATATA
1 TTAAAAATATA
40199922 CCTTCAACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 9 0.43
12 12 0.57
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (12 bp):
TTAAAAATATAA
Found at i:40202127 original size:35 final size:35
Alignment explanation
Indices: 40202088--40202162 Score: 132
Period size: 35 Copynumber: 2.1 Consensus size: 35
40202078 CCTTATTTTA
*
40202088 CTAGATTAGACTATCAACATTACATAAAGTATATG
1 CTAGATTAGAATATCAACATTACATAAAGTATATG
40202123 CTAGATTAGAATATCAACATTACATAAAGTATATG
1 CTAGATTAGAATATCAACATTACATAAAGTATATG
*
40202158 TTAGA
1 CTAGA
40202163 AAAAAATTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (35 bp):
CTAGATTAGAATATCAACATTACATAAAGTATATG
Found at i:40202829 original size:19 final size:19
Alignment explanation
Indices: 40202781--40202830 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
40202771 TGCAAAAAAA
40202781 AAAATGCCAAAATAAATTTT
1 AAAATGCC-AAATAAATTTT
* *
40202801 AACATCCCAAATAAA-TTT
1 AAAATGCCAAATAAATTTT
40202819 AAAATGTCCAAA
1 AAAATG-CCAAA
40202831 AGTCATGAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 7 0.28
19 12 0.48
20 6 0.24
ACGTcount: A:0.54, C:0.16, G:0.04, T:0.26
Consensus pattern (19 bp):
AAAATGCCAAATAAATTTT
Found at i:40204923 original size:30 final size:30
Alignment explanation
Indices: 40204887--40204949 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
40204877 TATTTTTTTA
*
40204887 AAACCACCCATATCCCCACTAACTCCCACT
1 AAACCACACATATCCCCACTAACTCCCACT
* *
40204917 AAACCACATATATCCCTACTAACTCCCACT
1 AAACCACACATATCCCCACTAACTCCCACT
40204947 AAA
1 AAA
40204950 TATGATTAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.38, C:0.43, G:0.00, T:0.19
Consensus pattern (30 bp):
AAACCACACATATCCCCACTAACTCCCACT
Found at i:40213942 original size:18 final size:20
Alignment explanation
Indices: 40213911--40213949 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
40213901 ACAAGTGCTA
*
40213911 AACATGCTCTTACATA-CAT
1 AACATGCTCATACATATCAT
40213930 AACA-GCTCATACATATCAT
1 AACATGCTCATACATATCAT
40213949 A
1 A
40213950 TTACACAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.41, C:0.26, G:0.05, T:0.28
Consensus pattern (20 bp):
AACATGCTCATACATATCAT
Found at i:40214529 original size:8 final size:8
Alignment explanation
Indices: 40214516--40214607 Score: 148
Period size: 8 Copynumber: 11.5 Consensus size: 8
40214506 TACAACACCA
40214516 GTATGCAT
1 GTATGCAT
40214524 GTATGCAT
1 GTATGCAT
40214532 GTATGCAT
1 GTATGCAT
40214540 GTATGCAT
1 GTATGCAT
40214548 GTATGCAT
1 GTATGCAT
*
40214556 GTATGCAG
1 GTATGCAT
*
40214564 GTATTCAT
1 GTATGCAT
40214572 GTATGCAT
1 GTATGCAT
40214580 GTATGCAT
1 GTATGCAT
40214588 GTATGCAT
1 GTATGCAT
* *
40214596 GCATGTAT
1 GTATGCAT
40214604 GTAT
1 GTAT
40214608 TGAATTCAAA
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 77 1.00
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (8 bp):
GTATGCAT
Found at i:40216727 original size:49 final size:49
Alignment explanation
Indices: 40216674--40216768 Score: 190
Period size: 49 Copynumber: 1.9 Consensus size: 49
40216664 TCAACACACT
40216674 CAAACTCTTCAAAATAAACACAATTTCGATTCTAACTTTAAGAAAAGAG
1 CAAACTCTTCAAAATAAACACAATTTCGATTCTAACTTTAAGAAAAGAG
40216723 CAAACTCTTCAAAATAAACACAATTTCGATTCTAACTTTAAGAAAA
1 CAAACTCTTCAAAATAAACACAATTTCGATTCTAACTTTAAGAAAA
40216769 AAGTGAAGAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.47, C:0.19, G:0.06, T:0.27
Consensus pattern (49 bp):
CAAACTCTTCAAAATAAACACAATTTCGATTCTAACTTTAAGAAAAGAG
Found at i:40217588 original size:46 final size:42
Alignment explanation
Indices: 40217525--40217610 Score: 120
Period size: 41 Copynumber: 2.0 Consensus size: 42
40217515 TTATGAAGGA
40217525 AATAAATACCTAATATAATAGAGAAAATAAATAAAACTAAAACTCTT
1 AATAAATACCTAATATAAT-----AAATAAATAAAACTAAAACTCTT
40217572 AATAAA-ACCTAATATAATAAATAAATAAAACTAAAACTC
1 AATAAATACCTAATATAATAAATAAATAAAACTAAAACTC
40217611 CTGTTGCAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
41 21 0.54
46 12 0.31
47 6 0.15
ACGTcount: A:0.62, C:0.12, G:0.02, T:0.24
Consensus pattern (42 bp):
AATAAATACCTAATATAATAAATAAATAAAACTAAAACTCTT
Found at i:40223782 original size:29 final size:29
Alignment explanation
Indices: 40223740--40223797 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
40223730 CTTAATGAGA
40223740 ATGATGACAAAGAAAATCACAAAGACAAT
1 ATGATGACAAAGAAAATCACAAAGACAAT
*
40223769 ATGATGACAAAGAAGATCACAAAGACAAT
1 ATGATGACAAAGAAAATCACAAAGACAAT
40223798 CACAATCAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.57, C:0.14, G:0.16, T:0.14
Consensus pattern (29 bp):
ATGATGACAAAGAAAATCACAAAGACAAT
Found at i:40224254 original size:3 final size:3
Alignment explanation
Indices: 40224246--40224271 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
40224236 AGATCTTTAA
40224246 CAT CAT CAT CAT CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CA
40224272 CCACCCTGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.31
Consensus pattern (3 bp):
CAT
Found at i:40225579 original size:13 final size:14
Alignment explanation
Indices: 40225548--40225580 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
40225538 ATATTACGTT
40225548 TTTTTCAAAACTAA
1 TTTTTCAAAACTAA
40225562 TTTTTCAAAA-TATA
1 TTTTTCAAAACTA-A
40225576 TTTTT
