Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009617.1 Hibiscus syriacus cultivar Beakdansim tig00117005_pilon, whole genome shotgun sequence
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: 3386631
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 16
Found at i:3247454 original size:27 final size:27
Alignment explanation
Indices: 3247414--3247491 Score: 97
Period size: 27 Copynumber: 2.9 Consensus size: 27
3247404 AAACGTTTTA
* *
3247414 TACTTAATTTTAATTTATAAAAATATG
1 TACTTTATTGTAATTTATAAAAATATG
* *
3247441 TACTTTTTTGTAATTTATAAAAAGTTTG
1 TACTTTATTGTAATTTATAAAAA-TATG
3247469 TACTTTATTGTAA-TTA-AAAAATA
1 TACTTTATTGTAATTTATAAAAATA
3247492 GTTTTATCCT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
25 1 0.02
26 5 0.11
27 23 0.52
28 15 0.34
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.49
Consensus pattern (27 bp):
TACTTTATTGTAATTTATAAAAATATG
Found at i:3247519 original size:84 final size:84
Alignment explanation
Indices: 3247367--3247520 Score: 186
Period size: 84 Copynumber: 1.8 Consensus size: 84
3247357 TCTTTTATCA
* * * * * * * *
3247367 TAATTTATAAATAGTTTTGTATTTTATTTTAATTTATAAACGTTTTATACTTAATTTTAATTTAT
1 TAATTTATAAAAAGTTTTGTACTTTATTGTAATTAAAAAAAGTTTTATACTTAATATAAATTTAT
3247432 AAAAATATGTACTTTTTTG
66 AAAAATATGTACTTTTTTG
* *
3247451 TAATTTATAAAAAG-TTTGTACTTTATTGTAATTAAAAAATAGTTTTATCCTTTATGATAAATTT
1 TAATTTATAAAAAGTTTTGTACTTTATTGTAATTAAAAAA-AGTTTTATACTTAAT-ATAAATTT
3247515 -TAAAAA
64 ATAAAAA
3247521 GTTTAGCCTT
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
83 21 0.36
84 31 0.53
85 6 0.10
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.51
Consensus pattern (84 bp):
TAATTTATAAAAAGTTTTGTACTTTATTGTAATTAAAAAAAGTTTTATACTTAATATAAATTTAT
AAAAATATGTACTTTTTTG
Found at i:3247541 original size:28 final size:27
Alignment explanation
Indices: 3247443--3247545 Score: 84
Period size: 28 Copynumber: 3.6 Consensus size: 27
3247433 AAAATATGTA
* *
3247443 CTTTTTTGTAATTTATAAAAAGTTT-GTA
1 CTTTATTGTAATTT-TAAAAAGTTTAG-C
** *
3247471 CTTTATTGTAATTAAAAAATAGTTTTATC
1 CTTTATTGTAATTTTAAAA-AG-TTTAGC
3247500 CTTTA-TGATAAATTTTAAAAAGTTTAGC
1 CTTTATTG-T-AATTTTAAAAAGTTTAGC
3247528 CTTTTATTGTAATTTTAA
1 C-TTTATTGTAATTTTAA
3247546 GTTTTTTAGT
Statistics
Matches: 60, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
27 4 0.07
28 30 0.50
29 16 0.27
30 10 0.17
ACGTcount: A:0.35, C:0.06, G:0.09, T:0.50
Consensus pattern (27 bp):
CTTTATTGTAATTTTAAAAAGTTTAGC
Found at i:3248641 original size:24 final size:24
Alignment explanation
Indices: 3248586--3248642 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
3248576 TTCAACATTG
3248586 TGAATTGTGTCTTGTAACTTATGT
1 TGAATTGTGTCTTGTAACTTATGT
** * *
3248610 TGTGTTGTTTCTTGTAACTTGTGT
1 TGAATTGTGTCTTGTAACTTATGT
3248634 CT-AATTGTG
1 -TGAATTGTG
3248643 CCTAAACTAG
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
24 24 0.96
25 1 0.04
ACGTcount: A:0.16, C:0.09, G:0.23, T:0.53
Consensus pattern (24 bp):
TGAATTGTGTCTTGTAACTTATGT
Found at i:3248765 original size:21 final size:21
Alignment explanation
Indices: 3248693--3248787 Score: 82
Period size: 21 Copynumber: 4.5 Consensus size: 21
3248683 AGGTTAAGAT
* * *
3248693 CTTTTGATAAAAGGAATTAAC
1 CTTTTCATGAAAGGACTTAAC
* * * **
3248714 CTTTTGATTAAAAGACTTCTC
1 CTTTTCATGAAAGGACTTAAC
*
3248735 CTTTTAATGAAAGGACTTAAC
1 CTTTTCATGAAAGGACTTAAC
* * *
3248756 CTTTTCATGAAAGAATTTAAT
1 CTTTTCATGAAAGGACTTAAC
3248777 CTTTTCATGAA
1 CTTTTCATGAA
3248788 GAGAATTGTT
Statistics
Matches: 60, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 60 1.00
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.39
Consensus pattern (21 bp):
CTTTTCATGAAAGGACTTAAC
Found at i:3252217 original size:21 final size:21
Alignment explanation
Indices: 3252193--3252238 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
3252183 AGGTTAAAAT
3252193 CTTTTGATGAAAGAAATTAAC
1 CTTTTGATGAAAGAAATTAAC
*
3252214 CTTTTGATGAATGAAATTAAC
1 CTTTTGATGAAAGAAATTAAC
3252235 CTTT
1 CTTT
3252239 CGATTAAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (21 bp):
CTTTTGATGAAAGAAATTAAC
Found at i:3252301 original size:22 final size:22
Alignment explanation
Indices: 3252254--3252308 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 22
3252244 AAAAGACTTC
* *
3252254 TCTTTTTGATGAAAGGGTTTAA
1 TCTTTTTCATGAAAGGATTTAA
*
3252276 -CTTTTTCATGAAAGTATTTAA
1 TCTTTTTCATGAAAGGATTTAA
3252297 TC-TTTTCATGAA
1 TCTTTTTCATGAA
3252309 GAGAATTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 28 0.97
22 1 0.03
ACGTcount: A:0.29, C:0.09, G:0.15, T:0.47
Consensus pattern (22 bp):
TCTTTTTCATGAAAGGATTTAA
Found at i:3253499 original size:16 final size:16
Alignment explanation
Indices: 3253478--3253512 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3253468 TTACCCGACC
* *
3253478 TGTTATTAACCTGATA
1 TGTTATAAACATGATA
3253494 TGTTATAAACATGATA
1 TGTTATAAACATGATA
3253510 TGT
1 TGT
3253513 AGTTTACTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (16 bp):
TGTTATAAACATGATA
Found at i:3253579 original size:16 final size:16
Alignment explanation
Indices: 3253560--3253590 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3253550 AACTGATTTA
*
3253560 ATATTTACTTAACTTG
1 ATATTTACCTAACTTG
3253576 ATATTTACCTAACTT
1 ATATTTACCTAACTT
3253591 ATAAGTTACA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.16, G:0.03, T:0.48
Consensus pattern (16 bp):
ATATTTACCTAACTTG
Found at i:3254620 original size:17 final size:18
Alignment explanation
Indices: 3254607--3254754 Score: 103
Period size: 19 Copynumber: 8.2 Consensus size: 18
3254597 ATGTATACTT
3254607 TATAATA-ATATATAATA
1 TATAATATATATATAATA
3254624 TAT-ATATATATAT-ATA
1 TATAATATATATATAATA
** *
3254640 TATATATATATATATGTGTG
1 TATA-ATATATATAT-AATA
* * *
3254660 TGTGTATATATATATATTA
1 TAT-AATATATATATAATA
* *
3254679 TATACT-TATAAGTATAATG
1 TATAATATAT-A-TATAATA
3254698 TAT-ATATATATAT-ATA
1 TATAATATATATATAATA
3254714 TAT-ATATATATATATATA
1 TATAATATATATATA-ATA
*
3254732 TATAACATATATATATATA
1 TATAATATATATATA-ATA
3254751 TATA
1 TATA
3254755 TTAACATATA
Statistics
Matches: 104, Mismatches: 15, Indels: 22
0.74 0.11 0.16
Matches are distributed among these distances:
16 24 0.23
17 15 0.14
18 20 0.19
19 32 0.31
20 13 0.12
ACGTcount: A:0.47, C:0.01, G:0.05, T:0.47
Consensus pattern (18 bp):
TATAATATATATATAATA
Found at i:3254765 original size:2 final size:2
Alignment explanation
Indices: 3254614--3254755 Score: 161
Period size: 2 Copynumber: 73.0 Consensus size: 2
3254604 CTTTATAATA
3254614 AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
3254655 GT GT GT GT GT AT AT AT AT AT AT -T AT AT ACT -T AT A- AGT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT A-T AT AT
*
3254695 AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
3254736 AC AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
3254756 TAACATATAT
Statistics
Matches: 127, Mismatches: 5, Indels: 16
0.86 0.03 0.11
Matches are distributed among these distances:
1 6 0.05
2 119 0.94
3 2 0.02
ACGTcount: A:0.46, C:0.01, G:0.05, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3254768 original size:10 final size:11
Alignment explanation
Indices: 3254703--3254765 Score: 65
Period size: 12 Copynumber: 5.5 Consensus size: 11
3254693 TAATGTATAT
*
3254703 ATATATATATAT
1 ATATATATA-AC
*
3254715 ATATATATATAT
1 ATATATATA-AC
3254727 ATATATATAAC
1 ATATATATAAC
*
3254738 ATATATAT-AT
1 ATATATATAAC
3254748 ATATATATTAAC
1 ATATATA-TAAC
3254760 ATATAT
1 ATATAT
3254766 TAAAATTATT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
10 8 0.17
11 10 0.22
12 28 0.61
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (11 bp):
ATATATATAAC
Found at i:3254976 original size:71 final size:69
Alignment explanation
Indices: 3254877--3255029 Score: 186
Period size: 71 Copynumber: 2.2 Consensus size: 69
3254867 CCTACATGTT
*
3254877 TATTTATTTA-A-TTATTAATTTATTCAATTTAGTCCTTAAAATTATACTTT-TATATGAAATTA
1 TATTTATTTATATTTATTAATTTATTCAATTTAGTCATTAAAATTAT-CTTTGTATATGAAATTA
3254939 GCCCA
65 GCCCA
* * * *
3254944 TATTTATTTATATTTTTGTAATTTACTTCAATTTTGTCATTGAAATTATGTTTGTATATGAAATT
1 TATTTATTTATATTTAT-TAATTTA-TTCAATTTAGTCATTAAAATTATCTTTGTATATGAAATT
