Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008656.1 Hibiscus syriacus cultivar Beakdansim tig00111650_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: 2456495
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 12
Found at i:2356443 original size:34 final size:33
Alignment explanation
Indices: 2356355--2356450 Score: 138
Period size: 33 Copynumber: 2.8 Consensus size: 33
2356345 AAAACAGACT
* **
2356355 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
*
2356389 ATCGCAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
2356422 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
2356451 CGAAACTCAT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
33 31 0.54
34 26 0.46
ACGTcount: A:0.42, C:0.21, G:0.24, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:2356446 original size:20 final size:19
Alignment explanation
Indices: 2356388--2356455 Score: 74
Period size: 19 Copynumber: 3.8 Consensus size: 19
2356378 GCAACGAGAG
2356388 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2356407 AATCGCAA--CG-AGTG--
1 AATCGCAATGCGAAATGAA
2356421 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
2356441 AATCGCAACGCGAAA
1 AATCGCAATGCGAAA
2356456 CTCATTGCGA
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
14 8 0.20
16 5 0.12
17 2 0.05
18 3 0.08
19 11 0.28
20 11 0.28
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:2356488 original size:20 final size:20
Alignment explanation
Indices: 2356460--2356731 Score: 129
Period size: 20 Copynumber: 14.6 Consensus size: 20
2356450 GCGAAACTCA
2356460 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCG
* * * *
2356480 TTACGATAGTCAATTCCGCA
1 TTGCGATAGTCATTTTCGCG
**
2356500 TTGCGATAGTCA-TTTCTATG
1 TTGCGATAGTCATTTTC-GCG
*
2356520 TTGCGATAGTCATATTCGCG
1 TTGCGATAGTCATTTTCGCG
2356540 TT--G-T-G--ATTTTCGCG
1 TTGCGATAGTCATTTTCGCG
* ** *
2356554 TTGCAATTTTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCG
*
2356574 TTGCGAT--TCA----CTCG
1 TTGCGATAGTCATTTTCGCG
** *
2356588 TTGCGATTTTCA-TTTCGCA
1 TTGCGATAGTCATTTTCGCG
* ** *
2356607 TTACGATTTTCA-TTTCGCA
1 TTGCGATAGTCATTTTCGCG
*
2356626 TTGCGAT--TC----TCTCG
1 TTGCGATAGTCATTTTCGCG
2356640 TTGCGATAGTCA-TTTCTGCG
1 TTGCGATAGTCATTTTC-GCG
* * * *
2356660 TTGTGATAGTCAATTCCGCA
1 TTGCGATAGTCATTTTCGCG
* *
2356680 TTGCGATAGTCATTTCCGTG
1 TTGCGATAGTCATTTTCGCG
*
2356700 TTGCGATAGTCATATTCGCG
1 TTGCGATAGTCATTTTCGCG
2356720 TTGCGATAGTCA
1 TTGCGATAGTCA
2356732 AATGAATGTC
Statistics
Matches: 196, Mismatches: 36, Indels: 40
0.72 0.13 0.15
Matches are distributed among these distances:
14 29 0.15
16 6 0.03
17 4 0.02
18 4 0.02
19 31 0.16
20 116 0.59
21 6 0.03
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.40
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCG
Found at i:2356572 original size:34 final size:34
Alignment explanation
Indices: 2356550--2356614 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 34
2356540 TTGTGATTTT
2356550 CGCGTTGCAATTTTCATTTTCGCATTGCGATTCA
1 CGCGTTGCAATTTTCATTTTCGCATTGCGATTCA
* * *
2356584 CTCGTTGCGATTTTCA-TTTCGCATTACGATT
1 CGCGTTGCAATTTTCATTTTCGCATTGCGATT
2356615 TTCATTTCGC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 14 0.50
34 14 0.50
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.43
Consensus pattern (34 bp):
CGCGTTGCAATTTTCATTTTCGCATTGCGATTCA
Found at i:2356615 original size:19 final size:19
Alignment explanation
Indices: 2356591--2356633 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
2356581 TCACTCGTTG
2356591 CGATTTTCATTTCGCATTA
1 CGATTTTCATTTCGCATTA
*
2356610 CGATTTTCATTTCGCATTG
1 CGATTTTCATTTCGCATTA
2356629 CGATT
1 CGATT
2356634 CTCTCGTTGC
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:0.19, C:0.21, G:0.14, T:0.47
Consensus pattern (19 bp):
CGATTTTCATTTCGCATTA
Found at i:2360165 original size:20 final size:20
Alignment explanation
Indices: 2360055--2360485 Score: 199
Period size: 20 Copynumber: 21.4 Consensus size: 20
2360045 CAGAATCTCG
2360055 TTGC-ATTTACAG-ATTCGCA
1 TTGCGATTTAC-GTATTCGCA
*
2360074 TTGCGATTTACAG-ATTCACA
1 TTGCGATTTAC-GTATTCGCA
*
2360094 TTGCGATTTATGTATTCGCA
1 TTGCGATTTACGTATTCGCA
2360114 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
*
2360134 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTATTCGCA
*
2360154 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTATTCGCA
* * *
2360174 TTGCGAATTAGGAAATTCGCA
1 TTGCGATTTACG-TATTCGCA
** ** * *
2360195 ACGCGAATTTGGGAAATCGCA
1 TTGCG-ATTTACGTATTCGCA
* * * *
2360216 ATGCGATAGT-CAG-AATCGCG
1 TTGCGAT-TTAC-GTATTCGCA
* * **
2360236 TTGCGA-AT-CTGGAAACTG-A
1 TTGCGATTTAC-GTATTC-GCA
* * *
2360255 TTTGCGA--TACCGAAGATCGCG
1 -TTGCGATTTA-CGTA-TTCGCA
* *
2360276 TTGCGAATTATCG-A-TCGCG
1 TTGCGATTTA-CGTATTCGCA
* * *
2360295 TTGCGATTTACGGATACGCG
1 TTGCGATTTACGTATTCGCA
*
2360315 TTGCGATTTTACGTATT-GTCG
1 TTGCGA-TTTACGTATTCG-CA
* *
2360336 TTGCGATTTACGGATACGCA
1 TTGCGATTTACGTATTCGCA
* *
2360356 TTGCGATTTACGTATTCTCG
1 TTGCGATTTACGTATTCGCA
*
2360376 TTGCGATTTACAG-ATACGCA
1 TTGCGATTTAC-GTATTCGCA
* *
2360396 TTGCGATTTACGTATTCTCG
1 TTGCGATTTACGTATTCGCA
* ** *
2360416 TTGCGATTTACGGATAGGCG
1 TTGCGATTTACGTATTCGCA
*
2360436 TTGCGATTTTACGTATT-GTCG
1 TTGCGA-TTTACGTATTCG-CA
* * *
2360457 TTGCGATTTACGGATACGCG
1 TTGCGATTTACGTATTCGCA
2360477 TTGCGATTT
1 TTGCGATTT
2360486 TACGGATACT
Statistics
Matches: 335, Mismatches: 52, Indels: 49
0.77 0.12 0.11
Matches are distributed among these distances:
18 5 0.01
19 25 0.07
20 235 0.70
21 61 0.18
22 9 0.03
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:2360200 original size:21 final size:21
Alignment explanation
Indices: 2360167--2360221 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
2360157 CGATTTACGT
**
2360167 AATCGCATTGCGAA-TTAGGA
1 AATCGCAACGCGAATTTAGGA
*
2360187 AATTCGCAACGCGAATTTGGGA
1 AA-TCGCAACGCGAATTTAGGA
*
2360209 AATCGCAATGCGA
1 AATCGCAACGCGA
2360222 TAGTCAGAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 2 0.07
21 20 0.69
22 7 0.24
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (21 bp):
AATCGCAACGCGAATTTAGGA
Found at i:2360343 original size:41 final size:41
Alignment explanation
Indices: 2360293--2360504 Score: 338
Period size: 41 Copynumber: 5.2 Consensus size: 41
2360283 TTATCGATCG
*
2360293 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
2360334 CGTTGCGATTTACGGATACGCATTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
2360374 CGTTGCGATTTACAGATACGCATTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
2360414 CGTTGCGATTTACGGATAGGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
2360455 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
2360496 CGTTGCGAT
1 CGTTGCGAT
2360505 AGTCAGAATC
Statistics
Matches: 159, Mismatches: 11, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
40 75 0.47
41 84 0.53
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.37
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:2360536 original size:20 final size:20
Alignment explanation
Indices: 2360513--2360565 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
2360503 ATAGTCAGAA
*
2360513 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
2360533 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
2360553 TCGCGTTGCGATT