1 TTTTT
40225581 TAAGGATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 2 0.11
14 16 0.89
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (14 bp):
TTTTTCAAAACTAA
Found at i:40225807 original size:19 final size:19
Alignment explanation
Indices: 40225783--40225825 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
40225773 TTAATACAAA
40225783 AAAATCAACCTTTGTGAGT
1 AAAATCAACCTTTGTGAGT
40225802 AAAATCAACCTTTGTGAGT
1 AAAATCAACCTTTGTGAGT
*
40225821 CAAAT
1 AAAAT
40225826 TTCTATCCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (19 bp):
AAAATCAACCTTTGTGAGT
Found at i:40227732 original size:27 final size:27
Alignment explanation
Indices: 40227661--40227940 Score: 345
Period size: 27 Copynumber: 10.4 Consensus size: 27
40227651 AGACCCTAAA
*
40227661 ATAGGGTAAAATGATCGAAATACCCC-
1 ATAGGGTAAAATGACCGAAATACCCCT
* *
40227687 ATAAGGTAAAATGATCGAAATACCCCT
1 ATAGGGTAAAATGACCGAAATACCCCT
40227714 ATAGGGTAAAATGACCGAAATA-CCCT
1 ATAGGGTAAAATGACCGAAATACCCCT
* *
40227740 CATAGGGTAAAATGATCGAAATACCCCC
1 -ATAGGGTAAAATGACCGAAATACCCCT
* * *
40227768 ATAGGGTAAAATAACCAAAATACCCCC
1 ATAGGGTAAAATGACCGAAATACCCCT
* *
40227795 ATAGGGTAAAATAACCAAAATACCCCT
1 ATAGGGTAAAATGACCGAAATACCCCT
*
40227822 ATAGGGTAAAATGACCAAAATACCCC-
1 ATAGGGTAAAATGACCGAAATACCCCT
*
40227848 ATAGGATAAAATGACCGAAATA-CCCT
1 ATAGGGTAAAATGACCGAAATACCCCT
* *
40227874 CATAGGGTAGAATGACGGAAATACTCCC-
1 -ATAGGGTAAAATGACCGAAATAC-CCCT
* *
40227902 ATAAGGTAAAATGACCGAAATACCCCC
1 ATAGGGTAAAATGACCGAAATACCCCT
*
40227929 ACAGGGTAAAAT
1 ATAGGGTAAAAT
40227941 AACTGTTATA
Statistics
Matches: 226, Mismatches: 20, Indels: 15
0.87 0.08 0.06
Matches are distributed among these distances:
25 3 0.01
26 52 0.23
27 165 0.73
28 3 0.01
29 3 0.01
ACGTcount: A:0.44, C:0.21, G:0.17, T:0.18
Consensus pattern (27 bp):
ATAGGGTAAAATGACCGAAATACCCCT
Found at i:40227896 original size:80 final size:78
Alignment explanation
Indices: 40227661--40227927 Score: 340
Period size: 80 Copynumber: 3.3 Consensus size: 78
40227651 AGACCCTAAA
* *
40227661 ATAGGGTAAAATGATCGAAATACCCCATAAGGTAAAATGATCGAAATACCCCTATAGGGTAAAAT
1 ATAGGGTAAAATGACCGAAATACCCCAT-AGGTAAAATGACCGAAATACCCC-ATAGGGTAAAAT
40227726 GACCGAAATA-CCCT
64 GACCGAAATACCCCT
* * *
40227740 CATAGGGTAAAATGATCGAAATACCCCCATAGGGTAAAATAACCAAAATACCCCCATAGGGTAAA
1 -ATAGGGTAAAATGACCGAAATA-CCCCATA-GGTAAAATGACCGAAATA-CCCCATAGGGTAAA
* *
40227805 ATAACCAAAATACCCCT
62 ATGACCGAAATACCCCT
* *
40227822 ATAGGGTAAAATGACCAAAATACCCCATAGGATAAAATGACCGAAATACCCTCATAGGGTAGAAT
1 ATAGGGTAAAATGACCGAAATACCCCATAGG-TAAAATGACCGAAATACCC-CATAGGGTAAAAT
*
40227887 GACGGAAATACTCCC-
64 GACCGAAATAC-CCCT
*
40227902 ATAAGGTAAAATGACCGAAATACCCC
1 ATAGGGTAAAATGACCGAAATACCCC
40227928 CACAGGGTAA
Statistics
Matches: 165, Mismatches: 15, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
79 5 0.03
80 88 0.53
81 64 0.39
82 8 0.05
ACGTcount: A:0.44, C:0.22, G:0.16, T:0.18
Consensus pattern (78 bp):
ATAGGGTAAAATGACCGAAATACCCCATAGGTAAAATGACCGAAATACCCCATAGGGTAAAATGA
CCGAAATACCCCT
Found at i:40227903 original size:134 final size:134
Alignment explanation
Indices: 40227661--40227943 Score: 417
Period size: 134 Copynumber: 2.1 Consensus size: 134
40227651 AGACCCTAAA
* * * * * *
40227661 ATAGGGTAAAATGATCGAAATACCCCATAAGGTAAAATGATCGAAATACCCCTATAGGGTAAAAT
1 ATAGGGTAAAATAACCAAAATACCCCATAAGGTAAAATGACCAAAATACCCCTATAGGATAAAAT
*
40227726 GACCGAAATACCCTCATAGGGTAAAATGATCGAAATACCCCCATAGGGTAAAATAACCAAAATAC
66 GACCGAAATACCCTCATAGGGTAAAATGATCGAAATACCCCCATAAGGTAAAATAACCAAAATAC
40227791 CCCC
131 CCCC
*
40227795 ATAGGGTAAAATAACCAAAATACCCCTATAGGGTAAAATGACCAAAATACCCC-ATAGGATAAAA
1 ATAGGGTAAAATAACCAAAATACCCC-ATAAGGTAAAATGACCAAAATACCCCTATAGGATAAAA
* * * *
40227859 TGACCGAAATACCCTCATAGGGTAGAATGA-CGGAAATACTCCCATAAGGTAAAATGACCGAAAT
65 TGACCGAAATACCCTCATAGGGTAAAATGATC-GAAATACCCCCATAAGGTAAAATAACCAAAAT
40227923 ACCCCC
129 ACCCCC
*
40227929 ACAGGGTAAAATAAC
1 ATAGGGTAAAATAAC
40227944 TGTTATACCC
Statistics
Matches: 134, Mismatches: 13, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
133 1 0.01
134 110 0.82
135 23 0.17
ACGTcount: A:0.44, C:0.22, G:0.17, T:0.18
Consensus pattern (134 bp):
ATAGGGTAAAATAACCAAAATACCCCATAAGGTAAAATGACCAAAATACCCCTATAGGATAAAAT
GACCGAAATACCCTCATAGGGTAAAATGATCGAAATACCCCCATAAGGTAAAATAACCAAAATAC
CCCC
Found at i:40227969 original size:54 final size:53
Alignment explanation
Indices: 40227661--40227940 Score: 380
Period size: 54 Copynumber: 5.2 Consensus size: 53
40227651 AGACCCTAAA
* * * *
40227661 ATAGGGTAAAATGATCGAAATACCCCATAAGGTAAAATGATCGAAATACCCCT
1 ATAGGGTAAAATGACCGAAATACCCCATAGGGTAAAATGACCGAAATACCCCC
*
40227714 ATAGGGTAAAATGACCGAAATACCCTCATAGGGTAAAATGATCGAAATACCCCC
1 ATAGGGTAAAATGACCGAAATACCC-CATAGGGTAAAATGACCGAAATACCCCC
* * * * *
40227768 ATAGGGTAAAATAACCAAAATACCCCCATAGGGTAAAATAACCAAAATACCCCT
1 ATAGGGTAAAATGACCGAAATA-CCCCATAGGGTAAAATGACCGAAATACCCCC
* * *
40227822 ATAGGGTAAAATGACCAAAATACCCCATAGGATAAAATGACCGAAATACCCTC
1 ATAGGGTAAAATGACCGAAATACCCCATAGGGTAAAATGACCGAAATACCCCC
* * *
40227875 ATAGGGTAGAATGACGGAAATACTCCCATAAGGTAAAATGACCGAAATACCCCC
1 ATAGGGTAAAATGACCGAAATAC-CCCATAGGGTAAAATGACCGAAATACCCCC
*
40227929 ACAGGGTAAAAT
1 ATAGGGTAAAAT
40227941 AACTGTTATA
Statistics