* *
3255009 TGCTCA
64 AGCCCA
*
3255015 TACTTATTTATATTT
1 TATTTATTTATATTT
3255030 GATCCCTCAG
Statistics
Matches: 73, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
67 10 0.14
68 1 0.01
69 3 0.04
70 10 0.14
71 49 0.67
ACGTcount: A:0.31, C:0.08, G:0.07, T:0.54
Consensus pattern (69 bp):
TATTTATTTATATTTATTAATTTATTCAATTTAGTCATTAAAATTATCTTTGTATATGAAATTAG
CCCA
Found at i:3255209 original size:16 final size:16
Alignment explanation
Indices: 3255188--3255221 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
3255178 TAAAAATTAC
3255188 AATTCATCGTTCATGA
1 AATTCATCGTTCATGA
3255204 AATTCATCGTTCATGA
1 AATTCATCGTTCATGA
3255220 AA
1 AA
3255222 GAGGAAAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (16 bp):
AATTCATCGTTCATGA
Found at i:3258610 original size:2 final size:2
Alignment explanation
Indices: 3258603--3258642 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3258593 TTAGTACACA
3258603 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3258643 GAAAAGGACT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3260934 original size:2 final size:2
Alignment explanation
Indices: 3260927--3260968 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3260917 ATACTAGCCA
3260927 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3260969 TCTCGATGAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3261210 original size:30 final size:32
Alignment explanation
Indices: 3261175--3261242 Score: 97
Period size: 30 Copynumber: 2.2 Consensus size: 32
3261165 AAAATATAAT
* *
3261175 ATATGATTTA-TTTTGTTTTTA-TTAATTAAG
1 ATATGATTGACTTTAGTTTTTATTTAATTAAG
3261205 ATATGA-TGACTTTAGTTTTTATTTAATTAAG
1 ATATGATTGACTTTAGTTTTTATTTAATTAAG
3261236 ATATGAT
1 ATATGAT
3261243 CATCATAGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 2 0.06
30 16 0.48
31 15 0.45
ACGTcount: A:0.32, C:0.01, G:0.12, T:0.54
Consensus pattern (32 bp):
ATATGATTGACTTTAGTTTTTATTTAATTAAG
Found at i:3261391 original size:27 final size:28
Alignment explanation
Indices: 3261359--3261430 Score: 74
Period size: 27 Copynumber: 2.5 Consensus size: 28
3261349 TATTTTTAAT
*
3261359 AAATTAAAATAAAAATGAAATAT-TTTA
1 AAATTAAAATAAAAATAAAATATATTTA
** *
3261386 AAATTAACTTAATAATAAAATATATTTA
1 AAATTAAAATAAAAATAAAATATATTTA
*
3261414 ATAAGTTAATATAAAAA
1 A-AA-TTAAAATAAAAA
3261431 ATATTTTTTT
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
27 19 0.54
28 5 0.14
29 2 0.06
30 9 0.26
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (28 bp):
AAATTAAAATAAAAATAAAATATATTTA
Found at i:3261430 original size:25 final size:26
Alignment explanation
Indices: 3261376--3261459 Score: 84
Period size: 25 Copynumber: 3.2 Consensus size: 26
3261366 AATAAAAATG
*
3261376 AAATATTTTAAAATTAACTTAATA-AT-A
1 AAATATTTT--AA-TAAGTTAATATATAA
3261403 AAATATATTTAATAAGTTAATATA-AA
1 AAATAT-TTTAATAAGTTAATATATAA
**
3261429 AAATATTTTTTTAAGTTAATATATAA
1 AAATATTTTAATAAGTTAATATATAA
3261455 AAATA
1 AAATA
3261460 ATTATGAATT
Statistics
Matches: 50, Mismatches: 3, Indels: 9
0.81 0.05 0.15
Matches are distributed among these distances:
25 24 0.48
26 17 0.34
27 6 0.12
28 3 0.06
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.42
Consensus pattern (26 bp):
AAATATTTTAATAAGTTAATATATAA
Found at i:3262308 original size:58 final size:59
Alignment explanation
Indices: 3262245--3262358 Score: 140
Period size: 58 Copynumber: 1.9 Consensus size: 59
3262235 AAATGGTCTT
* * * **
3262245 TCGACTATAGGGTATTGGTTTATTCAGTC-TCGGTTATTAAAAATTACAAAATGATTCA
1 TCGACTATAGGATATTGCTTTATTCAGTCACCGACTATTAAAAATTACAAAATGATTCA
* * * *
3262303 TCGACTATAGGATGTTGCTTTGTTGAGTCACCGACTATTAAAAGTTACAAAATGAT
1 TCGACTATAGGATATTGCTTTATTCAGTCACCGACTATTAAAAATTACAAAATGAT
3262359 CACCTAACTA
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
58 24 0.52
59 22 0.48
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.36
Consensus pattern (59 bp):
TCGACTATAGGATATTGCTTTATTCAGTCACCGACTATTAAAAATTACAAAATGATTCA
Found at i:3262927 original size:7 final size:7
Alignment explanation
Indices: 3262915--3262940 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3262905 TCTAATCAAC
3262915 ATTTTAA
1 ATTTTAA
3262922 ATTTTAA
1 ATTTTAA
3262929 ATTTTAA
1 ATTTTAA
3262936 ATTTT
1 ATTTT
3262941 GGTCGTGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (7 bp):
ATTTTAA
Found at i:3272757 original size:18 final size:17
Alignment explanation
Indices: 3272724--3272757 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3272714 TATTAGTTTT
*
3272724 ATTATTGTATTATGTTA
1 ATTATTGTAATATGTTA
3272741 ATTATTGTGAATATGTT
1 ATTATTGT-AATATGTT
3272758 TTAGTATTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.29, C:0.00, G:0.15, T:0.56
Consensus pattern (17 bp):
ATTATTGTAATATGTTA
Found at i:3278436 original size:42 final size:42
Alignment explanation
Indices: 3278373--3278456 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 42
3278363 TATCTATTTC
**
3278373 ATGCTTTTTTTTTTTTCTTAGATATAAAAAAATGCTCAACGT
1 ATGCTTTTTTTTCATTCTTAGATATAAAAAAATGCTCAACGT
3278415 ATGCTTTTATTTTCATT-TTAGATATAAAAAAATGCTCAACGT
1 ATGCTTTT-TTTTCATTCTTAGATATAAAAAAATGCTCAACGT
3278457 TTTATTCCAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
42 33 0.85
43 6 0.15
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (42 bp):
ATGCTTTTTTTTCATTCTTAGATATAAAAAAATGCTCAACGT
Found at i:3280463 original size:62 final size:62
Alignment explanation
Indices: 3280395--3280639 Score: 269
Period size: 62 Copynumber: 4.0 Consensus size: 62
3280385 ATTCGCGTTG
* * *
3280395 CATTTCGCGTTGCGATGGTTGGAAATCGCGTTGCGATTTTTCATTTCGCGTTGCGATAGTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTC
*
3280457 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTG
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTC
* ** * ** ** * * ** ** *
3280519 AAAATCGCGTTGCGAT-TTTCCATTTCGCGCTGCGATAGTTGAAAATCGCGTTGCGAT-TTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGAT-TTTCCATTTCGCGTTGCGATAGTTC
* * *
3280580 CATTTCGCGCTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCACATTGCGATAGT
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT
3280640 CTACATTGTC
Statistics
Matches: 142, Mismatches: 38, Indels: 6
0.76 0.20 0.03
Matches are distributed among these distances:
61 41 0.29
62 101 0.71
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.36
Consensus pattern (62 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTC
Found at i:3280465 original size:41 final size:41
Alignment explanation
Indices: 3280440--3280639 Score: 346
Period size: 41 Copynumber: 4.9 Consensus size: 41
3280430 ATTTTTCATT
*
3280440 TCGCGTTGCGATAGTTCCATTTCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATTTCGCGTTGCGATAGTTGAAAA
3280482 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
*
3280523 TCGCGTTGCGATTTTCCATTTCGCGCTGCGATAGTTGAAAA
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
*
3280564 TCGCGTTGCGATTTTCCATTTCGCGCTGCGATAGTTGAAAA
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
* *
3280605 TCGCGTTGCGATTTTCCATTTCACATTGCGATAGT
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT
3280640 CTACATTGTC
Statistics
Matches: 153, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
41 141 0.92
42 12 0.08
ACGTcount: A:0.20, C:0.21, G:0.24, T:0.35
Consensus pattern (41 bp):
TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
Found at i:3280653 original size:41 final size:40
Alignment explanation
Indices: 3280440--3280679 Score: 315
Period size: 41 Copynumber: 5.9 Consensus size: 40
3280430 ATTTTTCATT
*
3280440 TCGCGTTGCGATAGTTCCATTTCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATTTCGCGTTGCGATAGTT-AAAA
3280482 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTT-AAAA
*
3280523 TCGCGTTGCGATTTTCCATTTCGCGCTGCGATAGTTGAAAA
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTT-AAAA
*
3280564 TCGCGTTGCGATTTTCCATTTCGCGCTGCGATAGTTGAAAA
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTT-AAAA
* * *
3280605 TCGCGTTGCGATTTTCCATTTCACATTGCGATAGTCT-ACA
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT-TAAAA
* *
3280645 TTGTCGTTGCGATTTTCCAAATT--CGTTGCGATAGT
1 TCG-CGTTGCGATTTTCC-ATTTCGCGTTGCGATAGT
3280680 CTACAGTTGT
Statistics