1 TCGCGTTGCGATT
2360566 CTGAAAAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.13, C:0.19, G:0.25, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:2360557 original size:40 final size:40
Alignment explanation
Indices: 2360272--2360565 Score: 239
Period size: 40 Copynumber: 7.3 Consensus size: 40
2360262 TACCGAAGAT
* *
2360272 CGCGTTGCGAATTAT-CGATCGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTATACGTTCGCGTTGCGATTTACGGATA
*
2360311 CGCGTTGCGATTT-TACGTATTGTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTATACGT-TCG-CGTTGCGATTTACGGATA
* * *
2360352 CGCATTGCGA-TT-TACGTATTCTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTATACG--TTCGCGTTGCGATTTACGGATA
* *
2360392 CGCATTGCGA-TT-TACGTATTCTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTATACG--TTCGCGTTGCGATTTACGGATA
* *
2360432 GGCGTTGCGATTT-TACGTATTGTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTATACGT-TCG-CGTTGCGATTTACGGATA
* * * *
2360473 CGCGTTGCGATTT-TACGGATACTCGTTGCGATAGT-CAGA-A
1 CGCGTTGCGATTTATAC-G-TTCGCGTTGCGAT-TTACGGATA
* * ** *
2360513 TCGCGTTGCGATTTATATGTTCGCGTTGCGATTTTCATATT
1 -CGCGTTGCGATTTATACGTTCGCGTTGCGATTTACGGATA
2360554 CGCGTTGCGATT
1 CGCGTTGCGATT
2360566 CTGAAAAATC
Statistics
Matches: 216, Mismatches: 24, Indels: 29
0.80 0.09 0.11
Matches are distributed among these distances:
38 1 0.00
39 16 0.07
40 100 0.46
41 93 0.43
42 5 0.02
43 1 0.00
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.37
Consensus pattern (40 bp):
CGCGTTGCGATTTATACGTTCGCGTTGCGATTTACGGATA
Found at i:2360583 original size:21 final size:21
Alignment explanation
Indices: 2360559--2360610 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
2360549 ATATTCGCGT
2360559 TGCGATTCTGAAAAATCGCAA
1 TGCGATTCTGAAAAATCGCAA
* ** *
2360580 TGCGAATT-TGTACTATCGCAT
1 TGCG-ATTCTGAAAAATCGCAA
2360601 TGCGATTCTG
1 TGCGATTCTG
2360611 GGAACTGATT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 3 0.12
21 19 0.76
22 3 0.12
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (21 bp):
TGCGATTCTGAAAAATCGCAA
Found at i:2370071 original size:3 final size:3
Alignment explanation
Indices: 2370058--2370178 Score: 85
Period size: 3 Copynumber: 41.0 Consensus size: 3
2370048 ATATATTTGA
* * *
2370058 AAT AAT AAAT AAT AAT AAT -AT AGT AAT AAT AAA AAA AGAT AA- AAT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT
* *
2370103 GAA- AAT AAT AAAT ATT AAT TAT AAT AAT AA- AA- AAT AAT AAT AAT
1 -AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
2370147 AAAT ACT AAT AA- AAT AAT ATT AAT AA- AAT AAT
1 -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2370179 GATAGGGTAT
Statistics
Matches: 95, Mismatches: 12, Indels: 22
0.74 0.09 0.17
Matches are distributed among these distances:
2 14 0.15
3 68 0.72
4 13 0.14
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:2370086 original size:11 final size:11
Alignment explanation
Indices: 2370058--2370176 Score: 66
Period size: 10 Copynumber: 11.9 Consensus size: 11
2370048 ATATATTTGA
2370058 AATAATAA-AT
1 AATAATAATAT
2370068 AATAATAATAT
1 AATAATAATAT
*
2370079 AGTAATAATA-
1 AATAATAATAT
*
2370089 AA-AA-AAGAT
1 AATAATAATAT
*
2370098 AA-AATGA-A-
1 AATAATAATAT
2370106 AATAATAA-AT
1 AATAATAATAT
* *
2370116 ATTAATTATAAT
1 AATAATAAT-AT
*
2370128 AATAA-AAAAT
1 AATAATAATAT
2370138 AATAATAATA-
1 AATAATAATAT
* *
2370148 AATACTAATAA
1 AATAATAATAT
2370159 AATAAT-AT-T
1 AATAATAATAT
2370168 AATAA-AATA
1 AATAATAATA
2370177 ATGATAGGGT
Statistics
Matches: 84, Mismatches: 14, Indels: 22
0.70 0.12 0.18
Matches are distributed among these distances:
8 5 0.06
9 19 0.23
10 34 0.40
11 20 0.24
12 6 0.07
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (11 bp):
AATAATAATAT
Found at i:2370178 original size:14 final size:13
Alignment explanation
Indices: 2370058--2370174 Score: 78
Period size: 13 Copynumber: 8.8 Consensus size: 13
2370048 ATATATTTGA
*
2370058 AATAATAAATAAT
1 AATAATAAAAAAT
**
2370071 AATAATATAGTAAT
1 AATAATA-AAAAAT
2370085 AATAA-AAAAAGAT
1 AATAATAAAAA-AT
2370098 AA-AATGAAAATAAT
1 AATAAT-AAAA-AAT
* **
2370112 AA-ATATTAATTAT
1 AATA-ATAAAAAAT
2370125 AATAATAAAAAAT
1 AATAATAAAAAAT
*
2370138 AATAATAATAAAT
1 AATAATAAAAAAT
*
2370151 ACTAATAAAATAAT
1 AATAATAAAA-AAT
*
2370165 ATTAATAAAA
1 AATAATAAAA
2370175 TAATGATAGG
Statistics
Matches: 83, Mismatches: 13, Indels: 15
0.75 0.12 0.14
Matches are distributed among these distances:
12 4 0.05
13 42 0.51
14 34 0.41
15 3 0.04
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.29
Consensus pattern (13 bp):
AATAATAAAAAAT
Found at i:2371146 original size:102 final size:101
Alignment explanation
Indices: 2370931--2371187 Score: 333
Period size: 102 Copynumber: 2.6 Consensus size: 101
2370921 TCTATCTTAG
* * * * *
2370931 GTGAGAT-AATTGTT-TTTCGAATG-AACAATTTTAACTTGTGTGTTTCAAGGGAAAATATCTCA
1 GTGAGATGAATTTTTGTTTCGAGTGAAACAATTTCAAATTTTGTGTTTCAAGGGAAAATATCTCA
*
2370993 AGTGAGACAAGATTGATTTAAAAAAAACAATTTCAA
66 AGCGAGACAAGATTGATTTAAAAAAAACAATTTCAA
* * * * *
2371029 GTGAGATGAAATTTTGTTTCGAGTGAAACTATTTCAAGTTTTGTGTTCCAAGGGAAACTATCTCA
1 GTGAGATGAATTTTTGTTTCGAGTGAAACAATTTCAAATTTTGTGTTTCAAGGGAAAATATCTCA
*
2371094 AGCGAGACGAA-ATTGATTTTAAGAAAAACAATTTCAA
66 AGCGAGAC-AAGATTGA-TTTAAAAAAAACAATTTCAA
* * *
2371131 GTGAGATGAATTTTTGTTTCGAGTTAAACAATTACAAAATTTGTGTTTCAAGGGAAA
1 GTGAGATGAATTTTTGTTTCGAGTGAAACAATTTCAAATTTTGTGTTTCAAGGGAAA
2371188 TTGTTTTAAG
Statistics
Matches: 136, Mismatches: 18, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
98 7 0.05
99 5 0.04
100 8 0.06
101 45 0.33
102 71 0.52
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.34
Consensus pattern (101 bp):
GTGAGATGAATTTTTGTTTCGAGTGAAACAATTTCAAATTTTGTGTTTCAAGGGAAAATATCTCA
AGCGAGACAAGATTGATTTAAAAAAAACAATTTCAA
Found at i:2371199 original size:102 final size:101
Alignment explanation
Indices: 2370969--2371248 Score: 328
Period size: 102 Copynumber: 2.7 Consensus size: 101
2370959 TTTTAACTTG
* *
2370969 TGTGTTTCAAGGGAAAATATCTCAAGTGAGACAAGATTGA-TTTAAAAAAAACAATTTCAAGTGA
1 TGTGTTTCAAGGGAAAATATCTCAAGCGAGACAA-ATTGATTTTAAGAAAAACAATTTCAAGTGA
* * **
2371033 GATGAAATTTTGTTTCGAGTGAAACTATTTCAAGTTT
65 GATGAAATTTTGTTTCGAGTGAAACAATTACAAAATT
* *
2371070 TGTGTTCCAAGGGAAACTATCTCAAGCGAGACGAAATTGATTTTAAGAAAAACAATTTCAAGTGA
1 TGTGTTTCAAGGGAAAATATCTCAAGCGAGAC-AAATTGATTTTAAGAAAAACAATTTCAAGTGA
* *
2371135 GATGAATTTTTGTTTCGAGTTAAACAATTACAAAATT
65 GATGAAATTTTGTTTCGAGTGAAACAATTACAAAATT
* * * * * * * * *
2371172 TGTGTTTCAAGGGAAATTGTTTTAAGCGAGACATAATTTGTTTTTAAAGAAAAATAATCTCCACT
1 TGTGTTTCAAGGGAAAATATCTCAAGCGAGACA-AA-TTGATTTT-AAGAAAAACAATTTCAAGT
*
2371237 GAGATAAAATTT
63 GAGATGAAATTT
2371249 ATTGGATCAA
Statistics
Matches: 152, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
101 35 0.23
102 85 0.56
103 7 0.05
104 25 0.16
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.34
Consensus pattern (101 bp):
TGTGTTTCAAGGGAAAATATCTCAAGCGAGACAAATTGATTTTAAGAAAAACAATTTCAAGTGAG
ATGAAATTTTGTTTCGAGTGAAACAATTACAAAATT
Found at i:2371611 original size:160 final size:162
Alignment explanation
Indices: 2371296--2371913 Score: 966
Period size: 164 Copynumber: 3.9 Consensus size: 162
2371286 CATTTTCCCA
* *
2371296 AAAATATCATGCCTGAAGGTCTTACTGATTT-TTGGAATTAATTTACTAAG---G--ACTTTGGA