Matches: 201, Mismatches: 23, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
53 70 0.35
54 128 0.64
55 3 0.01
ACGTcount: A:0.44, C:0.21, G:0.17, T:0.18
Consensus pattern (53 bp):
ATAGGGTAAAATGACCGAAATACCCCATAGGGTAAAATGACCGAAATACCCCC
Found at i:40231793 original size:26 final size:27
Alignment explanation
Indices: 40231753--40231835 Score: 80
Period size: 26 Copynumber: 3.1 Consensus size: 27
40231743 TCAACTGGTA
*
40231753 AACACTAGCTAGCCAAACAGGCTAGCG
1 AACACTAGCTTGCCAAACAGGCTAGCG
* * *
40231780 AA-ACTAGCTTGCCAAATAGGTTAGTG
1 AACACTAGCTTGCCAAACAGGCTAGCG
* *
40231806 AACCCTTAG-TTCGCCAAACAGACTAGCG
1 AACAC-TAGCTT-GCCAAACAGGCTAGCG
40231834 AA
1 AA
40231836 GCCCTTACCA
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
26 22 0.50
27 5 0.11
28 17 0.39
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.18
Consensus pattern (27 bp):
AACACTAGCTTGCCAAACAGGCTAGCG
Found at i:40234152 original size:90 final size:91
Alignment explanation
Indices: 40234014--40234193 Score: 229
Period size: 90 Copynumber: 2.0 Consensus size: 91
40234004 GGTGGTCTAT
* * * * * **
40234014 CCACATATTATTTGACAACTTTTATCTGTAATTAAGTTGTGTATTCACAACCATTTGGTAGTGTA
1 CCACATATTATATGACAACTTTTATATGTAATTAAGTTGTGTACTCACAACCATCTGGCAGCATA
*
40234079 TTAACTTGCAA-ATTTAGGTGGTTCAC
66 TTAACCTGCAACATTT-GGTGGTTCAC
* * * *
40234105 CCACCTATTATATGA-AGCTTTTATATGTAATTATGTTGTGTGCTCACAACCATCTGGCAGCATA
1 CCACATATTATATGACAACTTTTATATGTAATTAAGTTGTGTACTCACAACCATCTGGCAGCATA
40234169 TTAACCTGCAACATTTGGTGGTTCA
66 TTAACCTGCAACATTTGGTGGTTCA
40234194 TCCATAACCC
Statistics
Matches: 76, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
90 59 0.78
91 17 0.22
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38
Consensus pattern (91 bp):
CCACATATTATATGACAACTTTTATATGTAATTAAGTTGTGTACTCACAACCATCTGGCAGCATA
TTAACCTGCAACATTTGGTGGTTCAC
Found at i:40237439 original size:146 final size:146
Alignment explanation
Indices: 40237259--40237599 Score: 539
Period size: 146 Copynumber: 2.3 Consensus size: 146
40237249 ATATATTTAT
* *
40237259 TAATTACAAA-TAAAA--AAAGCTTGAAACAACATGAAATAAAAA-AAAAATACAAATGT-GCTT
1 TAATTA-AAAGTAAAAGTAAAGCTTGAAACAAGATGAAATAAAAATAAAAAT-CAAA-GTAACTT
*
40237319 AGAAGAGAAATCAAACCTGAGATTCAATGATAAAATCACTATTAGTTAACCATCTAACCATTGGA
63 AGAAGAGAAATCAAACCTGAGATTCAATGATAAAATCACTATTAATTAACCATCTAACCATTGGA
40237384 GCTAATGTGTTAAAAATAA
128 GCTAATGTGTTAAAAATAA
* ***
40237403 TAATTAAAAGTAAAAGTAAAGCTTGAAACAAGATGAAATAAAAATACAAATGTGAGTAACTTAGA
1 TAATTAAAAGTAAAAGTAAAGCTTGAAACAAGATGAAATAAAAATAAAAATCAAAGTAACTTAGA
*
40237468 AGAGAAATCAAACCTGAGATTCAATGATAAAATCACTATTAATTAACCATCTAACTATTGGAGCT
66 AGAGAAATCAAACCTGAGATTCAATGATAAAATCACTATTAATTAACCATCTAACCATTGGAGCT
40237533 AATGTGTTAAAAATAA
131 AATGTGTTAAAAATAA
*
40237549 TAATTAAAAGTAAAAGTAAAGCTTGAAACAAGATGAAATAAAAATACAAAT
1 TAATTAAAAGTAAAAGTAAAGCTTGAAACAAGATGAAATAAAAATAAAAAT
40237600 GTGAGTAAGA
Statistics
Matches: 184, Mismatches: 8, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
143 3 0.02
144 11 0.06
145 2 0.01
146 163 0.89
147 5 0.03
ACGTcount: A:0.52, C:0.11, G:0.13, T:0.25
Consensus pattern (146 bp):
TAATTAAAAGTAAAAGTAAAGCTTGAAACAAGATGAAATAAAAATAAAAATCAAAGTAACTTAGA
AGAGAAATCAAACCTGAGATTCAATGATAAAATCACTATTAATTAACCATCTAACCATTGGAGCT
AATGTGTTAAAAATAA
Found at i:40237600 original size:146 final size:146
Alignment explanation
Indices: 40237316--40237607 Score: 566
Period size: 146 Copynumber: 2.0 Consensus size: 146
40237306 TACAAATGTG
*
40237316 CTTAGAAGAGAAATCAAACCTGAGATTCAATGATAAAATCACTATTAGTTAACCATCTAACCATT
1 CTTAGAAGAGAAATCAAACCTGAGATTCAATGATAAAATCACTATTAATTAACCATCTAACCATT
40237381 GGAGCTAATGTGTTAAAAATAATAATTAAAAGTAAAAGTAAAGCTTGAAACAAGATGAAATAAAA
66 GGAGCTAATGTGTTAAAAATAATAATTAAAAGTAAAAGTAAAGCTTGAAACAAGATGAAATAAAA
40237446 ATACAAATGTGAGTAA
131 ATACAAATGTGAGTAA
*
40237462 CTTAGAAGAGAAATCAAACCTGAGATTCAATGATAAAATCACTATTAATTAACCATCTAACTATT
1 CTTAGAAGAGAAATCAAACCTGAGATTCAATGATAAAATCACTATTAATTAACCATCTAACCATT
40237527 GGAGCTAATGTGTTAAAAATAATAATTAAAAGTAAAAGTAAAGCTTGAAACAAGATGAAATAAAA
66 GGAGCTAATGTGTTAAAAATAATAATTAAAAGTAAAAGTAAAGCTTGAAACAAGATGAAATAAAA
40237592 ATACAAATGTGAGTAA
131 ATACAAATGTGAGTAA
40237608 GAGAGGAACT
Statistics
Matches: 144, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
146 144 1.00
ACGTcount: A:0.50, C:0.11, G:0.14, T:0.26
Consensus pattern (146 bp):
CTTAGAAGAGAAATCAAACCTGAGATTCAATGATAAAATCACTATTAATTAACCATCTAACCATT
GGAGCTAATGTGTTAAAAATAATAATTAAAAGTAAAAGTAAAGCTTGAAACAAGATGAAATAAAA
ATACAAATGTGAGTAA
Found at i:40242189 original size:18 final size:18
Alignment explanation
Indices: 40242168--40242203 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
40242158 GTACAGTGAA
*
40242168 AGCGTAGTGGTGGAGTCT
1 AGCGTAGTAGTGGAGTCT
40242186 AGCGTAGTAGTGGAGTCT
1 AGCGTAGTAGTGGAGTCT
40242204 GTGTTATGCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.11, G:0.42, T:0.28
Consensus pattern (18 bp):
AGCGTAGTAGTGGAGTCT
Found at i:40243576 original size:81 final size:81
Alignment explanation
Indices: 40243414--40244014 Score: 672
Period size: 81 Copynumber: 7.4 Consensus size: 81
40243404 TCTAAAAATA
* * * * * * *
40243414 GGTAGAATGACCG-AATACCCCTATAGGGTAGACTGACCGAAATACCTCGTA-A-GGTATAATGA
1 GGTAAAATGACCGAAATACCCCCATAGGGTAAAATGACCAAAATACC-CCTATAGGGTAAAATGA