Matches: 186, Mismatches: 9, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
40 15 0.08
41 155 0.83
42 16 0.09
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.36
Consensus pattern (40 bp):
TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTAAAA
Found at i:3280653 original size:123 final size:123
Alignment explanation
Indices: 3280440--3280663 Score: 353
Period size: 123 Copynumber: 1.8 Consensus size: 123
3280430 ATTTTTCATT
* *
3280440 TCGCGTTGCGATAGTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCG
1 TCGCGTTGCGATAGTTCCATTTCGCGCTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCA
*
3280505 CGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGCTGCGATAGTTGAAAA
66 CATTGCGATAGTT-AAAATCGCGTTGCGATTTTCCATTTCGCGCTGCGATAGTTGAAAA
*
3280564 TCGCGTTGCGAT-TTTCCATTTCGCGCTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCA
1 TCGCGTTGCGATAGTTCCATTTCGCGCTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCA
* *
3280628 CATTGCGATAGTCT-ACATTGTCGTTGCGATTTTCCA
66 CATTGCGATAGT-TAAAATCG-CGTTGCGATTTTCCA
3280664 AATTCGTTGC
Statistics
Matches: 92, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
122 4 0.04
123 75 0.82
124 13 0.14
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.36
Consensus pattern (123 bp):
TCGCGTTGCGATAGTTCCATTTCGCGCTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCA
CATTGCGATAGTTAAAATCGCGTTGCGATTTTCCATTTCGCGCTGCGATAGTTGAAAA
Found at i:3280684 original size:40 final size:41
Alignment explanation
Indices: 3280608--3280697 Score: 121
Period size: 41 Copynumber: 2.2 Consensus size: 41
3280598 TTGAAAATCG
*
3280608 CGTTGCGATTTTCCATTTCACATTGCGATAGTCTACA-TTGT
1 CGTTGCGATTTTCCAATT-ACATTGCGATAGTCTACAGTTGT
*
3280649 CGTTGCGATTTTCCAAATT-CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCC-AATTACATTGCGATAGTCTACAGTTGT
*
3280690 TGTTGCGA
1 CGTTGCGA
3280698 AAGTATACAA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
40 16 0.36
41 25 0.57
42 3 0.07
ACGTcount: A:0.19, C:0.20, G:0.21, T:0.40
Consensus pattern (41 bp):
CGTTGCGATTTTCCAATTACATTGCGATAGTCTACAGTTGT
Found at i:3280696 original size:22 final size:22
Alignment explanation
Indices: 3280630--3280723 Score: 88
Period size: 22 Copynumber: 4.5 Consensus size: 22
3280620 CCATTTCACA
*
3280630 TTGCGATAGTCTAC-ATTGTCG
1 TTGCGATAGTATACAATTGTCG
* * *
3280651 TTGCGAT--TTTCCAAAT-TCG
1 TTGCGATAGTATACAATTGTCG
* * *
3280670 TTGCGATAGTCTACAGTTGTTG
1 TTGCGATAGTATACAATTGTCG
*
3280692 TTGCGAAAGTATACAATTGTCG
1 TTGCGATAGTATACAATTGTCG
3280714 TTGCGATAGT
1 TTGCGATAGT
3280724 TAAAAAAAAA
Statistics
Matches: 56, Mismatches: 13, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
19 13 0.23
20 2 0.04
21 12 0.21
22 29 0.52
ACGTcount: A:0.22, C:0.16, G:0.23, T:0.38
Consensus pattern (22 bp):
TTGCGATAGTATACAATTGTCG
Found at i:3280813 original size:6 final size:6
Alignment explanation
Indices: 3280802--3280862 Score: 108
Period size: 6 Copynumber: 10.5 Consensus size: 6
3280792 GACACGTATT
3280802 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
3280850 ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACC
3280863 CGAGACGGAC
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 10 0.18
6 45 0.82
ACGTcount: A:0.31, C:0.52, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:3281380 original size:6 final size:6
Alignment explanation
Indices: 3281359--3281401 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
3281349 TCTCGTCTCG
*
3281359 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCAT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
3281402 AATACGTGTC
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
5 10 0.28
6 26 0.72
ACGTcount: A:0.02, C:0.16, G:0.51, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:3281511 original size:19 final size:19
Alignment explanation
Indices: 3281487--3281533 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
3281477 TAACGAATTT
3281487 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
3281506 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
3281525 TCGCAACGA
1 TCGCAACGA
3281534 CAACTGTAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.19
Consensus pattern (19 bp):
TCGCAACGAATTTGGAAAA
Found at i:3281560 original size:22 final size:22
Alignment explanation
Indices: 3281524--3281599 Score: 63
Period size: 22 Copynumber: 3.6 Consensus size: 22
3281514 AATTTGGAAA
3281524 ATCGCAACGAC-AACTGTAGACT
1 ATCGCAACG-CGAACTGTAGACT
**
3281546 ATCGCAACGCGAACTG--GAAA
1 ATCGCAACGCGAACTGTAGACT
* *
3281566 ATCGCAACGCG-ATTTTCA-ACT
1 ATCGCAACGCGAACTGT-AGACT
3281587 ATCGCAACGCGAA
1 ATCGCAACGCGAA
3281600 ATGCAACGCG
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
19 2 0.05
20 13 0.30
21 13 0.30
22 15 0.35
ACGTcount: A:0.36, C:0.28, G:0.20, T:0.17
Consensus pattern (22 bp):
ATCGCAACGCGAACTGTAGACT
Found at i:3281568 original size:42 final size:41
Alignment explanation
Indices: 3281518--3281599 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 41
3281508 GCAACGAATT
3281518 TGGAAAATCGCAACGACAACTGT-AGACTATCGCAACGCGAAC
1 TGGAAAATCGCAACG-CAACTGTCA-ACTATCGCAACGCGAAC
* * *
3281560 TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAA
1 TGGAAAATCGCAACGCAACTGTCAACTATCGCAACGCGAA
3281600 ATGCAACGCG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
41 20 0.56
42 16 0.44
ACGTcount: A:0.37, C:0.26, G:0.21, T:0.17
Consensus pattern (41 bp):
TGGAAAATCGCAACGCAACTGTCAACTATCGCAACGCGAAC
Found at i:3281606 original size:21 final size:21
Alignment explanation
Indices: 3281543--3281606 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
3281533 ACAACTGTAG
* *
3281543 ACTATCGCAACGCGAACTGGA
1 ACTATCGCAACGCGAAATGCA
* ** *
3281564 A-AATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
3281584 ACTATCGCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
3281605 AC
1 AC
3281607 GCGAATTTGC
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
20 15 0.45
21 18 0.55
ACGTcount: A:0.36, C:0.28, G:0.19, T:0.17
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:3289124 original size:19 final size:19
Alignment explanation
Indices: 3289100--3289158 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 19
3289090 TTGGATATTT
3289100 TATGACTTATGGATTAATA
1 TATGACTTATGGATTAATA
3289119 TATGAC-T-T-G-TT--TA
1 TATGACTTATGGATTAATA
*
3289132 TTTGACTTATGGATTAATA
1 TATGACTTATGGATTAATA
3289151 TATGACTT
1 TATGACTT
3289159 GTTTATTTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
13 7 0.22
14 1 0.03
15 3 0.09
16 2 0.06
17 3 0.09
18 1 0.03
19 15 0.47
ACGTcount: A:0.31, C:0.07, G:0.15, T:0.47
Consensus pattern (19 bp):
TATGACTTATGGATTAATA
Found at i:3289138 original size:32 final size:32
Alignment explanation
Indices: 3289102--3289170 Score: 138
Period size: 32 Copynumber: 2.2 Consensus size: 32
3289092 GGATATTTTA
3289102 TGACTTATGGATTAATATATGACTTGTTTATT
1 TGACTTATGGATTAATATATGACTTGTTTATT
3289134 TGACTTATGGATTAATATATGACTTGTTTATT
1 TGACTTATGGATTAATATATGACTTGTTTATT
3289166 TGACT
1 TGACT
3289171 ATGTGTCTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.28, C:0.07, G:0.16, T:0.49
Consensus pattern (32 bp):
TGACTTATGGATTAATATATGACTTGTTTATT
Found at i:3290585 original size:12 final size:12
Alignment explanation
Indices: 3290568--3290593 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3290558 TATTATAAAG
3290568 CATCACCTGCCA
1 CATCACCTGCCA
3290580 CATCACCTGCCA
1 CATCACCTGCCA
3290592 CA
1 CA
3290594 AGCACATGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.50, G:0.08, T:0.15
Consensus pattern (12 bp):
CATCACCTGCCA
Found at i:3291544 original size:20 final size:21
Alignment explanation
Indices: 3291490--3291541 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
3291480 CCATGCACTC
* *
3291490 CCTCCTGCTCCTCGCGTGATT
1 CCTCTTGCCCCTCGCGTGATT
3291511 CCTCTTGCCCCTCGCGTGATT
1 CCTCTTGCCCCTCGCGTGATT
3291532 CCTCTTGCCC
1 CCTCTTGCCC
3291542 TCGGATGCCC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.04, C:0.46, G:0.17, T:0.33
Consensus pattern (21 bp):
CCTCTTGCCCCTCGCGTGATT
Found at i:3294429 original size:20 final size:19
Alignment explanation
Indices: 3294391--3294429 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