1 AAAATATCATGCCTGAAGGTCTTACTGATTTCTTGAAAATAATTTACTAAGTAAGAAACTTTGGA
* * *
2371355 AATCGTTTTCTTACTTTTCAAAAATTTCAATTTTAGGAAAGATTAAATGAGAAACTTTGAAAATC
66 AATCGTTTTCTTACTTTTCAAAAATTTCAATTTTGGGAAAGATTAAGTGAGAAACTTTGAAAATA
* *
2371420 GATTTCTCATTTTTTTC-AAAAATATCAAATG
131 AATTTCTCATTTTTTACAAAAAATATCAAATG
* * *
2371451 AAAATATTATGCCTGAAGGTCTTACTGATTTCATGAAAATAATTTACTACGTAAG-AACTTTGGA
1 AAAATATCATGCCTGAAGGTCTTACTGATTTCTTGAAAATAATTTACTAAGTAAGAAACTTTGGA
2371515 AATCGTTTTCTTACTTTTC-AAAATTTCAATTTTGGGAAAGATTAAGTGAGAAACTTTGAAAATA
66 AATCGTTTTCTTACTTTTCAAAAATTTCAATTTTGGGAAAGATTAAGTGAGAAACTTTGAAAATA
*
2371579 AATTTCTCATTTTTTCCAAAAAATATCAAATG
131 AATTTCTCATTTTTTACAAAAAATATCAAATG
*
2371611 AAAATATCATGCCTGAAGGTCTTACTGATTTCTTGAAAATAATTTACTAAGTAAGAAACTTTGAA
1 AAAATATCATGCCTGAAGGTCTTACTGATTTCTTGAAAATAATTTACTAAGTAAGAAACTTTGGA
* *
2371676 AATTGTTTTCTTACTTTTCAAAAATTTCAATTTTGGGAAAGATTAAGTGAGAAAATTTGAAAATC
66 AATCGTTTTCTTACTTTTCAAAAATTTCAATTTTGGGAAAGATTAAGTGAGAAACTTTGAAAAT-
** * *
2371741 AAATTTCTCATTTTAAAAAAAAAATATCATATG
130 AAATTTCTCATTTTTTACAAAAAATATCAAATG
2371774 AAAAATATCATGCCTGAAGGTCTTACTGATTTCTTGAAAATAATTTACTAAGTAAGAAACTTTGG
1 -AAAATATCATGCCTGAAGGTCTTACTGATTTCTTGAAAATAATTTACTAAGTAAGAAACTTTGG
* *
2371839 AAATTGTTTTCTTACTTTTCAAAAATTTCAATTTTGGGAAATATTAAGTGAGAAACTTTGAAAAT
65 AAATCGTTTTCTTACTTTTCAAAAATTTCAATTTTGGGAAAGATTAAGTGAGAAACTTTGAAAAT
*
2371904 CAATTTCTCA
130 AAATTTCTCA
2371914 CAAATCATAT
Statistics
Matches: 428, Mismatches: 25, Indels: 12
0.92 0.05 0.03
Matches are distributed among these distances:
155 30 0.07
156 15 0.04
159 58 0.14
160 93 0.22
161 26 0.06
162 43 0.10
163 37 0.09
164 126 0.29
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Consensus pattern (162 bp):
AAAATATCATGCCTGAAGGTCTTACTGATTTCTTGAAAATAATTTACTAAGTAAGAAACTTTGGA
AATCGTTTTCTTACTTTTCAAAAATTTCAATTTTGGGAAAGATTAAGTGAGAAACTTTGAAAATA
AATTTCTCATTTTTTACAAAAAATATCAAATG
Found at i:2377999 original size:81 final size:81
Alignment explanation
Indices: 2377878--2378320 Score: 608
Period size: 81 Copynumber: 5.5 Consensus size: 81
2377868 TCAAAAGTGT
* * * *
2377878 TTAA-CGTTCGTCCAACTAGCATAATTGACACATTTCTGCCAATTGCACAACTAGGCCATTTTTC
1 TTAACCGTTCATCTAACTAGCATAATTGACACCTTTCTGTCAATTGCACAACTAGGCCATTTTTC
*
2377942 TTTTACTCAACTGTAC
66 TTTTACTCAACGGTAC
* * * *
2377958 TTAACCGTTCATCTAACTAGCATAATTGAAACCTTTTTGCCAATTGCACAACTAAGCCATTTTTC
1 TTAACCGTTCATCTAACTAGCATAATTGACACCTTTCTGTCAATTGCACAACTAGGCCATTTTTC
2378023 TTTTACTCAACGGTAC
66 TTTTACTCAACGGTAC
* * **
2378039 TTAACCGTTCATCCAACTGGCATAATTGACATTTTTCTGTCAATTGCACAACTAGGCCATTTTTC
1 TTAACCGTTCATCTAACTAGCATAATTGACACCTTTCTGTCAATTGCACAACTAGGCCATTTTTC
2378104 TTTTACTCAACGGTAC
66 TTTTACTCAACGGTAC
* * * *** *
2378120 TTAACCGTTCATCTAACTGGCATAATTAACACCTTTCTATCAATTGCATTGCTAGGCCA---TTG
1 TTAACCGTTCATCTAACTAGCATAATTGACACCTTTCTGTCAATTGCACAACTAGGCCATTTTTC
*
2378182 TTTTACTCAATGGTAC
66 TTTTACTCAACGGTAC
* * * *
2378198 TTAACCGTTCATCTAACTGGCTTAATTGACACATTTCTGTCAATTGCACAGCTAGGCCATTTTTC
1 TTAACCGTTCATCTAACTAGCATAATTGACACCTTTCTGTCAATTGCACAACTAGGCCATTTTTC
2378263 TTTTACTCAACGGTAC
66 TTTTACTCAACGGTAC
*
2378279 ATAACCGTTCATCTAAC-AGGCATAATTGACACCTTTCTGTCA
1 TTAACCGTTCATCTAACTA-GCATAATTGACACCTTTCTGTCA
2378321 TATGTACAGT
Statistics
Matches: 321, Mismatches: 37, Indels: 9
0.87 0.10 0.02
Matches are distributed among these distances:
78 70 0.22
80 4 0.01
81 247 0.77
ACGTcount: A:0.27, C:0.25, G:0.12, T:0.36
Consensus pattern (81 bp):
TTAACCGTTCATCTAACTAGCATAATTGACACCTTTCTGTCAATTGCACAACTAGGCCATTTTTC
TTTTACTCAACGGTAC
Found at i:2378261 original size:159 final size:160
Alignment explanation
Indices: 2377878--2378316 Score: 632
Period size: 159 Copynumber: 2.7 Consensus size: 160
2377868 TCAAAAGTGT
* * *
2377878 TTAA-CGTTCGTCCAACTAGCATAATTGACACATTTCTGCCAATTGCACAACTAGGCCATTTTTC
1 TTAACCGTTCATCCAACTGGCATAATTGACACATTTCTGTCAATTGCACAACTAGGCCATTTTTC
* * * *
2377942 TTTTACTCAACTGTACTTAACCGTTCATCTAACTAGCATAATTGAA-ACCTTTTTGCCAATTGCA
66 TTTTACTCAACGGTACTTAACCGTTCATCTAACTGGCATAATT-AACACCTTTCTACCAATTGCA
2378006 CAACTAAGCCATTTTTCTTTTACTCAACGGTAC
130 CAACTAAGCCA--TTTCTTTTACTCAACGGTAC
**
2378039 TTAACCGTTCATCCAACTGGCATAATTGACATTTTTCTGTCAATTGCACAACTAGGCCATTTTTC
1 TTAACCGTTCATCCAACTGGCATAATTGACACATTTCTGTCAATTGCACAACTAGGCCATTTTTC
* *
2378104 TTTTACTCAACGGTACTTAACCGTTCATCTAACTGGCATAATTAACACCTTTCTATCAATTGCAT
66 TTTTACTCAACGGTACTTAACCGTTCATCTAACTGGCATAATTAACACCTTTCTACCAATTGCAC
** * * *
2378169 TGCTAGGCCA-TTGTTTTACTCAATGGTAC
131 AACTAAGCCATTTCTTTTACTCAACGGTAC
* * *
2378198 TTAACCGTTCATCTAACTGGCTTAATTGACACATTTCTGTCAATTGCACAGCTAGGCCATTTTTC
1 TTAACCGTTCATCCAACTGGCATAATTGACACATTTCTGTCAATTGCACAACTAGGCCATTTTTC
* * *
2378263 TTTTACTCAACGGTACATAACCGTTCATCTAACAGGCATAATTGACACCTTTCT
66 TTTTACTCAACGGTACTTAACCGTTCATCTAACTGGCATAATTAACACCTTTCT
2378317 GTCATATGTA
Statistics
Matches: 252, Mismatches: 24, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
159 128 0.51
161 6 0.02
162 118 0.47
ACGTcount: A:0.27, C:0.25, G:0.12, T:0.36
Consensus pattern (160 bp):
TTAACCGTTCATCCAACTGGCATAATTGACACATTTCTGTCAATTGCACAACTAGGCCATTTTTC
TTTTACTCAACGGTACTTAACCGTTCATCTAACTGGCATAATTAACACCTTTCTACCAATTGCAC
AACTAAGCCATTTCTTTTACTCAACGGTAC
Found at i:2378831 original size:68 final size:68
Alignment explanation
Indices: 2378286--2378818 Score: 841
Period size: 68 Copynumber: 7.8 Consensus size: 68
2378276 TACATAACCG
* * * * *
2378286 TTCATCTAACAGGCATAATTGACACCTTTCTGTCATATGTACAGTTAGGTCTCAAAGACACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCATATGCACAGTTAGGCCTCAAAGACACTTAG
2378351 TCT
66 TCT
* * *
2378354 TTCATCTAACTGGCATACATAATTGACACCTTTCTGTCATATGTACAGTTAGGTCTCAAAGACAC
1 TTCATCTAACTGGCAT--A-AA-TGACACATTTCTGTCATATGCACAGTTAGGCCTCAAAGACAC
2378419 TTAGTCT
62 TTAGTCT
* *
2378426 TTCATCTAACTGGCATAAATGACACCTTTCTATCATATGCACAGTTAGGCCTCAAAGACACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCATATGCACAGTTAGGCCTCAAAGACACTTAG
2378491 TCT
66 TCT
* *
2378494 TTCATCTAACTGGCATAAATGGCATATTTCTGTCATATGCACAGTTAGGCCTCAAAGACACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCATATGCACAGTTAGGCCTCAAAGACACTTAG
2378559 TCT
66 TCT
* *
2378562 TTCATCTAATTGGCATAAATGACACATTTCTGTCATATGCACAGTTAGGACTCAAAGACACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCATATGCACAGTTAGGCCTCAAAGACACTTAG
*
2378627 TAT
66 TCT
*
2378630 TTCATCTAACTGGCATAAATGACACATTTATGTCATATGCACAGTTAGGCCTCAAAGACACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCATATGCACAGTTAGGCCTCAAAGACACTTAG
2378695 TCT
66 TCT
* * *
2378698 TTTATCTAACTGACATAAATGACACATTTCTGTCATATGCACAGTTAGGCCTCAAAGACACTTAT
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCATATGCACAGTTAGGCCTCAAAGACACTTAG
2378763 TCT
66 TCT
* *
2378766 TTCATCTAACTGGCATAAATGACACATTTCTATCATATGTACAGTTAGGCCTC
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCATATGCACAGTTAGGCCTC
2378819 TTGATCTTTT
Statistics
Matches: 435, Mismatches: 26, Indels: 8
0.93 0.06 0.02
Matches are distributed among these distances:
68 365 0.84
69 2 0.00
70 2 0.00
71 1 0.00
72 65 0.15
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (68 bp):
TTCATCTAACTGGCATAAATGACACATTTCTGTCATATGCACAGTTAGGCCTCAAAGACACTTAG
TCT
Found at i:2379260 original size:58 final size:59
Alignment explanation
Indices: 2379185--2379357 Score: 235