*
40243476 CCGAAATACCCCTATAG
65 CCGAAATACCCCCATAG
* * *
40243493 GATACAATGACCGAAATACCCCCATAGGGTAAAATGATCAAAATACCCCTATAGGGTAAAATGAC
1 GGTAAAATGACCGAAATACCCCCATAGGGTAAAATGACCAAAATACCCCTATAGGGTAAAATGAC
*
40243558 TGAAATACCCCCATAG
66 CGAAATACCCCCATAG
* * * * *
40243574 GATAAAATGATCGAAATACCCCCATAGGGTAAAATAACTAAAATACCCCAATAGGGTAAAATGAC
1 GGTAAAATGACCGAAATACCCCCATAGGGTAAAATGACCAAAATACCCCTATAGGGTAAAATGAC
* * *
40243639 CAAAATATCCCGATAG
66 CGAAATACCCCCATAG
* * * * * * *
40243655 GGTAAAATGATCGAAATACCCCTATAGGGTAGAATGACCGAAATATCCTTATAGGGTAAAATGAT
1 GGTAAAATGACCGAAATACCCCCATAGGGTAAAATGACCAAAATACCCCTATAGGGTAAAATGAC
*
40243720 CGAAATACTCTCCATAG
66 CGAAATAC-CCCCATAG
* * * * *
40243737 GGTAAAATGACCGAAATATCCCCATAGGATAGAATGACCAAAATA-CCCTCATAGGATAGAATGA
1 GGTAAAATGACCGAAATACCCCCATAGGGTAAAATGACCAAAATACCCCT-ATAGGGTAAAATGA
*
40243801 CCGAAATACCCCAATAGG
65 CCGAAATACCCCCATA-G
* * * *
40243819 GGTAAAATGACCGAAATACCCCCATAGGATAAATTGACCAAAATACCCCTATGGGGTAAAATAAC
1 GGTAAAATGACCGAAATACCCCCATAGGGTAAAATGACCAAAATACCCCTATAGGGTAAAATGAC
* * *
40243884 TGAAATACCCTCATAA
66 CGAAATACCCCCATAG
* * * * *
40243900 GATAAAATGACCAAAATACCCCCATAGGGTAAAATGATCGAAATACCGC-ATAGGGTAAAATGAC
1 GGTAAAATGACCGAAATACCCCCATAGGGTAAAATGACCAAAATACCCCTATAGGGTAAAATGAC
* *
40243964 CGAAATAGCCTCATAG
66 CGAAATACCCCCATAG
* * *
40243980 GGTACAATAACCGAAATACCTCCATAGGGTAAAAT
1 GGTAAAATGACCGAAATACCCCCATAGGGTAAAAT
40244015 AACTGTTATA
Statistics
Matches: 441, Mismatches: 74, Indels: 13
0.84 0.14 0.02
Matches are distributed among these distances:
79 14 0.03
80 85 0.19
81 206 0.47
82 132 0.30
83 4 0.01
ACGTcount: A:0.42, C:0.21, G:0.18, T:0.19
Consensus pattern (81 bp):
GGTAAAATGACCGAAATACCCCCATAGGGTAAAATGACCAAAATACCCCTATAGGGTAAAATGAC
CGAAATACCCCCATAG
Found at i:40244017 original size:27 final size:26
Alignment explanation
Indices: 40243414--40244014 Score: 610
Period size: 27 Copynumber: 22.3 Consensus size: 26
40243404 TCTAAAAATA
*
40243414 GGTAGAATGACCG-AATACCCCTATAG
1 GGTAAAATGACCGAAATACCCC-ATAG
* * * * *
40243440 GGTAGACTGACCGAAATACCTCGTAA
1 GGTAAAATGACCGAAATACCCCATAG
*
40243466 GGTATAATGACCGAAATACCCCTATAG
1 GGTAAAATGACCGAAATACCCC-ATAG
* *
40243493 GATACAATGACCGAAATACCCCCATAG
1 GGTAAAATGACCGAAATA-CCCCATAG
* *
40243520 GGTAAAATGATCAAAATACCCCTATAG
1 GGTAAAATGACCGAAATACCCC-ATAG
*
40243547 GGTAAAATGACTGAAATACCCCCATAG
1 GGTAAAATGACCGAAATA-CCCCATAG
* *
40243574 GATAAAATGATCGAAATACCCCCATAG
1 GGTAAAATGACCGAAATA-CCCCATAG
* **
40243601 GGTAAAATAACTAAAATACCCCAATAG
1 GGTAAAATGACCGAAATACCCC-ATAG
* *
40243628 GGTAAAATGACCAAAATATCCCGATAG
1 GGTAAAATGACCGAAATA-CCCCATAG
*
40243655 GGTAAAATGATCGAAATACCCCTATAG
1 GGTAAAATGACCGAAATACCCC-ATAG
* **
40243682 GGTAGAATGACCGAAATATCCTTATAG
1 GGTAAAATGACCGAAATA-CCCCATAG
*
40243709 GGTAAAATGATCGAAATACTCTCCATAG
1 GGTAAAATGACCGAAATAC-C-CCATAG
40243737 GGTAAAATGACCGAAATATCCCCATAG
1 GGTAAAATGACCGAAATA-CCCCATAG
* * *
40243764 GATAGAATGACCAAAATACCCTCATAG
1 GGTAAAATGACCGAAATACCC-CATAG
* *
40243791 GATAGAATGACCGAAATACCCCAATAGG
1 GGTAAAATGACCGAAATACCCC-ATA-G
40243819 GGTAAAATGACCGAAATACCCCCATAG
1 GGTAAAATGACCGAAATA-CCCCATAG
* * * *
40243846 GATAAATTGACCAAAATACCCCTATGG
1 GGTAAAATGACCGAAATACCCC-ATAG
* * *
40243873 GGTAAAATAACTGAAATACCCTCATAA
1 GGTAAAATGACCGAAATACCC-CATAG
* *
40243900 GATAAAATGACCAAAATACCCCCATAG
1 GGTAAAATGACCGAAATA-CCCCATAG
* *
40243927 GGTAAAATGATCGAAATACCGCATAG
1 GGTAAAATGACCGAAATACCCCATAG
*
40243953 GGTAAAATGACCGAAATAGCCTCATAG
1 GGTAAAATGACCGAAATA-CCCCATAG
* *
40243980 GGTACAATAACCGAAATACCTCCATAG
1 GGTAAAATGACCGAAATACC-CCATAG
40244007 GGTAAAAT
1 GGTAAAAT
40244015 AACTGTTATA
Statistics
Matches: 481, Mismatches: 73, Indels: 41
0.81 0.12 0.07
Matches are distributed among these distances:
26 79 0.16
27 338 0.70
28 59 0.12
29 5 0.01
ACGTcount: A:0.42, C:0.21, G:0.18, T:0.19
Consensus pattern (26 bp):
GGTAAAATGACCGAAATACCCCATAG
Found at i:40250121 original size:22 final size:23
Alignment explanation
Indices: 40250086--40250143 Score: 82
Period size: 22 Copynumber: 2.5 Consensus size: 23
40250076 GTGACTAAGC
*
40250086 GTGCAAGTGATAGTGGCACTACA
1 GTGCAAGTGATAGTGACACTACA
*
40250109 GTGCAAGTG-TAGTGACACTTCA
1 GTGCAAGTGATAGTGACACTACA
40250131 GTGCAAAGTGATA
1 GTGC-AAGTGATA
40250144 TCCACACGTC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
22 15 0.48
23 14 0.45
24 2 0.06
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (23 bp):
GTGCAAGTGATAGTGACACTACA
Found at i:40251114 original size:11 final size:11
Alignment explanation
Indices: 40251098--40251129 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
40251088 GTAACTAATA
*
40251098 GATCCAAGTCT
1 GATCCAAATCT
40251109 GATCCAAATCT
1 GATCCAAATCT
40251120 GATCCAAATC
1 GATCCAAATC
40251130 GTAGGATGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.34, C:0.28, G:0.12, T:0.25
Consensus pattern (11 bp):
GATCCAAATCT
Found at i:40251392 original size:18 final size:18
Alignment explanation
Indices: 40251354--40251391 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
40251344 TTTATTTATC
*
40251354 AATTTTAAGTTAATATAA
1 AATTTTAAGTTAAGATAA
40251372 AATTTTAAGTTTAAGATAA
1 AATTTTAAG-TTAAGATAA
40251391 A
1 A
40251392 TAGTTAGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (18 bp):