3294381 CCAGTATGTT
*
3294391 CAGGGGGTACCGATTCCCC
1 CAGGGGGAACCGATTCCCC
*
3294410 CAGGGGGAATCGATTCCCC
1 CAGGGGGAACCGATTCCCC
3294429 C
1 C
3294430 TAAATGGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.18, C:0.36, G:0.31, T:0.15
Consensus pattern (19 bp):
CAGGGGGAACCGATTCCCC
Found at i:3295016 original size:2 final size:2
Alignment explanation
Indices: 3295009--3295082 Score: 148
Period size: 2 Copynumber: 37.0 Consensus size: 2
3294999 CATGAGTAAG
3295009 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3295051 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3295083 CAGAATTGGT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3299690 original size:21 final size:21
Alignment explanation
Indices: 3299665--3299704 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3299655 AGTATGTTCA
*
3299665 GGGGGTACCGATTCCCCCTGG
1 GGGGGAACCGATTCCCCCTGG
*
3299686 GGGGGAATCGATTCCCCCT
1 GGGGGAACCGATTCCCCCT
3299705 AAATGGAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.12, C:0.33, G:0.35, T:0.20
Consensus pattern (21 bp):
GGGGGAACCGATTCCCCCTGG
Found at i:3301308 original size:15 final size:15
Alignment explanation
Indices: 3301290--3301324 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
3301280 CGAGGGTATT
3301290 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
* *
3301305 GTAGTCCTTTGGTAC
1 GTAGTCCTTCGGGAC
3301320 GTAGT
1 GTAGT
3301325 GGTCCTACGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.14, C:0.20, G:0.31, T:0.34
Consensus pattern (15 bp):
GTAGTCCTTCGGGAC
Found at i:3302947 original size:13 final size:13
Alignment explanation
Indices: 3302929--3302954 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3302919 TATGACTTTT
3302929 TGGTCAAAGTCAA
1 TGGTCAAAGTCAA
3302942 TGGTCAAAGTCAA
1 TGGTCAAAGTCAA
3302955 CGGGTTGACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (13 bp):
TGGTCAAAGTCAA
Found at i:3304945 original size:21 final size:21
Alignment explanation
Indices: 3304906--3304946 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3304896 ATTATATTTT
* *
3304906 ATAACTTATTTAGTAGTATAA
1 ATAAATTATTTAATAGTATAA
*
3304927 ATAAATTATTTAATTGTATA
1 ATAAATTATTTAATAGTATA
3304947 TAAATTTAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.46
Consensus pattern (21 bp):
ATAAATTATTTAATAGTATAA
Found at i:3304977 original size:22 final size:20
Alignment explanation
Indices: 3304944--3304991 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 20
3304934 ATTTAATTGT
*
3304944 ATATAAATTTAAATTTTAAA
1 ATATAAATTTAAATTTAAAA
3304964 ATATCAAATATTAAATTTAAAA
1 ATAT-AAAT-TTAAATTTAAAA
*
3304986 ACATAA
1 ATATAA
3304992 TAACGTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 4 0.17
21 6 0.25
22 14 0.58
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (20 bp):
ATATAAATTTAAATTTAAAA
Found at i:3308092 original size:14 final size:13
Alignment explanation
Indices: 3308047--3308090 Score: 70
Period size: 13 Copynumber: 3.2 Consensus size: 13
3308037 AGTCTATTAA
3308047 AAAATTATTTTTT
1 AAAATTATTTTTT
3308060 AAAATTATTTTTT
1 AAAATTATTTTTT
3308073 AAAATTATAATTTTT
1 AAAATTAT--TTTTT
3308088 AAA
1 AAA
3308091 TTTTAAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
13 21 0.72
15 8 0.28
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
AAAATTATTTTTT
Found at i:3312666 original size:15 final size:15
Alignment explanation
Indices: 3312623--3312668 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
3312613 TTTCCCCTTT
3312623 ATAAAAATATATTT-
1 ATAAAAATATATTTA
*
3312637 -TGAAAAATAAAATTTA
1 AT-AAAAAT-ATATTTA
3312653 ATAAAAATATATTTA
1 ATAAAAATATATTTA
3312668 A
1 A
3312669 GCTCCCCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
13 1 0.04
14 6 0.23
15 12 0.46
16 6 0.23
17 1 0.04
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (15 bp):
ATAAAAATATATTTA
Found at i:3319116 original size:64 final size:64
Alignment explanation
Indices: 3319048--3319169 Score: 174
Period size: 64 Copynumber: 1.9 Consensus size: 64
3319038 ATTATTCAAG
* * * *
3319048 GTGTATCGATGCACATG-AGGTGTATCGATGCACTCTTTTAAAATAAAAACATCGAATGTCATTA
1 GTGTATCGATGCACAAGTA-GTGCATCGATGCACCCTCTTAAAATAAAAACATCGAATGTCATTA
* *
3319112 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCTCTTAAAATACAAACATTGAATG
1 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCTCTTAAAATAAAAACATCGAATG
3319170 AGATTTATGT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
64 50 0.98
65 1 0.02
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (64 bp):
GTGTATCGATGCACAAGTAGTGCATCGATGCACCCTCTTAAAATAAAAACATCGAATGTCATTA
Found at i:3319186 original size:64 final size:64
Alignment explanation
Indices: 3319048--3319210 Score: 170
Period size: 64 Copynumber: 2.5 Consensus size: 64
3319038 ATTATTCAAG
* * * * *
3319048 GTGTATCGATGCACATG-AGGTGTATCGATGCACTCTTTTAAAATAAAAACATCGAATGTCATTA
1 GTGTATCGATGCACAAGTA-GTGCATCGATGCACCCTCTTAAAATAAAAACATCGAATGACATTA
* * *
3319112 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCTCTTAAAATACAAACATTGAATGAGATTTA
1 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCTCTTAAAATAAAAACATCGAATGACA-TTA
* * * *
3319177 -TGTACCGATGCA-TAGATTGTGCATCAATGCACCC
1 GTGTATCGATGCACAAG-TAGTGCATCGATGCACCC
3319211 GTCAAGGGAT
Statistics
Matches: 84, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
63 2 0.02
64 78 0.93
65 4 0.05
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (64 bp):
GTGTATCGATGCACAAGTAGTGCATCGATGCACCCTCTTAAAATAAAAACATCGAATGACATTA
Found at i:3325998 original size:64 final size:64
Alignment explanation
Indices: 3325893--3326014 Score: 156
Period size: 64 Copynumber: 1.9 Consensus size: 64
3325883 ATTGTTCAAG
* * * *
3325893 GTGTATCGATGCACATGAGGTGTATCAATGCACTCCTTTAAAATAAAAACATCAAATGTCATTA
1 GTGTATCGATGCACAAGAGGTGCATCAATGCACCCCCTTAAAATAAAAACATCAAATGTCATTA
** * *
3325957 GTGTATCGATGCACAAGTA-GTGCATTGATGCACCCCCTTAAAATACAAACATCGAATG
1 GTGTATCGATGCACAAG-AGGTGCATCAATGCACCCCCTTAAAATAAAAACATCAAATG
3326015 GGATTTATGT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
64 48 0.98
65 1 0.02
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (64 bp):
GTGTATCGATGCACAAGAGGTGCATCAATGCACCCCCTTAAAATAAAAACATCAAATGTCATTA
Found at i:3332266 original size:30 final size:30
Alignment explanation
Indices: 3332224--3332281 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
3332214 TCAGCAGATG
* *
3332224 TGGAAGCGTGGATCTCTCGGTGTCTTTACA
1 TGGAAGCGTGGATATCTCGGCGTCTTTACA
3332254 TGGAAG-GCTGGATATCTCGGCGTCTTTA
1 TGGAAGCG-TGGATATCTCGGCGTCTTTA
3332282 ACGCAATTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 1 0.04
30 24 0.96
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (30 bp):
TGGAAGCGTGGATATCTCGGCGTCTTTACA
Found at i:3332381 original size:34 final size:34
Alignment explanation
Indices: 3332333--3332417 Score: 134
Period size: 34 Copynumber: 2.5 Consensus size: 34
3332323 TATGATTGAT
3332333 CTCTCGGCGTCTTCAGTTGGATTCTTCATAAGAA
1 CTCTCGGCGTCTTCAGTTGGATTCTTCATAAGAA
* * *
3332367 CTCTTGGCGTCTTCAGTTGGATTCTTCGTAGGAA
1 CTCTCGGCGTCTTCAGTTGGATTCTTCATAAGAA
*
3332401 ATCTCGGCGTCTTCAGT
1 CTCTCGGCGTCTTCAGT
3332418 GCTGTGCATG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (34 bp):
CTCTCGGCGTCTTCAGTTGGATTCTTCATAAGAA
Found at i:3332520 original size:23 final size:23
Alignment explanation
Indices: 3332494--3332537 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
3332484 TGAGCAGGGG
3332494 CTGCACGTCTGCATGTGGGGGTC
1 CTGCACGTCTGCATGTGGGGGTC
3332517 CTGCACGTCTGCATGTGGGGG
1 CTGCACGTCTGCATGTGGGGG
3332538 GCATGCAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.09, C:0.25, G:0.41, T:0.25
Consensus pattern (23 bp):
CTGCACGTCTGCATGTGGGGGTC
Found at i:3332544 original size:23 final size:22
Alignment explanation
Indices: 3332490--3332544 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 22
3332480 GGGTTGAGCA
3332490 GGGGCTGCACGTCTGCATGTGG
1 GGGGCTGCACGTCTGCATGTGG
*
3332512 GGGTCCTGCACGTCTGCATGTGG
1 GGG-GCTGCACGTCTGCATGTGG
3332535 GGGGCATGCA
1 GGGGC-TGCA
3332545 ATTGTTGGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 4 0.14
23 25 0.86
ACGTcount: A:0.11, C:0.24, G:0.44, T:0.22
Consensus pattern (22 bp):