Period size: 58 Copynumber: 3.0 Consensus size: 59
2379175 TATATTTCCC
* *
2379185 ATACGGAAATTCATACACTTAGTATGAATTTCTTATCCT-TTAGCACAC-AAGGTGCCCA
1 ATACAGAAATTCATACACTTAGTATGAATTTCTTATCATGTTAGCACACGAA-GTGCCCA
* * * *
2379243 ATATAGAAATTCTTACACTTATTATGAATTTCTTATCATGTTAGCACACGAAGTGCCCT
1 ATACAGAAATTCATACACTTAGTATGAATTTCTTATCATGTTAGCACACGAAGTGCCCA
* * *
2379302 ATACAAAAATTCATACACTTAGTATGAATTTCTTAACAT-TTTGCACACGAAGTGCC
1 ATACAGAAATTCATACACTTAGTATGAATTTCTTATCATGTTAGCACACGAAGTGCC
2379358 ATTTGGTAAT
Statistics
Matches: 101, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
58 50 0.50
59 49 0.49
60 2 0.02
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.34
Consensus pattern (59 bp):
ATACAGAAATTCATACACTTAGTATGAATTTCTTATCATGTTAGCACACGAAGTGCCCA
Found at i:2379319 original size:59 final size:58
Alignment explanation
Indices: 2379191--2379357 Score: 237
Period size: 59 Copynumber: 2.9 Consensus size: 58
2379181 TCCCATACGG
* * *
2379191 AAATTCATACACTTAGTATGAATTTCTTATCCTTTAGCACAC-AAGGTGCCCAATATAG
1 AAATTCATACACTTAGTATGAATTTCTTATCATTTAGCACACGAA-GTGCCCAATACAA
* * *
2379249 AAATTCTTACACTTATTATGAATTTCTTATCATGTTAGCACACGAAGTGCCCTATACAA
1 AAATTCATACACTTAGTATGAATTTCTTATCAT-TTAGCACACGAAGTGCCCAATACAA
* *
2379308 AAATTCATACACTTAGTATGAATTTCTTAACATTTTGCACACGAAGTGCC
1 AAATTCATACACTTAGTATGAATTTCTTATCATTTAGCACACGAAGTGCC
2379358 ATTTGGTAAT
Statistics
Matches: 97, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
58 46 0.47
59 49 0.51
60 2 0.02
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.34
Consensus pattern (58 bp):
AAATTCATACACTTAGTATGAATTTCTTATCATTTAGCACACGAAGTGCCCAATACAA
Found at i:2382993 original size:138 final size:137
Alignment explanation
Indices: 2382770--2383638 Score: 1204
Period size: 138 Copynumber: 6.3 Consensus size: 137
2382760 CTAAAAATGT
* * * * * *
2382770 AGGCTCTAATATTAA-CTTAAATTAATTTTAATCAATTATGTTATTCAAAAAATTAAATTGGAAC
1 AGGCTCTAATATTAATCCT-AATTAATTTTAATCAATTAT-TGAATCGAATAATTAATTTGGAAC
* ** * * * *
2382834 CTCAAGCATAAGTGAGGACCAAGTAAAAAATTCTCCTAATTTTAAGGACTAAAGGTGAAATTAGG
64 CTCGAGCA-AAAAGAGGACCAAATTAAGAATTCTCCTAATTTTAAGGACTAAATGTGAAATTAGG
*
2382899 CCTAAGGTGG
128 CCTAAGATGG
* * *
2382909 AGGCTCTAATATTAATCCTAATTATTTTTATTCGATTATTGAATCGAATAATTAATTTGGAACCT
1 AGGCTCTAATATTAATCCTAATTAATTTTAATCAATTATTGAATCGAATAATTAATTTGGAACCT
* *
2382974 TGAGGAAAAATGAGGACCAAATTAAGAATTCTCCTAATTTTAAGGACTAAATGTGAAATTAGGCC
66 CGAGCAAAAA-GAGGACCAAATTAAGAATTCTCCTAATTTTAAGGACTAAATGTGAAATTAGGCC
*
2383039 TAAGGTGG
130 TAAGATGG
**
2383047 AGGCTCTAATATTAATATTAATTAATTTTAATCAATTATTGAATCGAATAATTAATTTGGAACCT
1 AGGCTCTAATATTAATCCTAATTAATTTTAATCAATTATTGAATCGAATAATTAATTTGGAACCT
* *
2383112 CGAGCAAAAGCGAGGACCAAATTAAGAATTCTTCTAATTTTAAGGACTAAATGTGAAATTAGGCC
66 CGAGCAAAA-AGAGGACCAAATTAAGAATTCTCCTAATTTTAAGGACTAAATGTGAAATTAGGCC
2383177 TAAGATGG
130 TAAGATGG
* * * *
2383185 AGGCTATAATATTAATCCTAATTAATGTTAATCAATTATTGAATCGAATAATTAATTTAGAACTT
1 AGGCTCTAATATTAATCCTAATTAATTTTAATCAATTATTGAATCGAATAATTAATTTGGAACCT
* * *
2383250 CAAGC-ATAAGCAACGACCAAATTAAGAATTCTCCTAATTTTAAGGACTAAATGTGAAATTAGGC
66 CGAGCAAAAAG--AGGACCAAATTAAGAATTCTCCTAATTTTAAGGACTAAATGTGAAATTAGGC
*
2383314 CTAAGGTGG
129 CTAAGATGG
*
2383323 AGGCTCTAATATTAATACTAATTAATTTTAATCAATTATTGAATCGAATAATTAATTTGGAACCT
1 AGGCTCTAATATTAATCCTAATTAATTTTAATCAATTATTGAATCGAATAATTAATTTGGAACCT
* **
2383388 CGAGCAAAAGCGAGGACCAAATTAAGAATTCTTTTAATTTTAAGGACTAAATGTGAAATTAGGCC
66 CGAGCAAAA-AGAGGACCAAATTAAGAATTCTCCTAATTTTAAGGACTAAATGTGAAATTAGGCC
2383453 TAAGATGG
130 TAAGATGG
* * * *
2383461 AGGCTATAATATTAATCCTAATTAATGTTAATCAATTATTGAATCGAATAATTAATTTAGAACTT
1 AGGCTCTAATATTAATCCTAATTAATTTTAATCAATTATTGAATCGAATAATTAATTTGGAACCT
* * *
2383526 CAAGC-ATAAGCAACGACCAAATTAAGAATTCTCCTAATTTTAAGGACTAAATGTGAAATTAGGC
66 CGAGCAAAAAG--AGGACCAAATTAAGAATTCTCCTAATTTTAAGGACTAAATGTGAAATTAGGC
*
2383590 CTAAGATTG
129 CTAAGATGG
* * *
2383599 AAGCTCCAATATTAGTCCTAATTAATTTTAATCAATTATT
1 AGGCTCTAATATTAATCCTAATTAATTTTAATCAATTATT
2383639 ACTAGAAAAT
Statistics
Matches: 652, Mismatches: 69, Indels: 19
0.88 0.09 0.03
Matches are distributed among these distances:
136 2 0.00
137 6 0.01
138 607 0.93
139 34 0.05
140 3 0.00
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (137 bp):
AGGCTCTAATATTAATCCTAATTAATTTTAATCAATTATTGAATCGAATAATTAATTTGGAACCT
CGAGCAAAAAGAGGACCAAATTAAGAATTCTCCTAATTTTAAGGACTAAATGTGAAATTAGGCCT
AAGATGG
Found at i:2383270 original size:276 final size:276
Alignment explanation
Indices: 2382770--2383638 Score: 1368
Period size: 276 Copynumber: 3.1 Consensus size: 276
2382760 CTAAAAATGT
* * * * *
2382770 AGGCTCTAATATT-A-ACTTAAATTAATTTTAATCAATTATGTTATTCAAAAAATTAAATTGGAA
1 AGGCTCTAATATTAATAC-T-AATTAATTTTAATCAATTAT-TGAATCGAATAATTAATTTGGAA
* * * * * * * *
2382833 CCTCAAGCATAAGTGAGGACCAAGTAAAAAATTCTCCTAATTTTAAGGACTAAAGGTGAAATTAG
63 CCTCGAGCAAAAGCGAGGACCAAATTAAGAATTCTTCTAATTTTAAGGACTAAATGTGAAATTAG
* * * * * *
2382898 GCCTAAGGTGGAGGCTCTAATATTAATCCTAATTATTTTTATTCGATTATTGAATCGAATAATTA
128 GCCTAAGATGGAGGCTATAATATTAATCCTAATTAATGTTAATCAATTATTGAATCGAATAATTA
* * * * * *
2382963 ATTTGGAACCTTGAGGAAAAATG--AGGACCAAATTAAGAATTCTCCTAATTTTAAGGACTAAAT
193 ATTTAGAA-CTTCAAGCATAA-GCAACGACCAAATTAAGAATTCTCCTAATTTTAAGGACTAAAT
2383026 GTGAAATTAGGCCTAAGGTGG
256 GTGAAATTAGGCCTAAGGTGG
*
2383047 AGGCTCTAATATTAATATTAATTAATTTTAATCAATTATTGAATCGAATAATTAATTTGGAACCT
1 AGGCTCTAATATTAATACTAATTAATTTTAATCAATTATTGAATCGAATAATTAATTTGGAACCT
2383112 CGAGCAAAAGCGAGGACCAAATTAAGAATTCTTCTAATTTTAAGGACTAAATGTGAAATTAGGCC
66 CGAGCAAAAGCGAGGACCAAATTAAGAATTCTTCTAATTTTAAGGACTAAATGTGAAATTAGGCC
2383177 TAAGATGGAGGCTATAATATTAATCCTAATTAATGTTAATCAATTATTGAATCGAATAATTAATT
131 TAAGATGGAGGCTATAATATTAATCCTAATTAATGTTAATCAATTATTGAATCGAATAATTAATT
2383242 TAGAACTTCAAGCATAAGCAACGACCAAATTAAGAATTCTCCTAATTTTAAGGACTAAATGTGAA
196 TAGAACTTCAAGCATAAGCAACGACCAAATTAAGAATTCTCCTAATTTTAAGGACTAAATGTGAA
2383307 ATTAGGCCTAAGGTGG
261 ATTAGGCCTAAGGTGG
2383323 AGGCTCTAATATTAATACTAATTAATTTTAATCAATTATTGAATCGAATAATTAATTTGGAACCT
1 AGGCTCTAATATTAATACTAATTAATTTTAATCAATTATTGAATCGAATAATTAATTTGGAACCT
*
2383388 CGAGCAAAAGCGAGGACCAAATTAAGAATTCTTTTAATTTTAAGGACTAAATGTGAAATTAGGCC
66 CGAGCAAAAGCGAGGACCAAATTAAGAATTCTTCTAATTTTAAGGACTAAATGTGAAATTAGGCC
2383453 TAAGATGGAGGCTATAATATTAATCCTAATTAATGTTAATCAATTATTGAATCGAATAATTAATT
131 TAAGATGGAGGCTATAATATTAATCCTAATTAATGTTAATCAATTATTGAATCGAATAATTAATT
2383518 TAGAACTTCAAGCATAAGCAACGACCAAATTAAGAATTCTCCTAATTTTAAGGACTAAATGTGAA
196 TAGAACTTCAAGCATAAGCAACGACCAAATTAAGAATTCTCCTAATTTTAAGGACTAAATGTGAA
* *
2383583 ATTAGGCCTAAGATTG
261 ATTAGGCCTAAGGTGG
* * * *
2383599 AAGCTCCAATATTAGTCCTAATTAATTTTAATCAATTATT
1 AGGCTCTAATATTAATACTAATTAATTTTAATCAATTATT
2383639 ACTAGAAAAT
Statistics
Matches: 554, Mismatches: 34, Indels: 9
0.93 0.06 0.02
Matches are distributed among these distances:
274 1 0.00
275 8 0.01
276 509 0.92
277 33 0.06
278 2 0.00
279 1 0.00
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (276 bp):
AGGCTCTAATATTAATACTAATTAATTTTAATCAATTATTGAATCGAATAATTAATTTGGAACCT
CGAGCAAAAGCGAGGACCAAATTAAGAATTCTTCTAATTTTAAGGACTAAATGTGAAATTAGGCC
TAAGATGGAGGCTATAATATTAATCCTAATTAATGTTAATCAATTATTGAATCGAATAATTAATT
TAGAACTTCAAGCATAAGCAACGACCAAATTAAGAATTCTCCTAATTTTAAGGACTAAATGTGAA
ATTAGGCCTAAGGTGG
Found at i:2383863 original size:32 final size:30