AATTTTAAGTTAAGATAA
Found at i:40258576 original size:47 final size:47
Alignment explanation
Indices: 40258507--40258601 Score: 172
Period size: 47 Copynumber: 2.0 Consensus size: 47
40258497 AAAAGCGGCA
40258507 TTAAGTCAATCTCGAATCAAATGAACCTTATCCTCAGTCTCGGCCAC
1 TTAAGTCAATCTCGAATCAAATGAACCTTATCCTCAGTCTCGGCCAC
* *
40258554 TTAAGTCAATCTCGAATCAAATGAACCTTATCTTCAGTCTCTGCCAC
1 TTAAGTCAATCTCGAATCAAATGAACCTTATCCTCAGTCTCGGCCAC
40258601 T
1 T
40258602 AACGCAGGAC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.31
Consensus pattern (47 bp):
TTAAGTCAATCTCGAATCAAATGAACCTTATCCTCAGTCTCGGCCAC
Found at i:40263916 original size:31 final size:31
Alignment explanation
Indices: 40263878--40263941 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
40263868 TAGAAATAAC
40263878 AAAAAAGA-AACCACAAAGGGAGAAAAAGAAA
1 AAAAAAGAGAACCACAAAGGG-GAAAAAGAAA
* *
40263909 AAAAAAGAGAAGCACAAAGGGGGAAAAGAAA
1 AAAAAAGAGAACCACAAAGGGGAAAAAGAAA
40263940 AA
1 AA
40263942 CAAATGTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 19 0.63
32 11 0.37
ACGTcount: A:0.69, C:0.08, G:0.23, T:0.00
Consensus pattern (31 bp):
AAAAAAGAGAACCACAAAGGGGAAAAAGAAA
Found at i:40264756 original size:20 final size:18
Alignment explanation
Indices: 40264709--40264815 Score: 60
Period size: 19 Copynumber: 5.8 Consensus size: 18
40264699 CAAGATAAAC
40264709 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
40264726 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
** *
40264746 ATTAAATTAATAAAATACT
1 ATTAAATTAAT-ATTTAAT
*
40264765 ATTAAGA-TAAGTATTAAAT
1 ATTAA-ATTAA-TATTTAAT
* *
40264784 -TTAATTTAATATTAAACT
1 ATTAAATTAATATTTAA-T
*
40264802 ATTAAAATAATATT
1 ATTAAATTAATATT
40264816 ATTTTTACAA
Statistics
Matches: 69, Mismatches: 11, Indels: 18
0.70 0.11 0.18
Matches are distributed among these distances:
17 15 0.22
18 9 0.13
19 27 0.39
20 18 0.26
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:40278260 original size:17 final size:17
Alignment explanation
Indices: 40278240--40278272 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
40278230 ATTTTCCCTC
40278240 TCTCTCTTTT-TCCTTTT
1 TCTCT-TTTTCTCCTTTT
40278257 TCTCTTTTTCTCCTTT
1 TCTCTTTTTCTCCTTT
40278273 CATTTTTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (17 bp):
TCTCTTTTTCTCCTTTT
Found at i:40281971 original size:39 final size:39
Alignment explanation
Indices: 40281928--40282007 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
40281918 TGGACAATGA
40281928 AAGTCCATTAGAGAATTCATCCTTCACTTGGACCAAGTG
1 AAGTCCATTAGAGAATTCATCCTTCACTTGGACCAAGTG
40281967 AAGTCCATTAGAGAATTCATCCTTCACTTGGACCAAGTG
1 AAGTCCATTAGAGAATTCATCCTTCACTTGGACCAAGTG
40282006 AA
1 AA
40282008 CTAGATTAGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.28
Consensus pattern (39 bp):
AAGTCCATTAGAGAATTCATCCTTCACTTGGACCAAGTG
Found at i:40282016 original size:39 final size:39
Alignment explanation
Indices: 40281933--40282016 Score: 141
Period size: 39 Copynumber: 2.2 Consensus size: 39
40281923 AATGAAAGTC
* *
40281933 CATTAGAGAATTCATCCTTCACTTGGACCAAGTGAAGTC
1 CATTAGAGAATTCATCCTTCACTTGGACCAAGTGAACTA
40281972 CATTAGAGAATTCATCCTTCACTTGGACCAAGTGAACTA
1 CATTAGAGAATTCATCCTTCACTTGGACCAAGTGAACTA
*
40282011 GATTAG
1 CATTAG
40282017 GATTTGGGTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (39 bp):
CATTAGAGAATTCATCCTTCACTTGGACCAAGTGAACTA
Found at i:40289351 original size:20 final size:19
Alignment explanation
Indices: 40289307--40289363 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 19
40289297 AACACTATGA
* *
40289307 ACCACTCCATTCACTTTCTT
1 ACCA-TCCATTTACTTACTT
40289327 ACCATTCCATTTACTTACTT
1 ACCA-TCCATTTACTTACTT
*
40289347 TCCATCTCATTTACTTA
1 ACCATC-CATTTACTTA
40289364 GCATAAACTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 2 0.06
20 30 0.94
ACGTcount: A:0.23, C:0.33, G:0.00, T:0.44
Consensus pattern (19 bp):
ACCATCCATTTACTTACTT
Found at i:40291598 original size:42 final size:39
Alignment explanation
Indices: 40291541--40291636 Score: 138
Period size: 42 Copynumber: 2.4 Consensus size: 39
40291531 GCCCAAATAT
40291541 ATATTAAAATATTAAACACATTATATATCAATAATTATAAAA
1 ATATTAAAATATTAAACACATTATATAT---TAATTATAAAA
*
40291583 ATATTAAAATATTAAACACATTATATATTATTTATAAAA
1 ATATTAAAATATTAAACACATTATATATTAATTATAAAA
*
40291622 ATTATAAAAATATTA
1 A-TATTAAAATATTA
40291637 TTATAATAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
39 11 0.22
40 12 0.24
42 28 0.55
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (39 bp):
ATATTAAAATATTAAACACATTATATATTAATTATAAAA
Found at i:40291650 original size:23 final size:24
Alignment explanation
Indices: 40291607--40291651 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
40291597 AACACATTAT
40291607 ATATTATTTATAAAAATTATAAAA
1 ATATTATTTATAAAAATTATAAAA
40291631 ATATTA-TTATAATAAA-TATAA
1 ATATTATTTATAA-AAATTATAA
40291652 TATTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
ATATTATTTATAAAAATTATAAAA
Found at i:40292207 original size:22 final size:23
Alignment explanation
Indices: 40292182--40292232 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
40292172 TTTAATTAAA
*
40292182 ATTAAAGAGAA-TATCATGTGTC
1 ATTAAAGAGAAGTATCACGTGTC
* *
40292204 ATTAAAGAGAAGTGTCACGTGTT
1 ATTAAAGAGAAGTATCACGTGTC