GGGGCTGCACGTCTGCATGTGG
Found at i:3333164 original size:165 final size:171
Alignment explanation
Indices: 3332963--3333313 Score: 536
Period size: 172 Copynumber: 2.1 Consensus size: 171
3332953 TTGTAAAGTT
*
3332963 TTAGGGACCGTTTTGTAAAATTTAAGGAATTTAAGGAATAAGAGTAAATTATTAAAAGTTGCTAT
1 TTAGGGATCGTTTTGTAAAATTTAAGGAATTTAAGGAATAAGAGTAAATTA-TAAAAGTTGCTAT
* *
3333028 ACTATGCTGGAATTTAGTATTAGTATCCTTAATTGGTTAAA-TT-AGA-AATTTA-AAA-TT-T-
65 ACTATGCTGGAATTTAGTATTAATATCCTTAATTGGTTAAATTTGAAAGAATTTATAAATTTATG
*
3333086 ATTAAATTGCTAAGTTTGAAAATGTTGAGAACCAAATAGTAA
130 ATTAAATTGCAAAGTTTGAAAATGTTGAGAACCAAATAGTAA
* * *
3333128 TTAGGGATCGTTTTGTAAAATTTGAGGAATTTAAGGAATTAGAGTAAATTATAAAAGTTGGTATA
1 TTAGGGATCGTTTTGTAAAATTTAAGGAATTTAAGGAATAAGAGTAAATTATAAAAGTTGCTATA
* *
3333193 CTATGCTTGAATTTAGTATTAATATGCTTAATTGGTTAAATTTGAAAGAATTTATAAATTTAGTG
66 CTATGCTGGAATTTAGTATTAATATCCTTAATTGGTTAAATTTGAAAGAATTTATAAATTTA-TG
*
3333258 ATTAAATTGCAAAGTTTGAAAATGTTGAGAAGCAAATAGTAA
130 ATTAAATTGCAAAGTTTGAAAATGTTGAGAACCAAATAGTAA
*
3333300 TTAGGGATCATTTT
1 TTAGGGATCGTTTT
3333314 ATATTTGATG
Statistics
Matches: 167, Mismatches: 11, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
164 50 0.30
165 50 0.30
166 2 0.01
167 6 0.04
168 3 0.02
169 2 0.01
171 1 0.01
172 53 0.32
ACGTcount: A:0.39, C:0.05, G:0.18, T:0.38
Consensus pattern (171 bp):
TTAGGGATCGTTTTGTAAAATTTAAGGAATTTAAGGAATAAGAGTAAATTATAAAAGTTGCTATA
CTATGCTGGAATTTAGTATTAATATCCTTAATTGGTTAAATTTGAAAGAATTTATAAATTTATGA
TTAAATTGCAAAGTTTGAAAATGTTGAGAACCAAATAGTAA
Found at i:3335451 original size:8 final size:8
Alignment explanation
Indices: 3335438--3335787 Score: 114
Period size: 8 Copynumber: 47.8 Consensus size: 8
3335428 AGTAATTATT
3335438 ATTAAATC
1 ATTAAATC
3335446 ATTAAA--
1 ATTAAATC
3335452 ATTAAATC
1 ATTAAATC
3335460 ATTAAA--
1 ATTAAATC
* *
3335466 ATTAAGTA
1 ATTAAATC
*
3335474 ATT--ATT
1 ATTAAATC
*
3335480 ATT-AATT
1 ATTAAATC
3335487 ATTAAA--
1 ATTAAATC
3335493 ATTAAATC
1 ATTAAATC
3335501 ATTAAAGT-
1 ATTAAA-TC
*
3335509 ATT--ATT
1 ATTAAATC
3335515 ATTAAA-C
1 ATTAAATC
3335522 ATTAAATC
1 ATTAAATC
*
3335530 A-TAAAGTA
1 ATTAAA-TC
*
3335538 ATT--ATT
1 ATTAAATC
*
3335544 ATTAAAGC
1 ATTAAATC
3335552 ATTAAA--
1 ATTAAATC
*
3335558 GTTAAATC
1 ATTAAATC
*
3335566 ATTAAAGTA
1 ATTAAA-TC
*
3335575 ATT--ATT
1 ATTAAATC
3335581 ATTAAATC
1 ATTAAATC
3335589 ATTAAATC
1 ATTAAATC
*
3335597 ATTAAAGTA
1 ATTAAA-TC
*
3335606 ATT--ATT
1 ATTAAATC
*
3335612 ATTAAAGC
1 ATTAAATC
3335620 ATTAAA--
1 ATTAAATC
*
3335626 GTTAAATC
1 ATTAAATC
*
3335634 ATTAAAGTA
1 ATTAAA-TC
3335643 ATT--AT-
1 ATTAAATC
3335648 ATTAAATC
1 ATTAAATC
*
3335656 ATTAAAGTA
1 ATTAAA-TC
*
3335665 ATT--ATT
1 ATTAAATC
3335671 ATTAAATC
1 ATTAAATC
3335679 ATTAAA--
1 ATTAAATC
*
3335685 GTTAAATC
1 ATTAAATC
**
3335693 ATTAAAAA
1 ATTAAATC
3335701 ATTAAATC
1 ATTAAATC
*
3335709 ATTAAAGTA
1 ATTAAA-TC
*
3335718 ATT--ATT
1 ATTAAATC
3335724 ATTAAATC
1 ATTAAATC
3335732 ATT-AA--
1 ATTAAATC
3335737 ATTAAATC
1 ATTAAATC
*
3335745 ATTAAAGTA
1 ATTAAA-TC
*
3335754 ATT--ATT
1 ATTAAATC
3335760 ATTAAATC
1 ATTAAATC
3335768 ATTAAA--
1 ATTAAATC
*
3335774 GTTAAATC
1 ATTAAATC
3335782 ATTAAA
1 ATTAAA
3335788 GTAATTATAT
Statistics
Matches: 258, Mismatches: 37, Indels: 94
0.66 0.10 0.24
Matches are distributed among these distances:
5 7 0.03
6 72 0.28
7 27 0.10
8 126 0.49
9 26 0.10
ACGTcount: A:0.51, C:0.05, G:0.04, T:0.40
Consensus pattern (8 bp):
ATTAAATC
Found at i:3335462 original size:42 final size:42
Alignment explanation
Indices: 3335393--3335508 Score: 164
Period size: 41 Copynumber: 2.8 Consensus size: 42
3335383 GAATATTTAC
* * *
3335393 TATTATTATATCAGT-AAATAAAATCATTAAAGTCAAGTAAT
1 TATTATTAAATCATTAAAATTAAATCATTAAAGTCAAGTAAT
* *
3335434 TATTATTAAATCATTAAAATTAAATCATTAAAATTAAGTAAT
1 TATTATTAAATCATTAAAATTAAATCATTAAAGTCAAGTAAT
*
3335476 TATTATT-AATTATTAAAATTAAATCATTAAAGT
1 TATTATTAAATCATTAAAATTAAATCATTAAAGT
3335509 ATTATTATTA
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
41 37 0.55
42 30 0.45
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.41
Consensus pattern (42 bp):
TATTATTAAATCATTAAAATTAAATCATTAAAGTCAAGTAAT
Found at i:3335572 original size:37 final size:37
Alignment explanation
Indices: 3335427--3335804 Score: 431
Period size: 36 Copynumber: 10.5 Consensus size: 37
3335417 CATTAAAGTC
*
3335427 AAGTAATTATTATTAAATCATTAAAATTAAATCATTAAAA
1 AAGTAATTATTATTAAATCATTAAAGTTAAATCATT---A
* *
3335467 TTAAGTAATTATTATT-AATTATTAAAATTAAATCATTA
1 --AAGTAATTATTATTAAATCATTAAAGTTAAATCATTA
3335505 AAGT-ATTATTATTAAA-C-----A-TTAAATCA-TA
1 AAGTAATTATTATTAAATCATTAAAGTTAAATCATTA
*
3335533 AAGTAATTATTATTAAAGCATTAAAGTTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAGTTAAATCATTA
3335570 AAGTAATTATTATTAAATC-----A-TTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAGTTAAATCATTA
*
3335601 AAGTAATTATTATTAAAGCATTAAAGTTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAGTTAAATCATTA
*
3335638 AAGTAATTA-TATTAAATCATTAAAG-TAATTATTATTA
1 AAGTAATTATTATTAAATCATTAAAGTTAA--ATCATTA
* * *
3335675 AA-TCATTA-AAGTTAAATCATTAAAAAATTAAATCATTA
1 AAGTAATTATTA-TTAAATCATT--AAAGTTAAATCATTA
3335713 AAGTAATTATTATTAAATCATTAAA-TTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAGTTAAATCATTA
3335749 AAGTAATTATTATTAAATCATTAAAGTTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAGTTAAATCATTA
3335786 AAGTAATTA-TATTAAATCA
1 AAGTAATTATTATTAAATCA
3335805 AAGTTAATTA
Statistics
Matches: 299, Mismatches: 12, Indels: 56
0.81 0.03 0.15
Matches are distributed among these distances:
28 6 0.02
29 20 0.07
30 2 0.01
31 29 0.10
32 1 0.00
35 13 0.04
36 82 0.27
37 81 0.27
38 9 0.03
39 18 0.06
40 4 0.01
41 20 0.07
42 14 0.05
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.40
Consensus pattern (37 bp):
AAGTAATTATTATTAAATCATTAAAGTTAAATCATTA
Found at i:3335586 original size:15 final size:15
Alignment explanation
Indices: 3335566--3335618 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
3335556 AAGTTAAATC
3335566 ATTAAAGTAATTATT
1 ATTAAAGTAATTATT
* *
3335581 ATTAAA-TCATTAAATC
1 ATTAAAGTAATT--ATT
3335597 ATTAAAGTAATTATT
1 ATTAAAGTAATTATT
3335612 ATTAAAG
1 ATTAAAG
3335619 CATTAAAGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
14 4 0.13
15 15 0.48
16 8 0.26
17 4 0.13
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.42
Consensus pattern (15 bp):
ATTAAAGTAATTATT
Found at i:3335590 original size:59 final size:60
Alignment explanation
Indices: 3335469--3335775 Score: 375
Period size: 59 Copynumber: 5.1 Consensus size: 60
3335459 CATTAAAATT
* *
3335469 AAGTAATTATTATT-AATTATTAAAATTAAATCATTAAAGTATTATTATTAAACATTAAATCA-T
1 AAGTAATTATTATTAAATCATTAAAGTTAAATCATTAAAGTA--ATTATT----ATTAAATCATT
3335532 A
60 A
*
3335533 AAGTAATTATTATTAAAGCATTAAAGTTAAATCATTAAAGTAATTATTATTAAATCATTAAATCA
1 AAGTAATTATTATTAAATCATTAAAGTTAAATCATTAAAGT-A--ATTA-T---T-ATTAAATCA
3335598 TTA
58 TTA
*
3335601 AAGTAATTATTATTAAAGCATTAAAGTTAAATCATTAAAGTAATTA-TATTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAGTTAAATCATTAAAGTAATTATTATTAAATCATTA
3335660 AAGTAATTATTATTAAATCATTAAAGTTAAATCATT-AA--AA--A--ATTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAGTTAAATCATTAAAGTAATTATTATTAAATCATTA
3335713 AAGTAATTATTATTAAATCATTAAA-TTAAATCATTAAAGTAATTATTATTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAGTTAAATCATTAAAGTAATTATTATTAAATCATTA
3335772 AAGT
1 AAGT
3335776 TAAATCATTA
Statistics
Matches: 225, Mismatches: 4, Indels: 33
0.86 0.02 0.13
Matches are distributed among these distances:
52 10 0.04
53 39 0.17
54 1 0.00
55 2 0.01
56 2 0.01
57 1 0.00
58 2 0.01
59 63 0.28
60 1 0.00
64 14 0.06
65 27 0.12
66 7 0.03
67 12 0.05
68 43 0.19
70 1 0.00
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.40
Consensus pattern (60 bp):
AAGTAATTATTATTAAATCATTAAAGTTAAATCATTAAAGTAATTATTATTAAATCATTA
Found at i:3335600 original size:45 final size:45
Alignment explanation
Indices: 3335544--3335738 Score: 191
Period size: 45 Copynumber: 4.2 Consensus size: 45
3335534 AGTAATTATT
*
3335544 ATTAAAGCATTAAAGTTAAATCATTAAAGTAATTATTATTAAATC
1 ATTAAATCATTAAAGTTAAATCATTAAAGTAATTATTATTAAATC
* * *
3335589 ATTAAATCATTAAAG-TAATTATTATTAAAG-CATTA-AAGTTAAATC