Alignment explanation
Indices: 2383798--2383870 Score: 71
Period size: 31 Copynumber: 2.4 Consensus size: 30
2383788 AAAATGTAAG
*
2383798 TTTTGAAAGTTTAAGGGAAAAAATTTAATTT
1 TTTTAAAAGTTTAAGGGAAAAAATTTAA-TT
2383829 TTTGTAAAAGTTT-AGGGACTAAAAATGTT-A-T
1 TTT-TAAAAGTTTAAGGGA--AAAAAT-TTAATT
2383860 TTTTAAAAGTT
1 TTTTAAAAGTT
2383871 ATAAATTTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
30 8 0.22
31 12 0.32
32 8 0.22
33 7 0.19
34 2 0.05
ACGTcount: A:0.40, C:0.01, G:0.16, T:0.42
Consensus pattern (30 bp):
TTTTAAAAGTTTAAGGGAAAAAATTTAATT
Found at i:2387077 original size:118 final size:118
Alignment explanation
Indices: 2386784--2387115 Score: 459
Period size: 118 Copynumber: 2.8 Consensus size: 118
2386774 CCTAAAGGTA
* * * *
2386784 CACTAGTATCTATATTTTGATATGATTGCACTTTGTGTGCATATTATGATTATGATATGATAGCA
1 CACTAGTATATATATTCTGATATGATTACACTTTGTGTGCACATTATGATTATGATATGATAGCA
* * * *
2386849 CTGTGTGTTCTTATATTTTC-AATTCTTATATATTGTGGTGTACCGATGGGTG
66 CTGTGTGTCCTTATATATTCTAATTCTGATATATTGTGGTCTACCGATGGGTG
*
2386901 CACTAGTATATATATATTCTGATATGGTTACACTTTGTGTGCACATTATGATTATGATATGATAG
1 CACTAG--TATATATATTCTGATATGATTACACTTTGTGTGCACATTATGATTATGATATGATAG
* * *
2386966 CACCGTGTGTCCTTATATGTTCTAATTCTGATATATTGTGGTCTACCGGTGGGTG
64 CACTGTGTGTCCTTATATATTCTAATTCTGATATATTGTGGTCTACCGATGGGTG
* * * *
2387021 CGCTAGTATATATATCCTGATATGATTACACTTTGTGTGCACATTACGATTTTGATATGATAGCA
1 CACTAGTATATATATTCTGATATGATTACACTTTGTGTGCACATTATGATTATGATATGATAGCA
* * * *
2387086 ATGTGTGTGCTTATATATTCTGATTATGAT
66 CTGTGTGTCCTTATATATTCTAATTCTGAT
2387116 GATAGCACTG
Statistics
Matches: 190, Mismatches: 22, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
117 6 0.03
118 79 0.42
119 71 0.37
120 34 0.18
ACGTcount: A:0.25, C:0.13, G:0.20, T:0.43
Consensus pattern (118 bp):
CACTAGTATATATATTCTGATATGATTACACTTTGTGTGCACATTATGATTATGATATGATAGCA
CTGTGTGTCCTTATATATTCTAATTCTGATATATTGTGGTCTACCGATGGGTG
Found at i:2391752 original size:90 final size:88
Alignment explanation
Indices: 2391636--2391807 Score: 290
Period size: 90 Copynumber: 1.9 Consensus size: 88
2391626 TAATCCTGAA
* *
2391636 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAA-CCCTAATATGA-
2391701 TAGGGTAACTTGGATATAAGAGGAT
64 TAGGGTAACTTGGATATAAGAGGAT
*
2391726 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCGTAATATGATA
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATA
*
2391791 GGGTAACTTGGCTATAA
66 GGGTAACTTGGATATAA
2391808 AAGGGTGTGT
Statistics
Matches: 78, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
88 18 0.23
89 10 0.13
90 50 0.64
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (88 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATA
GGGTAACTTGGATATAAGAGGAT
Found at i:2393009 original size:37 final size:37
Alignment explanation
Indices: 2392959--2393033 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
2392949 GGGATTTAAA
2392959 GCCTAAACCCGATAGGAGGTATCGGTACCCATCTAGG
1 GCCTAAACCCGATAGGAGGTATCGGTACCCATCTAGG
*
2392996 GCCTAAACCCGATAGGGGGTATCGGTACCCATCTAGG
1 GCCTAAACCCGATAGGAGGTATCGGTACCCATCTAGG
2393033 G
1 G
2393034 TATCGATACA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.25, C:0.27, G:0.29, T:0.19
Consensus pattern (37 bp):
GCCTAAACCCGATAGGAGGTATCGGTACCCATCTAGG
Found at i:2393059 original size:21 final size:21
Alignment explanation
Indices: 2393033--2393092 Score: 95
Period size: 21 Copynumber: 2.9 Consensus size: 21
2393023 CCCATCTAGG
2393033 GTATCGATACATATTCAAGGT
1 GTATCGATACATATTCAAGGT
*
2393054 GTATCGATACATATTTAAGGT
1 GTATCGATACATATTCAAGGT
*
2393075 GTATCGATACCTA-TCAAG
1 GTATCGATACATATTCAAG
2393093 AGAGGTATCG
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
20 4 0.11
21 32 0.89
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Consensus pattern (21 bp):
GTATCGATACATATTCAAGGT
Found at i:2402261 original size:16 final size:16
Alignment explanation
Indices: 2402240--2402280 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
2402230 AAGAAGGCAG
*
2402240 CAGATTCTGCTCAACA
1 CAGATTCTGCTCAAAA
2402256 CAGATTCTGCTCAAAA
1 CAGATTCTGCTCAAAA
2402272 CAGATTCTG
1 CAGATTCTG
2402281 GAAATTGGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.32, C:0.27, G:0.15, T:0.27
Consensus pattern (16 bp):
CAGATTCTGCTCAAAA
Found at i:2404833 original size:3 final size:3
Alignment explanation
Indices: 2404825--2404866 Score: 50
Period size: 3 Copynumber: 13.7 Consensus size: 3
2404815 ATATATTTAA
*
2404825 AAT AAT AAT AAT AAT AAT AAT AA- ATAT AAGT AAT AAA AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AA-T AAT AAT AAT AA
2404867 AAAAGATAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 1 0.03
3 29 0.85
4 4 0.12
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:2405819 original size:98 final size:101
Alignment explanation
Indices: 2405665--2405919 Score: 297
Period size: 102 Copynumber: 2.6 Consensus size: 101
2405655 AGATAAAAAA
* * * *
2405665 TTCGAATG-AACAATTTCAACTTGTGTGTTTCAAGGGAAACTATCTCAAGCGAGACGAAATT-AT
1 TTCGAGTGAAACAATTTCAAATTTTGTGTTCCAAGGGAAACTATCTCAAGCGAGACGAAATTAAT
* **
2405728 TT-A-AAAAATAATTTCAAGTGAGGTGAAA-TTTTGT
66 TTAAGAAAAACAATTTCAAGTGA-GACAAATTTTTGT
* * * *
2405762 TTGGATTGAAACAATTTCAAGTTTTGTGTTCCAAGGGAAATTATCTCAAGCGAGACGAAATTAAT
1 TTCGAGTGAAACAATTTCAAATTTTGTGTTCCAAGGGAAACTATCTCAAGCGAGACGAAATTAAT
2405827 TTGAAGAAAAACAATTTCAAGTGAGACAAATTTTTGT
66 TT-AAGAAAAACAATTTCAAGTGAGACAAATTTTTGT
* * * * *
2405864 TTCGAGTGAAACAGTTTAAAAATTTT-TGTTCCAAGGGAAACTGTTTTAAGCGAGAC
1 TTCGAGTGAAACAATTT-CAAATTTTGTGTTCCAAGGGAAACTATCTCAAGCGAGAC
2405920 ATAATTTGTT
Statistics
Matches: 133, Mismatches: 18, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
97 6 0.05
98 49 0.37
99 4 0.03
101 5 0.04
102 63 0.47
103 6 0.05
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.33
Consensus pattern (101 bp):
TTCGAGTGAAACAATTTCAAATTTTGTGTTCCAAGGGAAACTATCTCAAGCGAGACGAAATTAAT
TTAAGAAAAACAATTTCAAGTGAGACAAATTTTTGT
Found at i:2405903 original size:29 final size:29
Alignment explanation
Indices: 2405854--2405909 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
2405844 CAAGTGAGAC
* * *
2405854 AAATTTTTGTTTCGAGTGAAACAGTTTAA
1 AAATTTTTGTTCCAAGGGAAACAGTTTAA
*
2405883 AAATTTTTGTTCCAAGGGAAACTGTTT
1 AAATTTTTGTTCCAAGGGAAACAGTTT
2405910 TAAGCGAGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.41
Consensus pattern (29 bp):
AAATTTTTGTTCCAAGGGAAACAGTTTAA
Found at i:2406544 original size:161 final size:162
Alignment explanation
Indices: 2405979--2406651 Score: 1007
Period size: 161 Copynumber: 4.2 Consensus size: 162
2405969 TGTATCAATA
* *
2405979 TGAGAAACTTTGAAAATCGATTTCTCA-TTTTTTCCAAAAATATCAAATGAAAATATCATGCCTG
1 TGAGAAACTTTGAAAATCAATTTCTCATTTTTTTACAAAAATATCAAATGAAAATATCATGCCTG
* * *
2406043 AAGGTCTTACTGATTT-TTGGAACTAATTTACTAAAGTAAG-GACTTTGGAAATCATTTTCTTAC
66 AAGGTCTTACTGATTTCTTGAAAATAATTTACT-AAGTAAGAAACTTTGGAAATCATTTTCTTAC
* * *
2406106 TTTACAAAAATTTCAATTTTCGGAAAGATTAAA
130 TTTTCAAAAATTTCAATTTTGGGAAAGATTAAG
** * * * * *
2406139 TGAGAAACTTTGAAAATTGATTTCTTATTTTTTTCCAAAAATACCAAATGAAACTATTATGCCTG
1 TGAGAAACTTTGAAAATCAATTTCTCATTTTTTTACAAAAATATCAAATGAAAATATCATGCCTG
* * *
2406204 AAGGTCGTACTGGTTTCTTGAAAATAATTTACTACGTAAGAAACTTTGGAAATCATTTTCTTACT
66 AAGGTCTTACTGATTTCTTGAAAATAATTTACTAAGTAAGAAACTTTGGAAATCATTTTCTTACT