40292227 ATTAAA
1 ATTAAA
40292233 ATAAATCGTC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 11 0.44
23 14 0.56
ACGTcount: A:0.41, C:0.08, G:0.20, T:0.31
Consensus pattern (23 bp):
ATTAAAGAGAAGTATCACGTGTC
Found at i:40293174 original size:21 final size:21
Alignment explanation
Indices: 40293109--40293184 Score: 79
Period size: 21 Copynumber: 3.6 Consensus size: 21
40293099 GTTTCAAACT
40293109 TTTTTATTTTTAAATTAATGT-
1 TTTTTATTTTT-AATTAATGTA
*
40293130 TTTGATGATATTTT--TTAAT-TA
1 TTT--TTAT-TTTTAATTAATGTA
40293151 TTTTTATTTTTAATTAATGTA
1 TTTTTATTTTTAATTAATGTA
40293172 TTTTTATTTTTAA
1 TTTTTATTTTTAA
40293185 ATATTTTATT
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
18 4 0.09
19 3 0.07
20 6 0.13
21 26 0.57
23 3 0.07
24 4 0.09
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (21 bp):
TTTTTATTTTTAATTAATGTA
Found at i:40293182 original size:37 final size:40
Alignment explanation
Indices: 40293109--40293200 Score: 104
Period size: 42 Copynumber: 2.4 Consensus size: 40
40293099 GTTTCAAACT
*
40293109 TTTTTATTTTTAAATTAATGTTTTGATGATATTTTTTAATTA
1 TTTTTATTTTTAAATTAATGTTTT-AT-ATATTTTTTAAATA
40293151 TTTTTATTTTT-AATTAATGTATTT-T-TA-TTTTTAAATA
1 TTTTTATTTTTAAATTAATGT-TTTATATATTTTTTAAATA
*
40293188 -TTTTATTTATAAA
1 TTTTTATTTTTAAA
40293201 ATCAAATAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
36 9 0.20
37 11 0.24
38 2 0.04
40 1 0.02
41 9 0.20
42 14 0.30
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.65
Consensus pattern (40 bp):
TTTTTATTTTTAAATTAATGTTTTATATATTTTTTAAATA
Found at i:40293189 original size:16 final size:16
Alignment explanation
Indices: 40293141--40293200 Score: 50
Period size: 21 Copynumber: 3.5 Consensus size: 16
40293131 TTGATGATAT
*
40293141 TTTTTAATTATTTTTA
1 TTTTTAAATATTTTTA
40293157 TTTTTAATTAATGTATTTTTA
1 TTTTT-A--AA--TATTTTTA
40293178 TTTTTAAATA-TTTTA
1 TTTTTAAATATTTTTA
*
40293193 TTTATAAA
1 TTTTTAAA
40293201 ATCAAATAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
15 12 0.32
16 7 0.19
17 1 0.03
18 2 0.05
19 1 0.03
20 1 0.03
21 13 0.35
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (16 bp):
TTTTTAAATATTTTTA
Found at i:40293194 original size:21 final size:21
Alignment explanation
Indices: 40293148--40293195 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
40293138 TATTTTTTAA
*
40293148 TTATTTTTATTTTTAATTAAT
1 TTATTTTTATTTTTAAATAAT
* *
40293169 GTATTTTTATTTTTAAATATT
1 TTATTTTTATTTTTAAATAAT
40293190 TTATTT
1 TTATTT
40293196 ATAAAATCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (21 bp):
TTATTTTTATTTTTAAATAAT
Found at i:40293482 original size:143 final size:141
Alignment explanation
Indices: 40293266--40293532 Score: 342
Period size: 143 Copynumber: 1.9 Consensus size: 141
40293256 AATAATTAAA
* * * * * *
40293266 AAAAAAACTTGAAGCAACATGAAATAAAAAATACAAATGTAAGTAGTAGATGAACCAAACTGGAG
1 AAAAAAACTTGAAACAACATGAAATAAAAAACACAAATATAAGGAGTAGAGGAACCAAACTCGAG
* *
40293331 ACTCAAGGATATAATTACAACTATCTAACCATCTAA-TGGAAA-AACTAGTATGTTAAAAAATAT
66 ACTCAAGGATATAATTACAACTATCTAACAATCTAACT--AAATAACTAATATGTTAAAAAATAT
40293394 TAATTAAAAATTT
129 TAATTAAAAATTT
* * *
40293407 AAAAAAA-TTGAAACAACATGAAATAAAAAAACACATAAATATGAGGAGTAGAGGTATCAAACTC
1 AAAAAAACTTGAAACAACATGAAAT-AAAAAACAC--AAATATAAGGAGTAGAGGAACCAAACTC
* * *
40293471 GAGACTTAAGGATGTAATTGCAACTATCTAACAATCTAACTAAATAACTAATATGTTAAAAA
63 GAGACTCAAGGATATAATTACAACTATCTAACAATCTAACTAAATAACTAATATGTTAAAAA
40293533 TTAAAAAACT
Statistics
Matches: 107, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
140 16 0.15
141 15 0.14
142 3 0.03
143 72 0.67
144 1 0.01
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.24
Consensus pattern (141 bp):
AAAAAAACTTGAAACAACATGAAATAAAAAACACAAATATAAGGAGTAGAGGAACCAAACTCGAG
ACTCAAGGATATAATTACAACTATCTAACAATCTAACTAAATAACTAATATGTTAAAAAATATTA
ATTAAAAATTT
Found at i:40300076 original size:26 final size:26
Alignment explanation
Indices: 40300047--40300158 Score: 98
Period size: 27 Copynumber: 4.2 Consensus size: 26
40300037 TGATTTTTGC
*
40300047 AAAATAGGGGAAAAATTATAAAATTTAA
1 AAAATAGGGGAAAAACTATAAAA-TT-A
* * * *
40300075 AAAAAATGGGCAAAACTATAAAATAA
1 AAAATAGGGGAAAAACTATAAAATTA
*
40300101 AAAATAGGGGTAAAACTATAAAATTAA
1 AAAATAGGGGAAAAACTATAAAATT-A
** * *
40300128 AAAATAAAGGCAAAACTGTAAAATCTA
1 AAAATAGGGGAAAAACTATAAAAT-TA
40300155 AAAA
1 AAAA
40300159 ATAGTGGCAA
Statistics
Matches: 69, Mismatches: 13, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
26 22 0.32
27 27 0.39
28 20 0.29
ACGTcount: A:0.62, C:0.05, G:0.12, T:0.20
Consensus pattern (26 bp):
AAAATAGGGGAAAAACTATAAAATTA
Found at i:40300121 original size:54 final size:54
Alignment explanation
Indices: 40300047--40300162 Score: 155
Period size: 54 Copynumber: 2.1 Consensus size: 54
40300037 TGATTTTTGC
* *
40300047 AAAATAGGGGAAAAATTATAAAATTTAAAAAA-AATGGGCAAAACTATAAAA-TAA
1 AAAATAGGGGAAAAACTATAAAA-TTAAAAAATAA-AGGCAAAACTATAAAACTAA
* *
40300101 AAAATAGGGGTAAAACTATAAAATTAAAAAATAAAGGCAAAACTGTAAAATCTAA
1 AAAATAGGGGAAAAACTATAAAATTAAAAAATAAAGGCAAAACTATAAAA-CTAA
40300156 AAAATAG
1 AAAATAG
40300163 TGGCAAAATT
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
53 22 0.40
54 23 0.42
55 10 0.18
ACGTcount: A:0.62, C:0.05, G:0.13, T:0.20
Consensus pattern (54 bp):