1 ATTAAATCATTAAAGTTAA--ATCATTAAAGTAATTATTA-TTAAATC
* *
3335634 ATTAAAGTAATTATA-TTAAATCATTAAAGTAATTATTATTAAATC
1 ATTAAA-TCATTAAAGTTAAATCATTAAAGTAATTATTATTAAATC
*
3335679 ATTAAAGTTAAATCATTAAAAAATTAAATCATTAAAGTAATTATTATTAAATC
1 -----A-TTAAATCATT--AAAGTTAAATCATTAAAGTAATTATTATTAAATC
3335732 ATTAAAT
1 ATTAAAT
3335739 TAAATCATTA
Statistics
Matches: 123, Mismatches: 11, Indels: 30
0.75 0.07 0.18
Matches are distributed among these distances:
44 13 0.11
45 42 0.34
46 19 0.15
47 6 0.05
48 1 0.01
50 5 0.04
51 5 0.04
52 2 0.02
53 30 0.24
ACGTcount: A:0.50, C:0.06, G:0.05, T:0.39
Consensus pattern (45 bp):
ATTAAATCATTAAAGTTAAATCATTAAAGTAATTATTATTAAATC
Found at i:3335712 original size:112 final size:112
Alignment explanation
Indices: 3335559--3335775 Score: 357
Period size: 112 Copynumber: 1.9 Consensus size: 112
3335549 AGCATTAAAG
* **
3335559 TTAAATCATTAAAGTAATTATTATTAAATCATTAAATCATTAAAGTAATTATTATTAAAGCATTA
1 TTAAATCATTAAAGTAA-TATCATTAAAAAATTAAATCATTAAAGTAATTATTATTAAAGCATTA
3335624 AAGTTAAATCATTAAAGTAATTA-TATTAAATCATTAAAGTAATTATTA
65 AA-TTAAATCATTAAAGTAATTATTATTAAATCATTAAAGTAATTATTA
*
3335672 TTAAATCATTAAAGTTAA-ATCATTAAAAAATTAAATCATTAAAGTAATTATTATTAAATCATTA
1 TTAAATCATTAAAG-TAATATCATTAAAAAATTAAATCATTAAAGTAATTATTATTAAAGCATTA
3335736 AATTAAATCATTAAAGTAATTATTATTAAATCATTAAAGT
65 AATTAAATCATTAAAGTAATTATTATTAAATCATTAAAGT
3335776 TAAATCATTA
Statistics
Matches: 98, Mismatches: 4, Indels: 5
0.92 0.04 0.05
Matches are distributed among these distances:
111 20 0.20
112 61 0.62
113 14 0.14
114 3 0.03
ACGTcount: A:0.50, C:0.06, G:0.05, T:0.40
Consensus pattern (112 bp):
TTAAATCATTAAAGTAATATCATTAAAAAATTAAATCATTAAAGTAATTATTATTAAAGCATTAA
ATTAAATCATTAAAGTAATTATTATTAAATCATTAAAGTAATTATTA
Found at i:3335788 original size:14 final size:14
Alignment explanation
Indices: 3335439--3335789 Score: 173
Period size: 14 Copynumber: 27.1 Consensus size: 14
3335429 GTAATTATTA
*
3335439 TTAAATCATTAAAA
1 TTAAATCATTAAAG
*
3335453 TTAAATCATTAAAA
1 TTAAATCATTAAAG
* * *
3335467 TTAAGTAATTATTA-
1 TTAAATCATTA-AAG
* *
3335481 TT-AATTATTAAAA
1 TTAAATCATTAAAG
3335494 TTAAATCATTAAAG
1 TTAAATCATTAAAG
* * *
3335508 -TATTATTATTAAACA
1 TTA-AATCATTAAA-G
3335523 TTAAATCA-TAAAG
1 TTAAATCATTAAAG
*
3335536 -T-AATTATT--A-
1 TTAAATCATTAAAG
*
3335545 TTAAAGCATTAAAG
1 TTAAATCATTAAAG
3335559 TTAAATCATTAAAG
1 TTAAATCATTAAAG
* *
3335573 -TAATTATTATTAAATCA
1 TTAA--ATCATTAAA--G
3335590 TTAAATCATTAAAG
1 TTAAATCATTAAAG
*
3335604 -T-AATTATT--A-
1 TTAAATCATTAAAG
*
3335613 TTAAAGCATTAAAG
1 TTAAATCATTAAAG
3335627 TTAAATCATTAAAG
1 TTAAATCATTAAAG
*
3335641 -T--A--ATTATA-
1 TTAAATCATTAAAG
3335649 TTAAATCATTAAAG
1 TTAAATCATTAAAG
*
3335663 -T-AATTATT--A-
1 TTAAATCATTAAAG
3335672 TTAAATCATTAAAG
1 TTAAATCATTAAAG
*
3335686 TTAAATCATTAAAAAA
1 TTAAATCATT--AAAG
3335702 TTAAATCATTAAAG
1 TTAAATCATTAAAG
*
3335716 -T-AATTATT--A-
1 TTAAATCATTAAAG
3335725 TTAAATCATTAAA-
1 TTAAATCATTAAAG
3335738 TTAAATCATTAAAG
1 TTAAATCATTAAAG
*
3335752 -T-AATTATT--A-
1 TTAAATCATTAAAG
3335761 TTAAATCATTAAAG
1 TTAAATCATTAAAG
3335775 TTAAATCATTAAAG
1 TTAAATCATTAAAG
3335789 T
1 T
3335790 AATTATATTA
Statistics
Matches: 256, Mismatches: 36, Indels: 90
0.67 0.09 0.24
Matches are distributed among these distances:
9 6 0.02
10 10 0.04
11 34 0.13
12 27 0.11
13 41 0.16
14 100 0.39
15 12 0.05
16 23 0.09
18 3 0.01
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.40
Consensus pattern (14 bp):
TTAAATCATTAAAG
Found at i:3335794 original size:23 final size:22
Alignment explanation
Indices: 3335491--3335775 Score: 205
Period size: 23 Copynumber: 12.8 Consensus size: 22
3335481 TTAATTATTA
3335491 AAATTAAATCATTAAAGT-ATT
1 AAATTAAATCATTAAAGTCATT
*
3335512 ATTATTAAA-CATTAAA-TCA-T
1 A-AATTAAATCATTAAAGTCATT
* *
3335532 AAAGTAATTATTATTAAAG-CATT
1 AAATTAA--ATCATTAAAGTCATT
*
3335555 AAAGTTAAATCATTAAAGTAATT
1 AAA-TTAAATCATTAAAGTCATT
*
3335578 ATTATTAAATCATTAAA-TCATT
1 A-AATTAAATCATTAAAGTCATT
* *
3335600 AAAGTAATTATTATTAAAG-CATT
1 AAATTAA--ATCATTAAAGTCATT
*
3335623 AAAGTTAAATCATTAAAGTAATT
1 AAA-TTAAATCATTAAAGTCATT
* *
3335646 ATATTAAATCATTAAAGTAATT
1 AAATTAAATCATTAAAGTCATT
* *
3335668 ATTATTAAATCATTAAAGT--TA
1 A-AATTAAATCATTAAAGTCATT
**
3335689 AATCATTAAAAAATTAAA-TCATT
1 AA--ATTAAATCATTAAAGTCATT
* *
3335712 AAAGTAATTATTATTAAA-TCATT
1 AAATTAA--ATCATTAAAGTCATT
*
3335735 AAATTAAATCATTAAAGTAATT
1 AAATTAAATCATTAAAGTCATT
*
3335757 ATTATTAAATCATTAAAGT
1 A-AATTAAATCATTAAAGT
3335776 TAAATCATTA
Statistics
Matches: 212, Mismatches: 28, Indels: 46
0.74 0.10 0.16
Matches are distributed among these distances:
19 4 0.02
20 3 0.01
21 29 0.14
22 74 0.35
23 95 0.45
24 7 0.03
ACGTcount: A:0.50, C:0.06, G:0.05, T:0.39
Consensus pattern (22 bp):
AAATTAAATCATTAAAGTCATT
Found at i:3335832 original size:33 final size:34
Alignment explanation
Indices: 3335672--3335833 Score: 169
Period size: 36 Copynumber: 4.8 Consensus size: 34
3335662 GTAATTATTA
*
3335672 TTAAATCATTAAAGTTAA--ATCATTAAA--AAA-
1 TTAAATCATTAAAG-TAATTATTATTAAATCAAAG
*
3335702 TTAAATCATTAAAGTAATTATTATTAAATCATTAAA
1 TTAAATCATTAAAGTAATTATTATTAAATCA--AAG
3335738 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAG
1 TTAAATCATTAAAGTAATTATTATTAAATC---AAAG
3335775 TTAAATCATTAAAGTAATTA-TATTAAATCAAAG
1 TTAAATCATTAAAGTAATTATTATTAAATCAAAG
* *
3335808 TTAATTAATTTAAA-T-ATTATTATTAA
1 TTAAATCA-TTAAAGTAATTATTATTAA
3335834 TATGTACTCG
Statistics
Matches: 116, Mismatches: 4, Indels: 21
0.82 0.03 0.15
Matches are distributed among these distances:
29 3 0.03
30 14 0.12
31 8 0.07
32 4 0.03
33 18 0.16
34 5 0.04
35 2 0.02
36 39 0.34
37 22 0.19
39 1 0.01
ACGTcount: A:0.51, C:0.05, G:0.04, T:0.41
Consensus pattern (34 bp):
TTAAATCATTAAAGTAATTATTATTAAATCAAAG
Found at i:3339298 original size:42 final size:42
Alignment explanation
Indices: 3339239--3339342 Score: 136
Period size: 42 Copynumber: 2.4 Consensus size: 42
3339229 AACAAATCTC
* * *
3339239 ACGCTTCAGGCGAATCTCACCCTTCGGCCCCAAAGCATACAG
1 ACGCTTCAGACGAATCTCACCCTTCGGCCACAAAGAATACAG
*
3339281 ACGCTTCAGACGAATCTCACGCTTCGGCCACAAAGAATACAG
1 ACGCTTCAGACGAATCTCACCCTTCGGCCACAAAGAATACAG
* *
3339323 ATGCATGCAGAACGAATCTC
1 ACGC-TTCAG-ACGAATCTC
3339343 GGAGGAAGAA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
42 41 0.76
43 4 0.07
44 9 0.17
ACGTcount: A:0.31, C:0.33, G:0.19, T:0.17
Consensus pattern (42 bp):
ACGCTTCAGACGAATCTCACCCTTCGGCCACAAAGAATACAG
Found at i:3348539 original size:14 final size:16
Alignment explanation
Indices: 3348516--3348561 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 16
3348506 GATTCGCAAT
3348516 GCGAACTTCGACTATC
1 GCGAACTTCGACTATC
*
3348532 GCG-A-TTCG--TAAC
1 GCGAACTTCGACTATC
3348544 GCGAACTTCGACTATC
1 GCGAACTTCGACTATC
3348560 GC
1 GC
3348562 ATTGCGATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 8
0.71 0.06 0.24
Matches are distributed among these distances:
12 6 0.25
13 1 0.04
14 8 0.33
15 1 0.04
16 8 0.33
ACGTcount: A:0.24, C:0.30, G:0.22, T:0.24
Consensus pattern (16 bp):
GCGAACTTCGACTATC
Found at i:3348547 original size:28 final size:28
Alignment explanation
Indices: 3348506--3348561 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
3348496 TCAGTTTCCA
*
3348506 GATTCGCAATGCGAACTTCGACTATCGC
1 GATTCGCAACGCGAACTTCGACTATCGC
*
3348534 GATTCGTAACGCGAACTTCGACTATCGC
1 GATTCGCAACGCGAACTTCGACTATCGC
3348562 ATTGCGATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (28 bp):
GATTCGCAACGCGAACTTCGACTATCGC
Found at i:3358077 original size:15 final size:16
Alignment explanation
Indices: 3358049--3358078 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3358039 TATTAGTCGT
3358049 ACAAATTCAAATAAAA
1 ACAAATTCAAATAAAA
3358065 ACAAATT-AAATAAA
1 ACAAATTCAAATAAA
3358079 TTAAAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.70, C:0.10, G:0.00, T:0.20
Consensus pattern (16 bp):
ACAAATTCAAATAAAA
Found at i:3359349 original size:3 final size:3
Alignment explanation
Indices: 3359341--3359411 Score: 135
Period size: 3 Copynumber: 24.0 Consensus size: 3
3359331 TGGGTTTGTA
3359341 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3359388 AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT
3359412 GGTTGAAAAA
Statistics