**
2406269 TTTCAAAAAAACTCAATTTTGGGAAAGATTAAG
131 TTTC-AAAAATTTCAATTTTGGGAAAGATTAAG
*
2406302 TGAGAAACTTTGAAAATCAATTTCTCATTTTTTTCCAAAAAATATCAAATGAAAATATC-TGCCT
1 TGAGAAACTTTGAAAATCAATTTCTCATTTTTTTAC-AAAAATATCAAATGAAAATATCATGCCT
* * *
2406366 GAAGGTCTTACTGATTTCTTGAAAAAAATTTACTAAGTAAGAAACTTTGAAAATCGTTTTCTTAC
65 GAAGGTCTTACTGATTTCTTGAAAATAATTTACTAAGTAAGAAACTTTGGAAATCATTTTCTTAC
2406431 TTTTCAAAAATTTCAA-TTTGGGAAAGATTAAG
130 TTTTCAAAAATTTCAATTTTGGGAAAGATTAAG
*
2406463 TGAGAAACTTTGAAAATCAATTTCTCATTTTTTTATAAAAATATCAAATGAAAATATCATGCCTG
1 TGAGAAACTTTGAAAATCAATTTCTCATTTTTTTACAAAAATATCAAATGAAAATATCATGCCTG
* **
2406528 AAGGTATTGTTGATTTCTTGAAAATAATTTACTAAGTAAGAAACTTTGGAAAT-AGTTTTCTTAC
66 AAGGTCTTACTGATTTCTTGAAAATAATTTACTAAGTAAGAAACTTTGGAAATCA-TTTTCTTAC
2406592 TTTTCAAAAATTTCAATTTTGGGAAAGATTAAG
130 TTTTCAAAAATTTCAATTTTGGGAAAGATTAAG
*
2406625 TGAGACACTTTGAAAATCAATTTCTCA
1 TGAGAAACTTTGAAAATCAATTTCTCA
2406652 CAAATCATAT
Statistics
Matches: 466, Mismatches: 39, Indels: 14
0.90 0.08 0.03
Matches are distributed among these distances:
160 47 0.10
161 183 0.39
162 91 0.20
163 126 0.27
164 19 0.04
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (162 bp):
TGAGAAACTTTGAAAATCAATTTCTCATTTTTTTACAAAAATATCAAATGAAAATATCATGCCTG
AAGGTCTTACTGATTTCTTGAAAATAATTTACTAAGTAAGAAACTTTGGAAATCATTTTCTTACT
TTTCAAAAATTTCAATTTTGGGAAAGATTAAG
Found at i:2406595 original size:324 final size:322
Alignment explanation
Indices: 2405979--2406651 Score: 1021
Period size: 324 Copynumber: 2.1 Consensus size: 322
2405969 TGTATCAATA
*
2405979 TGAGAAACTTTGAAAATCGATTTCTCATTTTTTCCAAAAATATCAAATGAAAATATCATGCCTGA
1 TGAGAAACTTTGAAAATCAATTTCTCATTTTTTCCAAAAATATCAAATGAAAATATCATGCCTGA
* ** * *
2406044 AGGTCTTACTGATTTTTGGAACTAATTTACTAAAGTAAGGACTTTGGAAATCATTTTCTTACTTT
66 AGGTCTTACTGATTTTTGAAAAAAATTTACTAAAGTAAGAACTTTGAAAATCATTTTCTTACTTT
** * *
2406109 ACAAAAATTTCAATTTTCGGAAAGATTAAATGAGAAACTTTGAAAATTGATTTCTTATTTTTTTC
131 ACAAAAATTTCAATTTTCGGAAAGATTAAATGAGAAACTTTGAAAATCAATTTCTCATTTTTTTA
* * * * *
2406174 CAAAAATACCAAATGAAACTATTATGCCTGAAGGTCGTACTGGTTTCTTGAAAATAATTTACTAC
196 CAAAAATACCAAATGAAAATATCATGCCTGAAGGTAGTACTGATTTCTTGAAAATAATTTACTAA
2406239 GTAAGAAACTTTGGAAATCATTTTCTTACTTTTCAAAAAAACTCAATTTTGGGAAAGATTAAG
261 GTAAGAAACTTTGGAAATCATTTTCTTACTTTTC-AAAAAACTCAATTTTGGGAAAGATTAAG
2406302 TGAGAAACTTTGAAAATCAATTTCTCATTTTTTTCCAAAAAATATCAAATGAAAATATC-TGCCT
1 TGAGAAACTTTGAAAATCAATTTCTCA-TTTTTTCC-AAAAATATCAAATGAAAATATCATGCCT
*
2406366 GAAGGTCTTACTGATTTCTTGAAAAAAATTTACT-AAGTAAGAAACTTTGAAAATCGTTTTCTTA
64 GAAGGTCTTACTGATTT-TTGAAAAAAATTTACTAAAGTAAG-AACTTTGAAAATCATTTTCTTA
* * *
2406430 CTTTTCAAAAATTTCAA-TTTGGGAAAGATTAAGTGAGAAACTTTGAAAATCAATTTCTCATTTT
127 CTTTACAAAAATTTCAATTTTCGGAAAGATTAAATGAGAAACTTTGAAAATCAATTTCTCATTTT
* * * **
2406494 TTTATAAAAATATCAAATGAAAATATCATGCCTGAAGGTATTGTTGATTTCTTGAAAATAATTTA
192 TTTACAAAAATACCAAATGAAAATATCATGCCTGAAGGTAGTACTGATTTCTTGAAAATAATTTA
**
2406559 CTAAGTAAGAAACTTTGGAAAT-AGTTTTCTTACTTTTCAAAAATTTCAATTTTGGGAAAGATTA
257 CTAAGTAAGAAACTTTGGAAATCA-TTTTCTTACTTTTCAAAAAACTCAATTTTGGGAAAGATTA
2406623 AG
321 AG
*
2406625 TGAGACACTTTGAAAATCAATTTCTCA
1 TGAGAAACTTTGAAAATCAATTTCTCA
2406652 CAAATCATAT
Statistics
Matches: 318, Mismatches: 27, Indels: 10
0.90 0.08 0.03
Matches are distributed among these distances:
323 79 0.25
324 169 0.53
325 70 0.22
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (322 bp):
TGAGAAACTTTGAAAATCAATTTCTCATTTTTTCCAAAAATATCAAATGAAAATATCATGCCTGA
AGGTCTTACTGATTTTTGAAAAAAATTTACTAAAGTAAGAACTTTGAAAATCATTTTCTTACTTT
ACAAAAATTTCAATTTTCGGAAAGATTAAATGAGAAACTTTGAAAATCAATTTCTCATTTTTTTA
CAAAAATACCAAATGAAAATATCATGCCTGAAGGTAGTACTGATTTCTTGAAAATAATTTACTAA
GTAAGAAACTTTGGAAATCATTTTCTTACTTTTCAAAAAACTCAATTTTGGGAAAGATTAAG
Found at i:2415883 original size:118 final size:118
Alignment explanation
Indices: 2415718--2416081 Score: 437
Period size: 118 Copynumber: 3.1 Consensus size: 118
2415708 TGAGGTGGAG
* * * * *
2415718 TGATTCTGATATACTG-GGTGTCACCTGAAG-GTACACTAGTATCTATATTATGATCTTATTGCA
1 TGATTCTGATATATTGTGGTG-CACC-GATGAGTGCACTAGTATATATATTATGATCTCATTGCA
* * *
2415781 CTTTGTGTGCACATTACAATTCTGATATGATAGCACTATGTGTGCTTATATGTTC
64 CTTTGTGTGCACATTACGATTATGATATGATAGCACTGTGTGTGCTTATATGTTC
* * * * **
2415836 TGATTCTGATATATTGTGGTGTATCGGTGAGTGCACTAGTATATATATTTTGATCTGGTTGCACT
1 TGATTCTGATATATTGTGGTGCACCGATGAGTGCACTAGTATATATATTATGATCTCATTGCACT
* *
2415901 TTGTGTGCACATTACGATTATGATATGATAACA-TCGTGTGTCCTTATATGTTC
66 TTGTGTGCACATTACGATTATGATATGATAGCACT-GTGTGTGCTTATATGTTC
** * ** * *
2415954 CAATTCTGATATATTGTGGTGCACCGATGGGTGCACTAGTATATATATCCTGATCTCATTACACG
1 TGATTCTGATATATTGTGGTGCACCGATGAGTGCACTAGTATATATATTATGATCTCATTGCACT
* * *
2416019 TTGTGTGCACATTCCGATTTTGATATGATAGCACTGTGTGTGCTTATATATTC
66 TTGTGTGCACATTACGATTATGATATGATAGCACTGTGTGTGCTTATATGTTC
*
2416072 TGATTATGAT
1 TGATTCTGAT
2416082 GATAGCAATG
Statistics
Matches: 207, Mismatches: 35, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
117 3 0.01
118 199 0.96
119 5 0.02
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.40
Consensus pattern (118 bp):
TGATTCTGATATATTGTGGTGCACCGATGAGTGCACTAGTATATATATTATGATCTCATTGCACT
TTGTGTGCACATTACGATTATGATATGATAGCACTGTGTGTGCTTATATGTTC
Found at i:2420258 original size:121 final size:118
Alignment explanation
Indices: 2419972--2420291 Score: 500
Period size: 118 Copynumber: 2.7 Consensus size: 118
2419962 CCTGAAGGTA
* *
2419972 CACTAGTATATATATTCTGATCTGATTGCACTTTGTGTGCACATTACGATTCTGATATGATAACA
1 CACTAGTATATATATTCTGATCTGATTGCACTTTGTGTGCACATTACGATTATGATATGATAGCA
*
2420037 TTGTGTGTGCTTATATGTTCCGATTCTGATATAATATGGTGTACTGGTGGGTG
66 TTGTGTGTGCTTATATGTTCCAATTCTGATATAATATGGTGTACTGGTGGGTG
* *
2420090 CACTACTATATATATTATGATCTGATTGCACTTTGTGTGCACATTACGATTATGATATGATAGCA
1 CACTAGTATATATATTCTGATCTGATTGCACTTTGTGTGCACATTACGATTATGATATGATAGCA
* *
2420155 CTT-TGTGTGCTTATATGTTCCAATTCTGATATATTGTGGTGTACTGGTGGTGGGTG
66 -TTGTGTGTGCTTATATGTTCCAATTCTGATATAATATGGTGTAC---TGGTGGGTG
*
2420211 CACTAGTATATATATTCTGATCTGATTACACTTTGTGTGCACATTACGA-TATTGATATGATAGC
1 CACTAGTATATATATTCTGATCTGATTGCACTTTGTGTGCACATTACGATTA-TGATATGATAGC
*
2420275 ATTGTGTGTGGTTATAT
65 ATTGTGTGTGCTTATAT
2420292 ATTATGATTA
Statistics
Matches: 185, Mismatches: 11, Indels: 9
0.90 0.05 0.04
Matches are distributed among these distances:
118 99 0.54
119 2 0.01
120 4 0.02
121 80 0.43
ACGTcount: A:0.24, C:0.13, G:0.21, T:0.41
Consensus pattern (118 bp):
CACTAGTATATATATTCTGATCTGATTGCACTTTGTGTGCACATTACGATTATGATATGATAGCA
TTGTGTGTGCTTATATGTTCCAATTCTGATATAATATGGTGTACTGGTGGGTG
Found at i:2421289 original size:21 final size:20
Alignment explanation
Indices: 2421265--2421304 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2421255 AATACTAAAT
*
2421265 TAAACTAAATTAAAAGGCAAA
1 TAAAATAAATT-AAAGGCAAA
*
2421286 TAAAATGAATTAAAGGCAA
1 TAAAATAAATTAAAGGCAA
2421305 TTAATTGACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.60, C:0.07, G:0.12, T:0.20
Consensus pattern (20 bp):
TAAAATAAATTAAAGGCAAA
Found at i:2421461 original size:23 final size:22
Alignment explanation
Indices: 2421434--2421481 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
2421424 TAAAGTTAGA
* *
2421434 AATTAAAGGATTAAAATACAAGC
1 AATTAAAGAAATAAAA-ACAAGC
*
2421457 AATTAAATAAATAAAAACAAGC
1 AATTAAAGAAATAAAAACAAGC