AAAATAGGGGAAAAACTATAAAATTAAAAAATAAAGGCAAAACTATAAAACTAA
Found at i:40300181 original size:28 final size:27
Alignment explanation
Indices: 40300047--40300179 Score: 142
Period size: 28 Copynumber: 4.9 Consensus size: 27
40300037 TGATTTTTGC
* *
40300047 AAAATAGGGGAAAAATTATAAAATTTAA
1 AAAATAGGGGCAAAACTATAAAA-TTAA
* *
40300075 AAAAAATGGGCAAAACTATAAAA-TAA
1 AAAATAGGGGCAAAACTATAAAATTAA
*
40300101 AAAATAGGGGTAAAACTATAAAATTAA
1 AAAATAGGGGCAAAACTATAAAATTAA
** *
40300128 AAAATAAAGGCAAAACTGTAAAATCTAA
1 AAAATAGGGGCAAAACTATAAAAT-TAA
* * *
40300156 AAAATAGTGGCAAAATTGTAAAAT
1 AAAATAGGGGCAAAACTATAAAAT
40300180 CTGAAAAACA
Statistics
Matches: 89, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
26 23 0.26
27 23 0.26
28 43 0.48
ACGTcount: A:0.60, C:0.05, G:0.14, T:0.21
Consensus pattern (27 bp):
AAAATAGGGGCAAAACTATAAAATTAA
Found at i:40300589 original size:43 final size:43
Alignment explanation
Indices: 40300538--40300759 Score: 297
Period size: 43 Copynumber: 5.2 Consensus size: 43
40300528 TCTTTGGAAG
*
40300538 CGCCGCTAAAGGTCATGTTCTTTAGCGACGCTTTTCTTACAAA
1 CGCCGCTAAAGGTCATGTTCTTTAGCGACGCTTTTCTCACAAA
* ** *
40300581 CGTCGCTAAAGGTCATGTTCTTTAGCGGTGCTTTTCCCACAAA
1 CGCCGCTAAAGGTCATGTTCTTTAGCGACGCTTTTCTCACAAA
* * * * * *
40300624 TGCCGCTAAAGGTCGTGTTTTTTAGCGTCGCTTTCCT-TCAAA
1 CGCCGCTAAAGGTCATGTTCTTTAGCGACGCTTTTCTCACAAA
*
40300666 CGCCGCTAAAGGTCATGTTCTTTAGCGACACTTTTCTCACAAA
1 CGCCGCTAAAGGTCATGTTCTTTAGCGACGCTTTTCTCACAAA
40300709 CGCCGCTAAAGGTCATGTTCTTTAGCTG-CGCTTTT-TCCACAAA
1 CGCCGCTAAAGGTCATGTTCTTTAGC-GACGCTTTTCT-CACAAA
40300752 CGCCGCTA
1 CGCCGCTA
40300760 TTATTTGGCT
Statistics
Matches: 154, Mismatches: 22, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
42 36 0.23
43 117 0.76
44 1 0.01
ACGTcount: A:0.21, C:0.27, G:0.19, T:0.32
Consensus pattern (43 bp):
CGCCGCTAAAGGTCATGTTCTTTAGCGACGCTTTTCTCACAAA
Found at i:40300591 original size:71 final size:71
Alignment explanation
Indices: 40300467--40300603 Score: 222
Period size: 71 Copynumber: 1.9 Consensus size: 71
40300457 TAGAAATAAA
* * *
40300467 CGCCTCTAAAGGTCATGTTCTTTAGCGGCGCTTTTCCTACAAACGCAGTTAAAGGTCATGTTCTT
1 CGCCGCTAAAGGTCATGTTCTTTAGCGACGCTTTTCCTACAAACGCAGCTAAAGGTCATGTTCTT
40300532 TGGAAG
66 TGGAAG
*
40300538 CGCCGCTAAAGGTCATGTTCTTTAGCGACGCTTTTCTTACAAACGTC-GCTAAAGGTCATGTTCT
1 CGCCGCTAAAGGTCATGTTCTTTAGCGACGCTTTTCCTACAAACG-CAGCTAAAGGTCATGTTCT
40300602 TT
65 TT
40300604 AGCGGTGCTT
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
71 60 0.98
72 1 0.02
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.34
Consensus pattern (71 bp):
CGCCGCTAAAGGTCATGTTCTTTAGCGACGCTTTTCCTACAAACGCAGCTAAAGGTCATGTTCTT
TGGAAG
Found at i:40300688 original size:85 final size:85
Alignment explanation
Indices: 40300538--40300759 Score: 295
Period size: 85 Copynumber: 2.6 Consensus size: 85
40300528 TCTTTGGAAG
* * *
40300538 CGCCGCTAAAGGTCATGTTCTTTAGCGACGCTTTTCTTACAAACGTCGCTAAAGGTCATGTTCTT
1 CGCCGCTAAAGGTCATGTTCTTTAGCGTCGCTTTCCTT-CAAACGCCGCTAAAGGTCATGTTCTT
***
40300603 TAGCGGTGCTTTTCCCACAAA
65 TAGCGACACTTTTCCCACAAA
* * *
40300624 TGCCGCTAAAGGTCGTGTTTTTTAGCGTCGCTTTCCTTCAAACGCCGCTAAAGGTCATGTTCTTT
1 CGCCGCTAAAGGTCATGTTCTTTAGCGTCGCTTTCCTTCAAACGCCGCTAAAGGTCATGTTCTTT
*
40300689 AGCGACACTTTTCTCACAAA
66 AGCGACACTTTTCCCACAAA
*
40300709 CGCCGCTAAAGGTCATGTTCTTTAGC-TGCGCTTTTTCC-ACAAACGCCGCTA
1 CGCCGCTAAAGGTCATGTTCTTTAGCGT-CGC--TTTCCTTCAAACGCCGCTA
40300760 TTATTTGGCT
Statistics
Matches: 119, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
84 1 0.01
85 68 0.57
86 45 0.38
87 5 0.04
ACGTcount: A:0.21, C:0.27, G:0.19, T:0.32
Consensus pattern (85 bp):
CGCCGCTAAAGGTCATGTTCTTTAGCGTCGCTTTCCTTCAAACGCCGCTAAAGGTCATGTTCTTT
AGCGACACTTTTCCCACAAA
Found at i:40301131 original size:21 final size:21
Alignment explanation
Indices: 40301107--40301177 Score: 88
Period size: 21 Copynumber: 3.4 Consensus size: 21
40301097 TTCTGCGCTG
*
40301107 CTCTGCTTCCCTTGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* *
40301128 CTCTGCTTCTCTCGCTACAGC
1 CTCTGCTTCCCTCGCTGCAGC
* * *
40301149 CTCTACTTCCCTCACTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
40301170 CTCTGCTT
1 CTCTGCTT
40301178 TAAGTTGTAG
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.07, C:0.45, G:0.14, T:0.34
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:40304985 original size:270 final size:268
Alignment explanation
Indices: 40304505--40305137 Score: 777
Period size: 270 Copynumber: 2.3 Consensus size: 268
40304495 TTAATTTCTA
* *
40304505 AAATTTTTCTAAGTTAAAAATCGTATACAGAAACGACACCGTTTACACATTATTTTAATACCTTT
1 AAATTTTTCTAAGTTAAAAATCGTGTACAGAAACGACACCGTTTACACACTATTTTAATACCTTT
* * * *
40304570 TGCGGCATTTTCTGTAAAAACGCCGCTATTGCTTCCACATCTTCGGCGTTTTCCTAAAAACGCCA
66 TGCGGCATTTACTGTAAAAACGCCACTATTGCTTCCAAATCTCCGGCGTTTTCCTAAAAACGCCA
* * * * * * *
40304635 CTAAAAGTTCAAGTTTTAAATAGAAACAATGCCGTTTTGTTAGTCTCAAATTGCATTATTTCTTG
131 CAAAAAGTTAAAGTTGTAAATAGAAACAACGCCATTTTGCTAGTCTCAAATTGCATTATTTCTAG
** *
40304700 CGTTTTATGTAAAAACGCCACTAATACCTAATTTACTTTAACCCAAACGGTGATGTTTTAAATAA
196 CGTTTTATGTAAAAACGCCACTAATACCTAACGTACTTTAACCCAAACGGTGACGTTTTAAATAA
40304765 ATAAATCT
261 ATAAATCT
* * *
40304773 CAAATTTTTCTAAGTTAAAAATCGTGTACAGAAATGGCACCGTTTAGACACTATTTTAATACCCT