Matches: 67, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 65 0.97
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:3366401 original size:42 final size:41
Alignment explanation
Indices: 3366327--3366425 Score: 126
Period size: 42 Copynumber: 2.4 Consensus size: 41
3366317 TCTTATGGAG
* * *
3366327 GACCCGAAGGATTTATCATCTTGCTCTAAAGGCTTACAGAT
1 GACCCGGAGGATTTATCATCATGCTCGAAAGGCTTACAGAT
* *
3366368 GACCCGGAGGATTTAATCATCATGCTCGGAAGGCTTACTGAT
1 GACCCGGAGGATTT-ATCATCATGCTCGAAAGGCTTACAGAT
* *
3366410 GGCCCGGAGGACTTAT
1 GACCCGGAGGATTTAT
3366426 AAATTGGGAA
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
41 15 0.30
42 35 0.70
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.26
Consensus pattern (41 bp):
GACCCGGAGGATTTATCATCATGCTCGAAAGGCTTACAGAT
Found at i:3366614 original size:41 final size:41
Alignment explanation
Indices: 3366555--3366632 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
3366545 CGAAGGACTT
* *
3366555 ATCATCTTGCTCTAAAGGCCTACAGATGACCCGGAGGTTTA
1 ATCATCATGCTCGAAAGGCCTACAGATGACCCGGAGGTTTA
* * * *
3366596 ATCATCATGCTCGGAAGGCTTACTGATGGCCCGGAGG
1 ATCATCATGCTCGAAAGGCCTACAGATGACCCGGAGG
3366633 ACTTATAAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (41 bp):
ATCATCATGCTCGAAAGGCCTACAGATGACCCGGAGGTTTA
Found at i:3366922 original size:214 final size:214
Alignment explanation
Indices: 3366298--3367680 Score: 2304
Period size: 214 Copynumber: 6.5 Consensus size: 214
3366288 ATCCTGGTGA
* *
3366298 AAAACATCCTGCCCGAAGGTCTTATGGA-GGACCCGAAGGATTTATCATCTTGCTCTAAAGGCTT
1 AAAACATCCTACCCGAAGGTCTTATGGATGG-CCCGAAGGACTTATCATCTTGCTCTAAAGGCTT
3366362 ACAGATGACCCGGAGGATTTAATCATCATGCTCGGAAGGCTTACTGATGGCCCGGAGGACTTATA
65 ACAGATGACCCGGAGGATTTAATCATCATGCTCGGAAGGCTTACTGATGGCCCGGAGGACTTATA
* *
3366427 AATTGGGAAATTTTGAAACTTGCATTCTTTGTTTTCAAAAAATCCATCTTCTTAAAACATCATTT
130 AATTGGGAAATTTTGAAACTCGCATTCTTCGTTTTCAAAAAATCCATCTTCTTAAAACATCATTT
3366492 TTCTTTTTCAAATTCATTTG
195 TTCTTTTTCAAATTCATTTG
*
3366512 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCCTA
1 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
3366577 CAGATGACCCGGAGG-TTTAATCATCATGCTCGGAAGGCTTACTGATGGCCCGGAGGACTTATAA
66 CAGATGACCCGGAGGATTTAATCATCATGCTCGGAAGGCTTACTGATGGCCCGGAGGACTTATAA
* *
3366641 ATTGGGAAATTTTGAAACTCGCATTCTTCGTTTTCAAAAAAACCATCTTCTTAAAACATTATTTT
131 ATTGGGAAATTTTGAAACTCGCATTCTTCGTTTTCAAAAAATCCATCTTCTTAAAACATCATTTT
3366706 TCTTTTTCAAATTCATTTG
196 TCTTTTTCAAATTCATTTG
*
3366725 AAAACATCCTACCCGAAGGTCTTATGGATGGCTCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
1 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
* * * *
3366790 CAGATGACCCGGAGGATTTAAGCATCATGCTTGAAAGACTTACTGATGGCCCGGAGGACTTATAA
66 CAGATGACCCGGAGGATTTAATCATCATGCTCGGAAGGCTTACTGATGGCCCGGAGGACTTATAA
3366855 ATTGGGAAATTTTGAAACTCGCATTCTTCGTTTTCAAAAAATCCATCTTCTTAAAACATCATTTT
131 ATTGGGAAATTTTGAAACTCGCATTCTTCGTTTTCAAAAAATCCATCTTCTTAAAACATCATTTT
3366920 TCTTTTTCAAATTCATTTG
196 TCTTTTTCAAATTCATTTG
*
3366939 AAAACATCCTACCCGTAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
1 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
* *
3367004 TAGATGACCCGGAGGATTTAATCATCATGCTCGTAAGGCTTACTGATGGCCCGGAGGACTTATAA
66 CAGATGACCCGGAGGATTTAATCATCATGCTCGGAAGGCTTACTGATGGCCCGGAGGACTTATAA
3367069 ATTGGGAAATTTTGAAACTCGCATTCTTCGTTTTCAAAAAA--C-TC--C----AACATCATTTT
131 ATTGGGAAATTTTGAAACTCGCATTCTTCGTTTTCAAAAAATCCATCTTCTTAAAACATCA-TTT
*
3367125 TTCATTTTCAAATTCATTTG
195 TTCTTTTTCAAATTCATTTG
*
3367145 AAAACATCCAACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
1 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
3367210 CAGATGACCCGGAGGATTTAATCATCATGCTCGGAAGGCTTACTGATGGCCCGGAGGACTTATAA
66 CAGATGACCCGGAGGATTTAATCATCATGCTCGGAAGGCTTACTGATGGCCCGGAGGACTTATAA
* *
3367275 ATTGGGAAATTTTGAAACTCTCATTCTTCGTTTTCAAAAAAATCCATCTTCTTAAAACGTCATTT
131 ATTGGGAAATTTTGAAACTCGCATTCTTCGTTTTC-AAAAAATCCATCTTCTTAAAACATCATTT
* *
3367340 TTCATTTTCAATTTCATTTG
195 TTCTTTTTCAAATTCATTTG
* *
3367360 AAAACATCCTACCCAAAGGTCTTATGGATGGCCCAAAGGACTTATCATCTTGCTCTAAAGGCTTA
1 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
* * * * *
3367425 TAGATGACCCAGAGGATTTAATCATCATGCTTGAAAGACTTACTGATGGCCCGGAGGACTTATAA
66 CAGATGACCCGGAGGATTTAATCATCATGCTCGGAAGGCTTACTGATGGCCCGGAGGACTTATAA
3367490 ATTGGGAAATTTTGAAACTCGCATTCTTCGTTTTC-AAAAA--C-TC--C----AACATCATTTT
131 ATTGGGAAATTTTGAAACTCGCATTCTTCGTTTTCAAAAAATCCATCTTCTTAAAACATCA--TT
*
3367545 TTTTTATTTTCAAATTCATTTG
194 TTTCT-TTTTCAAATTCATTTG
3367567 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
1 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
3367632 CAGATGACCCGGAGGATTTAATCATCATGCTCGGAAGGCTTACTGATGG
66 CAGATGACCCGGAGGATTTAATCATCATGCTCGGAAGGCTTACTGATGG
3367681 ATTTACTTCA
Statistics
Matches: 1103, Mismatches: 50, Indels: 39
0.93 0.04 0.03
Matches are distributed among these distances:
204 6 0.01
205 7 0.01
206 187 0.17
207 128 0.12
208 1 0.00
209 2 0.00
210 4 0.00
211 3 0.00
212 2 0.00
213 212 0.19
214 365 0.33
215 180 0.16
216 6 0.01
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (214 bp):
AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
CAGATGACCCGGAGGATTTAATCATCATGCTCGGAAGGCTTACTGATGGCCCGGAGGACTTATAA
ATTGGGAAATTTTGAAACTCGCATTCTTCGTTTTCAAAAAATCCATCTTCTTAAAACATCATTTT
TCTTTTTCAAATTCATTTG
Found at i:3367029 original size:42 final size:40
Alignment explanation
Indices: 3366959--3367066 Score: 128
Period size: 42 Copynumber: 2.6 Consensus size: 40
3366949 ACCCGTAGGT
* *
3366959 CTTATGGATGGCCCGAAGGACTTATCATCTTGCTC-TAAAGG
1 CTTAT-GATGGCCCGGAGGACTTATCATCATGCTCGT-AAGG
* *
3367000 CTTATAGATGACCCGGAGGATTTAATCATCATGCTCGTAAGG
1 CTTAT-GATGGCCCGGAGGACTT-ATCATCATGCTCGTAAGG
3367042 CTTACTGATGGCCCGGAGGACTTAT
1 CTTA-TGATGGCCCGGAGGACTTAT
3367067 AAATTGGGAA
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
41 21 0.37
42 34 0.60
43 2 0.04
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (40 bp):
CTTATGATGGCCCGGAGGACTTATCATCATGCTCGTAAGG
Found at i:3367110 original size:427 final size:421
Alignment explanation
Indices: 3366298--3367680 Score: 2364
Period size: 427 Copynumber: 3.3 Consensus size: 421
3366288 ATCCTGGTGA
* *
3366298 AAAACATCCTGCCCGAAGGTCTTATGGA-GGACCCGAAGGATTTATCATCTTGCTCTAAAGGCTT
1 AAAACATCCTACCCGAAGGTCTTATGGATGG-CCCGAAGGACTTATCATCTTGCTCTAAAGGCTT
3366362 ACAGATGACCCGGAGGATTTAATCATCATGCTCGGAAGGCTTACTGATGGCCCGGAGGACTTATA
65 ACAGATGACCCGGAGGATTTAATCATCATGCTCGGAAGGCTTACTGATGGCCCGGAGGACTTATA
* *
3366427 AATTGGGAAATTTTGAAACTTGCATTCTTTGTTTTCAAAAAATCCATCTTCTTAAAACATCATTT
130 AATTGGGAAATTTTGAAACTCGCATTCTTCGTTTTCAAAAAATCCATCTTCTTAAAACATCATTT
3366492 TTCTTTTTCAAATTCATTTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTAT
195 TTCTTTTTCAAATTCATTTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTAT
* * *
3366557 CATCTTGCTCTAAAGGCCTACAGATGACCCGGAGG-TTTAATCATCATGCTCGGAAGGCTTACTG
260 CATCTTGCTCTAAAGGCTTATAGATGACCCGGAGGATTTAATCATCATGCTCGAAAGGCTTACTG
3366621 ATGGCCCGGAGGACTTATAAATTGGGAAATTTTGAAACTCGCATTCTTCGTTTTCAAAAAAACCA
325 ATGGCCCGGAGGACTTATAAATTGGGAAATTTTGAAACTCGCATTCTTCGTTTTC-AAAAAA-C-
3366686 TCTTCTTAAAACATTATTTTTCTTTTTCAAATTCATTTG
387 TC--C--AAAACATTATTTTTCTTTTTCAAATTCATTTG
*
3366725 AAAACATCCTACCCGAAGGTCTTATGGATGGCTCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
1 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
* * * *
3366790 CAGATGACCCGGAGGATTTAAGCATCATGCTTGAAAGACTTACTGATGGCCCGGAGGACTTATAA
66 CAGATGACCCGGAGGATTTAATCATCATGCTCGGAAGGCTTACTGATGGCCCGGAGGACTTATAA
3366855 ATTGGGAAATTTTGAAACTCGCATTCTTCGTTTTCAAAAAATCCATCTTCTTAAAACATCATTTT
131 ATTGGGAAATTTTGAAACTCGCATTCTTCGTTTTCAAAAAATCCATCTTCTTAAAACATCATTTT
*
3366920 TCTTTTTCAAATTCATTTGAAAACATCCTACCCGTAGGTCTTATGGATGGCCCGAAGGACTTATC
196 TCTTTTTCAAATTCATTTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATC
*
3366985 ATCTTGCTCTAAAGGCTTATAGATGACCCGGAGGATTTAATCATCATGCTCGTAAGGCTTACTGA
261 ATCTTGCTCTAAAGGCTTATAGATGACCCGGAGGATTTAATCATCATGCTCGAAAGGCTTACTGA
3367050 TGGCCCGGAGGACTTATAAATTGGGAAATTTTGAAACTCGCATTCTTCGTTTTCAAAAAACTCC-
326 TGGCCCGGAGGACTTATAAATTGGGAAATTTTGAAACTCGCATTCTTCGTTTTCAAAAAACTCCA
* *
3367114 -AACATCATTTTTTCATTTTCAAATTCATTTG
391 AAACATTA-TTTTTCTTTTTCAAATTCATTTG
*