2421479 AAT
1 AAT
2421482 CGAATCAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.62, C:0.08, G:0.08, T:0.21
Consensus pattern (22 bp):
AATTAAAGAAATAAAAACAAGC
Found at i:2421479 original size:22 final size:24
Alignment explanation
Indices: 2421445--2421496 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
2421435 ATTAAAGGAT
*
2421445 TAAAATACAAGCAATTAAAT-AAA
1 TAAAATACAAGCAATCAAATCAAA
*
2421468 TAAAA-ACAAGCAATCGAATCAAA
1 TAAAATACAAGCAATCAAATCAAA
2421491 TAAAAT
1 TAAAAT
2421497 GGTATGAGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 12 0.48
23 13 0.52
ACGTcount: A:0.63, C:0.12, G:0.06, T:0.19
Consensus pattern (24 bp):
TAAAATACAAGCAATCAAATCAAA
Found at i:2437927 original size:74 final size:74
Alignment explanation
Indices: 2437753--2437938 Score: 239
Period size: 74 Copynumber: 2.5 Consensus size: 74
2437743 TAAGTAAGGA
* *
2437753 GGTACCGATACCCCTCATAGGGTGTACCGATACCCCTAAGCCAATTTTGGCTCCAAGAAAAACAG
1 GGTACCGATACCCC-CATAAGG-GTACCGATACCCCTAAGCAAATTTTGGCTCCAAGAAAAACAG
*
2437818 ATTGCCCAATG
64 AATGCCCAATG
* * * * *
2437829 GGTACCGATACCCTACAT-AGGGTACCAATACCCCTATGCAAATTTTGGCTCCGAGAAAAATAGA
1 GGTACCGATACCC-CCATAAGGGTACCGATACCCCTAAGCAAATTTTGGCTCCAAGAAAAACAGA
*
2437893 ATGCCCTATG
65 ATGCCCAATG
* *
2437903 GGTACCGATACCCCCTTAAAGGTACCGATACCCCTA
1 GGTACCGATACCCCCATAAGGGTACCGATACCCCTA
2437939 GTCATTTAAC
Statistics
Matches: 95, Mismatches: 13, Indels: 6
0.83 0.11 0.05
Matches are distributed among these distances:
73 2 0.02
74 75 0.79
75 2 0.02
76 16 0.17
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.22
Consensus pattern (74 bp):
GGTACCGATACCCCCATAAGGGTACCGATACCCCTAAGCAAATTTTGGCTCCAAGAAAAACAGAA
TGCCCAATG
Found at i:2438003 original size:21 final size:21
Alignment explanation
Indices: 2437977--2438026 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
2437967 TTACACTGTA
2437977 GGTACCGAGACTCATTGAAGG
1 GGTACCGAGACTCATTGAAGG
2437998 GGTACCGAGACTCATTGAAGG
1 GGTACCGAGACTCATTGAAGG
2438019 GGTACCGA
1 GGTACCGA
2438027 TACCCCACGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.28, C:0.20, G:0.34, T:0.18
Consensus pattern (21 bp):
GGTACCGAGACTCATTGAAGG
Found at i:2440592 original size:6 final size:6
Alignment explanation
Indices: 2440583--2440733 Score: 71
Period size: 6 Copynumber: 24.5 Consensus size: 6
2440573 ATATATATTA
* *
2440583 AATAAT AATAAT AATAAT AA-ATAT AAGTAAT AAAAAT AA-AAA AGATAA-
1 AATAAT AATAAT AATAAT AATA-AT AA-TAAT AATAAT AATAAT A-ATAAT
* * * * *
2440631 AATACA- AATAAT AAATATT AATTAT AAAAAT AAAAAT AATAAAT TATAAAT
1 AATA-AT AATAAT -AATAAT AATAAT AATAAT AATAAT AAT-AAT AAT-AAT
* * * *
2440682 TATAATT AATAAT AATTAAGT AATAAT TATAA- AATAAT ATTAGT AA-AAT
1 AATAA-T AATAAT AA-TAA-T AATAAT AATAAT AATAAT AATAAT AATAAT
2440731 AAT
1 AAT
2440734 GATAGGGTAT
Statistics
Matches: 115, Mismatches: 16, Indels: 28
0.72 0.10 0.18
Matches are distributed among these distances:
5 16 0.14
6 61 0.53
7 34 0.30
8 4 0.03
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.32
Consensus pattern (6 bp):
AATAAT
Found at i:2440646 original size:7 final size:7
Alignment explanation
Indices: 2440581--2440720 Score: 73
Period size: 7 Copynumber: 20.3 Consensus size: 7
2440571 ATATATATAT
2440581 TAAATAA
1 TAAATAA
2440588 T-AATAA
1 TAAATAA
2440594 T-AATAA
1 TAAATAA
2440600 TAAAT-A
1 TAAATAA
*
2440606 TAAGTAA
1 TAAATAA
2440613 TAAA-AA
1 TAAATAA
*
2440619 TAAAAAAGA
1 T-AAATA-A
2440628 TAAA-ATA
1 TAAATA-A
*
2440635 CAAATAA
1 TAAATAA
*
2440642 TAAATAT
1 TAAATAA
2440649 TAATTATAA
1 TAA--ATAA
2440658 -AAATAA
1 TAAATAA
2440664 -AAATAA
1 TAAATAA
*
2440670 TAAATTA
1 TAAATAA
*
2440677 TAAATTA
1 TAAATAA
*
2440684 TAATTAA
1 TAAATAA
2440691 T-AATAA
1 TAAATAA
*
2440697 TTAAGTAA
1 -TAAATAA
*
2440705 T-AATTA
1 TAAATAA
2440711 TAAAATAA
1 T-AAATAA
2440719 TA
1 TA
2440721 TTAGTAAAAT
Statistics
Matches: 105, Mismatches: 15, Indels: 26
0.72 0.10 0.18
Matches are distributed among these distances:
6 38 0.36
7 46 0.44
8 16 0.15
9 5 0.05
ACGTcount: A:0.66, C:0.01, G:0.02, T:0.31
Consensus pattern (7 bp):
TAAATAA
Found at i:2440675 original size:22 final size:22
Alignment explanation
Indices: 2440590--2440680 Score: 89
Period size: 22 Copynumber: 4.2 Consensus size: 22
2440580 TTAAATAATA
* * *
2440590 ATAATAATAATAAATATAAGTA
1 ATAAAAATAATAAATATAAATT
* *
2440612 ATAAAAATAAAAAAGATAAA--
1 ATAAAAATAATAAATATAAATT
* *
2440632 ATACAAATAATAAATATTAATT
1 ATAAAAATAATAAATATAAATT
2440654 ATAAAAATAA-AAATAATAAATT
1 ATAAAAATAATAAAT-ATAAATT
2440676 ATAAA
1 ATAAA
2440681 TTATAATTAA
Statistics
Matches: 56, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
20 16 0.29
21 4 0.07
22 36 0.64
ACGTcount: A:0.69, C:0.01, G:0.02, T:0.27
Consensus pattern (22 bp):
ATAAAAATAATAAATATAAATT
Found at i:2440940 original size:2 final size:2
Alignment explanation
Indices: 2440933--2440963 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2440923 TGCAACCCAT
2440933 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2440964 GGAGTAAGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2441615 original size:60 final size:60
Alignment explanation
Indices: 2441551--2441681 Score: 192
Period size: 60 Copynumber: 2.2 Consensus size: 60
2441541 TAGAAAGGGG
* *
2441551 GTCATAGTTTAGGGATAAAATTAGAATATTCAAAAATTTAAAGA-CTAATTTATAATGAGA
1 GTCATAGTTTAGGGATAAAATTAAAATATTCAAAAATTTAAAGATC-AATTTAAAATGAGA
* *
2441611 GTCATAGTTTAGTGATAAAATTAAAATATTTAAAAATTTAAAGATCAATTTAAAATGAGA
1 GTCATAGTTTAGGGATAAAATTAAAATATTCAAAAATTTAAAGATCAATTTAAAATGAGA
**
2441671 GTTGTAGTTTA
1 GTCATAGTTTA
2441682 AATTTTGTCG
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
60 63 0.98
61 1 0.02
ACGTcount: A:0.46, C:0.04, G:0.15, T:0.36
Consensus pattern (60 bp):
GTCATAGTTTAGGGATAAAATTAAAATATTCAAAAATTTAAAGATCAATTTAAAATGAGA
Found at i:2441920 original size:6 final size:6
Alignment explanation
Indices: 2441909--2441934 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2441899 TTATTATAAG
2441909 TTAAAA TTAAAA TTAAAA TTAAAA TT
1 TTAAAA TTAAAA TTAAAA TTAAAA TT
2441935 TGAAATTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (6 bp):
TTAAAA
Found at i:2443811 original size:22 final size:22
Alignment explanation
Indices: 2443779--2443840 Score: 108
Period size: 22 Copynumber: 2.9 Consensus size: 22
2443769 CGGTACCGTA
2443779 ATAG-AGTATTGATACCATAGT
1 ATAGTAGTATTGATACCATAGT
2443800 ATAGTAGTATTGATACCATAGT
1 ATAGTAGTATTGATACCATAGT
*
2443822 ATAGTAGTATCGATACCAT
1 ATAGTAGTATTGATACCAT
2443841 GATGGGAGTA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
21 4 0.10
22 35 0.90
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.34
Consensus pattern (22 bp):
ATAGTAGTATTGATACCATAGT
Found at i:2444240 original size:54 final size:54
Alignment explanation
Indices: 2444182--2444284 Score: 179
Period size: 54 Copynumber: 1.9 Consensus size: 54
2444172 TTACCAAATA
*
2444182 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTC
1 GGCACTAAGTGTGCATTTCAAGGAATTCATCCTATGTGGATGAATAACCATTTC
* *
2444236 GGCACTAAGTGTGTATTTCAAGGAATTCATCCTATGTTGATGAATAACC
1 GGCACTAAGTGTGCATTTCAAGGAATTCATCCTATGTGGATGAATAACC
2444285 GTACAGACAC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.32
Consensus pattern (54 bp):
GGCACTAAGTGTGCATTTCAAGGAATTCATCCTATGTGGATGAATAACCATTTC