1 -AAATTTTTCTAAGTTAAAAATCGTGTACAGAAACGACACCGTTTACACACTATTTTAATA-CCT
** * *
40304838 TTTGCGGTGTTTACTGTACAAACGCCACTATTGCTTCCAAAGT-TCCGGCATTTTTCC-AAAAAC
64 TTTGCGGCATTTACTGTAAAAACGCCACTATTGCTTCCAAA-TCTCCGGC-GTTTTCCTAAAAAC
* * * *
40304901 GCCACAAAAATTTAAAGTTGTAAATAGAAACGACGTCATTTTGCTAGTCTCAAATTGCATTGTTT
127 GCCACAAAAAGTTAAAGTTGTAAATAGAAACAACGCCATTTTGCTAGTCTCAAATTGCATTATTT
* * *
40304966 CTAGCGTTTTATGTAAAAACGCCACTAATACTTAACGTACTTTAAGCCAAACTGTGACGTTTTAA
192 CTAGCGTTTTATGTAAAAACGCCACTAATACCTAACGTACTTTAACCCAAACGGTGACGTTTTAA
* *
40305031 GTAAATAATTCT
257 ATAAATAAATCT
* * * **** * ** *
40305043 AAACTTTTTATAAGTTAAAAATCGTGGAGAGAAACGGGGTCGTTTACTCAAAATTTTAAGACACT
1 AAA-TTTTTCTAAGTTAAAAATCGTGTACAGAAACGACACCGTTTACACACTATTTTAATAC-CT
* *
40305108 TTTGCGGCGTTT-CTTGTAAAAACACCACTA
64 TTTGCGGCATTTAC-TGTAAAAACGCCACTA
40305138 ATGCATCCCA
Statistics
Matches: 311, Mismatches: 47, Indels: 11
0.84 0.13 0.03
Matches are distributed among these distances:
269 60 0.19
270 244 0.78
271 7 0.02
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34
Consensus pattern (268 bp):
AAATTTTTCTAAGTTAAAAATCGTGTACAGAAACGACACCGTTTACACACTATTTTAATACCTTT
TGCGGCATTTACTGTAAAAACGCCACTATTGCTTCCAAATCTCCGGCGTTTTCCTAAAAACGCCA
CAAAAAGTTAAAGTTGTAAATAGAAACAACGCCATTTTGCTAGTCTCAAATTGCATTATTTCTAG
CGTTTTATGTAAAAACGCCACTAATACCTAACGTACTTTAACCCAAACGGTGACGTTTTAAATAA
ATAAATCT
Found at i:40305245 original size:270 final size:270
Alignment explanation
Indices: 40304505--40305214 Score: 669
Period size: 270 Copynumber: 2.6 Consensus size: 270
40304495 TTAATTTCTA
* ** * ** *
40304505 AAATTTTTCTAAGTTAAAAATCGTATACAGAAACGACACCGTTTACACATTATTTTAATAC-CTT
1 AAATTTTTATAAGTTAAAAATCGTGGACAGAAACGGCACCGTTTACACAAAATTTTAAGACACTT
* * * * * * * * * *
40304569 TTGCGGCATTTTCTGTAAAAACGCCGCTATTGCTTCCACA-TCTTCGGCGTTTT-CCTAAAAACG
66 TTGCGGCGTTTACTGTAAAAACACCACTAATGCTCCCAAAGT-TCCGGCATTTTAAC-AAAAACG
* * * * * * * * * *
40304632 CCACTAAAAGTTCAAGTTTTAAATAGAAACAATGCCGTTTTGTTAGTCTCAAATTGCATTA-TTT
129 CCACAAAAATTTAAACTTGTAAATAAAAACGACGCCATTTTGCTAGTCTCAAATTGCA-TAGTTT
* ** *
40304696 CTTGCGTTTTATGTAAAAACGCCACTAATACCTAATTTACTTTAACCCAAACGGTGATGTTTTAA
193 CTAGCGTTTTATGTAAAAACGCCACTAATACCTAACGTACTTTAACCCAAACGGTGACGTTTTAA
40304761 ATAAATAAATCTC
258 ATAAATAAATCTC
* * * * ** * *
40304774 AAATTTTTCTAAGTTAAAAATCGTGTACAGAAATGGCACCGTTTAGACACTATTTTAATACCCTT
1 AAATTTTTATAAGTTAAAAATCGTGGACAGAAACGGCACCGTTTACACAAAATTTTAAGACACTT
* * * * * **
40304839 TTGCGGTGTTTACTGTACAAACGCCACTATTGCTTCCAAAGTTCCGGCATTTTTCCAAAAACGCC
66 TTGCGGCGTTTACTGTAAAAACACCACTAATGCTCCCAAAGTTCCGGCATTTTAACAAAAACGCC
* * * *
40304904 ACAAAAATTTAAAGTTGTAAATAGAAACGACGTCATTTTGCTAGTCTCAAATTGCATTGTTTCTA
131 ACAAAAATTTAAACTTGTAAATAAAAACGACGCCATTTTGCTAGTCTCAAATTGCATAGTTTCTA
* * * *
40304969 GCGTTTTATGTAAAAACGCCACTAATACTTAACGTACTTTAAGCCAAACTGTGACGTTTTAAGTA
196 GCGTTTTATGTAAAAACGCCACTAATACCTAACGTACTTTAACCCAAACGGTGACGTTTTAAATA
*
40305034 AATAATTCT-
261 AATAAATCTC
* *** *
40305043 AAACTTTTTATAAGTTAAAAATCGTGGAGAGAAACGGGGTCGTTTACTCAAAATTTTAAGACACT
1 AAA-TTTTTATAAGTTAAAAATCGTGGACAGAAACGGCACCGTTTACACAAAATTTTAAGACACT
* * ** * *
40305108 TTTGCGGCGTTT-CTTGTAAAAACACCACTAATGCATCCCACATTTGTGGCGTTTTAATAAAAAC
65 TTTGCGGCGTTTAC-TGTAAAAACACCACTAATGC-TCCCAAAGTTCCGGCATTTTAACAAAAAC
* * * *
40305172 GCCACTAAAATTTTAACTAT-TCATTCAAAAACGACGCCATTTT
128 GCCACAAAAATTTAAACT-TGTAAAT-AAAAACGACGCCATTTT
40305215 CTTAAGCTAT
Statistics
Matches: 367, Mismatches: 65, Indels: 15
0.82 0.15 0.03
Matches are distributed among these distances:
269 61 0.17
270 249 0.68
271 41 0.11
272 16 0.04
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (270 bp):
AAATTTTTATAAGTTAAAAATCGTGGACAGAAACGGCACCGTTTACACAAAATTTTAAGACACTT
TTGCGGCGTTTACTGTAAAAACACCACTAATGCTCCCAAAGTTCCGGCATTTTAACAAAAACGCC
ACAAAAATTTAAACTTGTAAATAAAAACGACGCCATTTTGCTAGTCTCAAATTGCATAGTTTCTA
GCGTTTTATGTAAAAACGCCACTAATACCTAACGTACTTTAACCCAAACGGTGACGTTTTAAATA
AATAAATCTC
Found at i:40305623 original size:7 final size:7
Alignment explanation
Indices: 40305595--40305663 Score: 57
Period size: 7 Copynumber: 9.4 Consensus size: 7
40305585 CCCTAAATTA
40305595 TTAACCC
1 TTAACCC
40305602 ATTAACCCC
1 -TTAA-CCC
*
40305611 TAAACCC
1 TTAACCC
40305618 TTAACCC
1 TTAACCC
*
40305625 GTAACCC
1 TTAACCC
*
40305632 TTAAATCC
1 TT-AACCC
*
40305640 TAAACCC
1 TTAACCC
*
40305647 CTAACCC
1 TTAACCC
*
40305654 CTAACCC
1 TTAACCC
40305661 TTA
1 TTA
40305664 TATCCCAAAC
Statistics
Matches: 49, Mismatches: 10, Indels: 5
0.77 0.16 0.08
Matches are distributed among these distances:
7 34 0.69
8 12 0.24
9 3 0.06
ACGTcount: A:0.33, C:0.42, G:0.01, T:0.23
Consensus pattern (7 bp):
TTAACCC
Found at i:40305623 original size:15 final size:14
Alignment explanation
Indices: 40305596--40305663 Score: 73
Period size: 15 Copynumber: 4.6 Consensus size: 14
40305586 CCTAAATTAT
40305596 TAACCCATTAACCCC
1 TAACCC-TTAACCCC
*
40305611 TAAACCCTTAACCCG
1 T-AACCCTTAACCCC
**
40305626 TAACCCTTAAATCC
1 TAACCCTTAACCCC
*
40305640 TAAACCCCTAACCCC
1 T-AACCCTTAACCCC
40305655 TAACCCTTA
1 TAACCCTTA
40305664 TATCCCAAAC
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
14 18 0.42
15 20 0.47
16 5 0.12
ACGTcount: A:0.34, C:0.43, G:0.01, T:0.22
Consensus pattern (14 bp):
TAACCCTTAACCCC
Done.