3367145 AAAACATCCAACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
1 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
3367210 CAGATGACCCGGAGGATTTAATCATCATGCTCGGAAGGCTTACTGATGGCCCGGAGGACTTATAA
66 CAGATGACCCGGAGGATTTAATCATCATGCTCGGAAGGCTTACTGATGGCCCGGAGGACTTATAA
* *
3367275 ATTGGGAAATTTTGAAACTCTCATTCTTCGTTTTCAAAAAAATCCATCTTCTTAAAACGTCATTT
131 ATTGGGAAATTTTGAAACTCGCATTCTTCGTTTTC-AAAAAATCCATCTTCTTAAAACATCATTT
* * * *
3367340 TTCATTTTCAATTTCATTTGAAAACATCCTACCCAAAGGTCTTATGGATGGCCCAAAGGACTTAT
195 TTCTTTTTCAAATTCATTTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTAT
* * *
3367405 CATCTTGCTCTAAAGGCTTATAGATGACCCAGAGGATTTAATCATCATGCTTGAAAGACTTACTG
260 CATCTTGCTCTAAAGGCTTATAGATGACCCGGAGGATTTAATCATCATGCTCGAAAGGCTTACTG
3367470 ATGGCCCGGAGGACTTATAAATTGGGAAATTTTGAAACTCGCATTCTTCGTTTTC-AAAAACTCC
325 ATGGCCCGGAGGACTTATAAATTGGGAAATTTTGAAACTCGCATTCTTCGTTTTCAAAAAACTCC
* *
3367534 AACATCATT-TTTTTTTATTTTCAAATTCATTTG
390 AA-AACATTATTTTTCT-TTTTCAAATTCATTTG
3367567 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
1 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
3367632 CAGATGACCCGGAGGATTTAATCATCATGCTCGGAAGGCTTACTGATGG
66 CAGATGACCCGGAGGATTTAATCATCATGCTCGGAAGGCTTACTGATGG
3367681 ATTTACTTCA
Statistics
Matches: 911, Mismatches: 37, Indels: 21
0.94 0.04 0.02
Matches are distributed among these distances:
419 6 0.01
420 189 0.21
421 209 0.23
422 129 0.14
423 5 0.01
425 2 0.00
426 1 0.00
427 285 0.31
428 85 0.09
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (421 bp):
AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
CAGATGACCCGGAGGATTTAATCATCATGCTCGGAAGGCTTACTGATGGCCCGGAGGACTTATAA
ATTGGGAAATTTTGAAACTCGCATTCTTCGTTTTCAAAAAATCCATCTTCTTAAAACATCATTTT
TCTTTTTCAAATTCATTTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATC
ATCTTGCTCTAAAGGCTTATAGATGACCCGGAGGATTTAATCATCATGCTCGAAAGGCTTACTGA
TGGCCCGGAGGACTTATAAATTGGGAAATTTTGAAACTCGCATTCTTCGTTTTCAAAAAACTCCA
AAACATTATTTTTCTTTTTCAAATTCATTTG
Found at i:3367248 original size:42 final size:41
Alignment explanation
Indices: 3367171--3367272 Score: 132
Period size: 42 Copynumber: 2.5 Consensus size: 41
3367161 AGGTCTTATG
* * *
3367171 GATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACA
1 GATGGCCCGGAGGACTTATCATCATGCTCGAAAGGCTTACA
* * * *
3367212 GATGACCCGGAGGATTTAATCATCATGCTCGGAAGGCTTACT
1 GATGGCCCGGAGGACTT-ATCATCATGCTCGAAAGGCTTACA
3367254 GATGGCCCGGAGGACTTAT
1 GATGGCCCGGAGGACTTAT
3367273 AAATTGGGAA
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
41 16 0.31
42 35 0.69
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.25
Consensus pattern (41 bp):
GATGGCCCGGAGGACTTATCATCATGCTCGAAAGGCTTACA
Found at i:3367449 original size:42 final size:42
Alignment explanation
Indices: 3367374--3367455 Score: 103
Period size: 41 Copynumber: 2.0 Consensus size: 42
3367364 CATCCTACCC
* * *
3367374 AAAGGTCTTATGGATGGCCCAAAGGACTTATCATCTTGCTCT
1 AAAGGTCTTATAGATGACCCAAAGGACTTATCATCATGCTCT
* *
3367416 AAAGG-CTTATAGATGACCCAGAGGATTTAATCATCATGCT
1 AAAGGTCTTATAGATGACCCAAAGGACTT-ATCATCATGCT
3367456 TGAAAGACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
41 19 0.56
42 15 0.44
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (42 bp):
AAAGGTCTTATAGATGACCCAAAGGACTTATCATCATGCTCT
Found at i:3367670 original size:42 final size:41
Alignment explanation
Indices: 3367593--3367679 Score: 102
Period size: 42 Copynumber: 2.1 Consensus size: 41
3367583 AGGTCTTATG
* * *
3367593 GATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACA
1 GATGACCCGAAGGACTTATCATCATGCTCGAAAGGCTTACA
* * * *
3367634 GATGACCCGGAGGATTTAATCATCATGCTCGGAAGGCTTACT
1 GATGACCCGAAGGACTT-ATCATCATGCTCGAAAGGCTTACA
3367676 GATG
1 GATG
3367680 GATTTACTTC
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 14 0.37
42 24 0.63
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.26
Consensus pattern (41 bp):
GATGACCCGAAGGACTTATCATCATGCTCGAAAGGCTTACA
Found at i:3368977 original size:16 final size:16
Alignment explanation
Indices: 3368956--3368988 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3368946 AGCTGCAAGG
3368956 ACTTTTCACGTTTGAA
1 ACTTTTCACGTTTGAA
*
3368972 ACTTTTCATGTTTGAA
1 ACTTTTCACGTTTGAA
3368988 A
1 A
3368989 ATGTTTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.45
Consensus pattern (16 bp):
ACTTTTCACGTTTGAA
Found at i:3369912 original size:5 final size:5
Alignment explanation
Indices: 3369902--3369956 Score: 74
Period size: 5 Copynumber: 10.2 Consensus size: 5
3369892 ATTTTCAATT
3369902 TTTTC TTTTC TTTTC TTTTC TTTTC TTTCTTC TTTTC TTTTCC TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC -TT-TTC TTTTC TTTT-C TTTTC
3369950 TCTTTC T
1 T-TTTC T
3369957 ACATTTCTCT
Statistics
Matches: 46, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
5 29 0.63
6 14 0.30
7 3 0.07
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTTC
Found at i:3369956 original size:22 final size:20
Alignment explanation
Indices: 3369902--3369956 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 20
3369892 ATTTTCAATT
3369902 TTTTCTTTTCTTTTCTTTTC
1 TTTTCTTTTCTTTTCTTTTC
3369922 TTTTCTTTCTTCTTTTCTTTTCC
1 TTTTC-TT-TTCTTTTCTTTT-C
3369945 TTTTCTCTTTCT
1 TTTTCT-TTTCT
3369957 ACATTTCTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
20 5 0.16
21 2 0.06
22 17 0.55
23 7 0.23
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTCTTTTCTTTTCTTTTC
Found at i:3369963 original size:25 final size:23
Alignment explanation
Indices: 3369913--3369976 Score: 76
Period size: 25 Copynumber: 2.7 Consensus size: 23
3369903 TTTCTTTTCT
* *
3369913 TTTCTTTTCTTT-TCTTTCTTCT
1 TTTCTTTTCTTTCTCTTTCTACA
3369935 TTTCTTTTCCTTTTCTCTTTCTACA
1 TTTCTTTT-C-TTTCTCTTTCTACA
*
3369960 TTTCTCTTCTTTCTCTT
1 TTTCTTTTCTTTCTCTT
3369977 CATAATGACA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
22 8 0.22
23 9 0.25
24 4 0.11
25 15 0.42
ACGTcount: A:0.03, C:0.27, G:0.00, T:0.70
Consensus pattern (23 bp):
TTTCTTTTCTTTCTCTTTCTACA
Found at i:3369964 original size:33 final size:28
Alignment explanation
Indices: 3369893--3369955 Score: 83
Period size: 27 Copynumber: 2.2 Consensus size: 28
3369883 ATTTTCCTCA
*
3369893 TTTTCAATTTTTTCTTTTCTTTTCTTTTC
1 TTTTC-ATTTCTTCTTTTCTTTTCTTTTC
3369922 TTTTC-TTTCTTCTTTTCTTTTCCTTTTC
1 TTTTCATTTCTTCTTTTCTTTT-CTTTTC
3369950 TCTTTC
1 T-TTTC
3369956 TACATTTCTC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 15 0.48
28 7 0.23
29 9 0.29
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.75
Consensus pattern (28 bp):
TTTTCATTTCTTCTTTTCTTTTCTTTTC
Found at i:3372010 original size:21 final size:21
Alignment explanation
Indices: 3371962--3372121 Score: 200
Period size: 21 Copynumber: 7.7 Consensus size: 21
3371952 TCCATGCGAT
* *
3371962 ATGGTCTTCTCGTCTTTACGA
1 ATGGTCTTCTCGTCTTGATGA
*
3371983 A-GGTCTTCTCGTCTTTATGA
1 ATGGTCTTCTCGTCTTGATGA
*
3372003 AGGGTCTTCTCGTCTTGATGA
1 ATGGTCTTCTCGTCTTGATGA
3372024 ATGG-CATTCTCGTCTTGATGA
1 ATGGTC-TTCTCGTCTTGATGA
*
3372045 ATGGCCTTCTCGTCTTGATGA
1 ATGGTCTTCTCGTCTTGATGA
* *
3372066 ATGGTATTCTCATCTTGATGA
1 ATGGTCTTCTCGTCTTGATGA
*
3372087 AT-GACATTCTCGTCTTGATGA
1 ATGGTC-TTCTCGTCTTGATGA
*
3372108 ATGCTCTTCTCGTC
1 ATGGTCTTCTCGTC
3372122 CTTGGTACGA
Statistics
Matches: 123, Mismatches: 11, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
20 21 0.17
21 100 0.81
22 2 0.02
ACGTcount: A:0.17, C:0.21, G:0.21, T:0.41
Consensus pattern (21 bp):
ATGGTCTTCTCGTCTTGATGA
Found at i:3382417 original size:8 final size:8
Alignment explanation
Indices: 3382404--3382431 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
3382394 AGATTCTCCC
3382404 ATATGTAT
1 ATATGTAT
3382412 ATATGTAT
1 ATATGTAT
3382420 ATATGTAT
1 ATATGTAT
3382428 ATAT
1 ATAT
3382432 CTTCTTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (8 bp):
ATATGTAT
Found at i:3385937 original size:13 final size:13
Alignment explanation
Indices: 3385921--3385945 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3385911 ATGAGTGAAA
3385921 AAAAAATAAAAAT
1 AAAAAATAAAAAT
3385934 AAAAAATAAAAA
1 AAAAAATAAAAA
3385946 ATGATGAAAA
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:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAAATAAAAAT
Done.