Found at i:2444331 original size:55 final size:55
Alignment explanation
Indices: 2444257--2444739 Score: 728
Period size: 55 Copynumber: 8.9 Consensus size: 55
2444247 TGTATTTCAA
* * *
2444257 GGAATTCATCCT-ATGTTGATGAATAACCGTACAGACACTATGTGTTCAAATCCAC
1 GGAATTCATCATGA-GTTGATGAATAACCGTACAGGCACTATGTGTGCAAATCCAC
* **
2444312 GGAATTCATCATGAGTTGATGAATAACAGTACATACACTATGTGTGCAAATCCAC
1 GGAATTCATCATGAGTTGATGAATAACCGTACAGGCACTATGTGTGCAAATCCAC
* *
2444367 GTAATTCATCATGAGTTGATGAATAACCGTACATGCACTATGTGTGCAAAT-C-C
1 GGAATTCATCATGAGTTGATGAATAACCGTACAGGCACTATGTGTGCAAATCCAC
*
2444420 --AATTCATCATGAGTTGATGAATAACCGTACAGGCACTATGTGTTCAAATCCAC
1 GGAATTCATCATGAGTTGATGAATAACCGTACAGGCACTATGTGTGCAAATCCAC
* * *
2444473 GGAATTCATCATGAGTTGATGAATAATCGTACAGACACTATGTGTACAAATCCAC
1 GGAATTCATCATGAGTTGATGAATAACCGTACAGGCACTATGTGTGCAAATCCAC
2444528 GGAATTCATCATGAGTTGATGAATAACCGTACAGGCACTATGTGTGCAAATCCAC
1 GGAATTCATCATGAGTTGATGAATAACCGTACAGGCACTATGTGTGCAAATCCAC
*
2444583 GGAATTCATCACGAGTTGATGAATAACCGTACAGGCACTATGTGTGCAAATCCAC
1 GGAATTCATCATGAGTTGATGAATAACCGTACAGGCACTATGTGTGCAAATCCAC
* * * *
2444638 GAAATTCATCATAAGTTGATGAATAACCGTACAGGCACGATGTGTGC-AACCCAC
1 GGAATTCATCATGAGTTGATGAATAACCGTACAGGCACTATGTGTGCAAATCCAC
* *
2444692 GGAATTCATCATGAGTTGATGAACT-ACCGTATAGGCACTACGTGTGCA
1 GGAATTCATCATGAGTTGATGAA-TAACCGTACAGGCACTATGTGTGCA
2444740 TCTTAATAAA
Statistics
Matches: 395, Mismatches: 26, Indels: 14
0.91 0.06 0.03
Matches are distributed among these distances:
51 47 0.12
52 1 0.00
53 2 0.01
54 47 0.12
55 297 0.75
56 1 0.00
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.27
Consensus pattern (55 bp):
GGAATTCATCATGAGTTGATGAATAACCGTACAGGCACTATGTGTGCAAATCCAC
Found at i:2444473 original size:161 final size:163
Alignment explanation
Indices: 2444258--2444739 Score: 733
Period size: 161 Copynumber: 3.0 Consensus size: 163
2444248 GTATTTCAAG
* *
2444258 GAATTCATC-CTATGTTGATGAATAACCGTACAGACACTATGTGTTCAAATCCACGGAATTCATC
1 GAATTCATCACGA-GTTGATGAATAACCGTACAGGCACTATGTGTTCAAATCCACGGAATTCATC
* *
2444322 ATGAGTTGATGAATAACAGTACATACACTATGTGTGCAAATCCACGTAATTCATCATGAGTTGAT
65 ATGAGTTGATGAATAAC-GTACAGACACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGAT
*
2444387 GAATAACCGTACATGCACTATGTGTGCAAAT-C-C
129 GAATAACCGTACAGGCACTATGTGTGCAAATCCAC
*
2444420 -AATTCATCATGAGTTGATGAATAACCGTACAGGCACTATGTGTTCAAATCCACGGAATTCATCA
1 GAATTCATCACGAGTTGATGAATAACCGTACAGGCACTATGTGTTCAAATCCACGGAATTCATCA
*
2444484 TGAGTTGATGAATAATCGTACAGACACTATGTGTACAAATCCACGGAATTCATCATGAGTTGATG
66 TGAGTTGATGAATAA-CGTACAGACACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATG
2444549 AATAACCGTACAGGCACTATGTGTGCAAATCCAC
130 AATAACCGTACAGGCACTATGTGTGCAAATCCAC
* *
2444583 GGAATTCATCACGAGTTGATGAATAACCGTACAGGCACTATGTGTGCAAATCCACGAAATTCATC
1 -GAATTCATCACGAGTTGATGAATAACCGTACAGGCACTATGTGTTCAAATCCACGGAATTCATC
* * * *
2444648 ATAAGTTGATGAATAACCGTACAGGCACGATGTGTGC-AACCCACGGAATTCATCATGAGTTGAT
65 ATGAGTTGATGAATAA-CGTACAGACACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGAT
* *
2444712 GAACT-ACCGTATAGGCACTACGTGTGCA
129 GAA-TAACCGTACAGGCACTATGTGTGCA
2444740 TCTTAATAAA
Statistics
Matches: 295, Mismatches: 18, Indels: 12
0.91 0.06 0.04
Matches are distributed among these distances:
161 148 0.50
162 3 0.01
163 1 0.00
164 50 0.17
165 93 0.32
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.27
Consensus pattern (163 bp):
GAATTCATCACGAGTTGATGAATAACCGTACAGGCACTATGTGTTCAAATCCACGGAATTCATCA
TGAGTTGATGAATAACGTACAGACACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGA
ATAACCGTACAGGCACTATGTGTGCAAATCCAC
Found at i:2444578 original size:216 final size:218
Alignment explanation
Indices: 2444257--2444736 Score: 745
Period size: 216 Copynumber: 2.2 Consensus size: 218
2444247 TGTATTTCAA
* *
2444257 GGAATTCATCCT-ATGTTGATGAATAACCGTACAGACACTATGTGTTCAAATCCACGGAATTCAT
1 GGAATTCATCATGA-GTTGATGAATAACCGTACAGACACTATGTGTACAAATCCACGGAATTCAT
* * *
2444321 CATGAGTTGATGAATAACAGTACATACACTATGTGTGCAAATCCACGTAATTCATCATGAGTTGA
65 CATGAGTTGATGAATAACAGTACAGACACTATGTGTGCAAATCCACGGAATTCATCACGAGTTGA
* *
2444386 TGAATAACCGTACATGCACTATGTGTGCAAAT-C-C-AATTCATCATGAGTTGATGAATAACCGT
130 TGAATAACCGTACAGGCACTATGTGTGCAAATCCACAAATTCATCATAAGTTGATGAATAACCGT
* * *
2444448 ACAGGCACTATGTGTTCAAATCCAC
195 ACAGGCACGATGTGTGC-AACCCAC
*
2444473 GGAATTCATCATGAGTTGATGAATAATCGTACAGACACTATGTGTACAAATCCACGGAATTCATC
1 GGAATTCATCATGAGTTGATGAATAACCGTACAGACACTATGTGTACAAATCCACGGAATTCATC
* *
2444538 ATGAGTTGATGAATAACCGTACAGGCACTATGTGTGCAAATCCACGGAATTCATCACGAGTTGAT
66 ATGAGTTGATGAATAACAGTACAGACACTATGTGTGCAAATCCACGGAATTCATCACGAGTTGAT
2444603 GAATAACCGTACAGGCACTATGTGTGCAAATCCACGAAATTCATCATAAGTTGATGAATAACCGT
131 GAATAACCGTACAGGCACTATGTGTGCAAATCCAC-AAATTCATCATAAGTTGATGAATAACCGT
2444668 ACAGGCACGATGTGTGCAACCCAC
195 ACAGGCACGATGTGTGCAACCCAC
* * *
2444692 GGAATTCATCATGAGTTGATGAACT-ACCGTATAGGCACTACGTGT
1 GGAATTCATCATGAGTTGATGAA-TAACCGTACAGACACTATGTGT
2444737 GCATCTTAAT
Statistics
Matches: 241, Mismatches: 17, Indels: 9
0.90 0.06 0.03
Matches are distributed among these distances:
216 150 0.62
217 2 0.01
218 1 0.00
219 45 0.19
220 43 0.18
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.27
Consensus pattern (218 bp):
GGAATTCATCATGAGTTGATGAATAACCGTACAGACACTATGTGTACAAATCCACGGAATTCATC
ATGAGTTGATGAATAACAGTACAGACACTATGTGTGCAAATCCACGGAATTCATCACGAGTTGAT
GAATAACCGTACAGGCACTATGTGTGCAAATCCACAAATTCATCATAAGTTGATGAATAACCGTA
CAGGCACGATGTGTGCAACCCAC
Found at i:2445245 original size:45 final size:45
Alignment explanation
Indices: 2445181--2445314 Score: 137
Period size: 45 Copynumber: 3.0 Consensus size: 45
2445171 TGTATAGAAT
*
2445181 GGCATGAAAGGATGCCATAAATAAAATGCATATGGGTGCATTAAC
1 GGCATGAAAAGATGCCATAAATAAAATGCATATGGGTGCATTAAC
* * * * * **
2445226 GGCATGAAAAGATACCATAATTGAAATTCATATGAGTGCATTATT
1 GGCATGAAAAGATGCCATAAATAAAATGCATATGGGTGCATTAAC
* *
2445271 GGCAAG-AAAGAATGTCATAAATGAAAATGCATAAT-GGTGCATTA
1 GGCATGAAAAG-ATGCCATAAAT-AAAATGCAT-ATGGGTGCATTA
2445315 TAAGTACGAA
Statistics
Matches: 71, Mismatches: 15, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
44 4 0.06
45 50 0.70
46 15 0.21
47 2 0.03
ACGTcount: A:0.42, C:0.11, G:0.22, T:0.25
Consensus pattern (45 bp):
GGCATGAAAAGATGCCATAAATAAAATGCATATGGGTGCATTAAC
Found at i:2447622 original size:3 final size:3
Alignment explanation
Indices: 2447614--2447639 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2447604 AGGAAGGGCA
2447614 GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GA
2447640 AGAAGAAGAA
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:0.00, G:0.35, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:2447687 original size:3 final size:3
Alignment explanation
Indices: 2447638--2447673 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
2447628 TGATGATGAT
2447638 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
2447674 ATAGAGGGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:2450185 original size:41 final size:41
Alignment explanation
Indices: 2450100--2450191 Score: 100
Period size: 41 Copynumber: 2.2 Consensus size: 41
2450090 GGTTACCAAT
* * *
2450100 AAAAATATTATGAATAAGGTAATATTTTCGATTCAACCG-A
1 AAAAATATTAAGAAAAAGGTAATATTTTAGATTCAACCGAA
*
2450140 AAAAATATTAAGAAAAAAGTTAATATTTTAGATTGC-ACC-ACA
1 AAAAATATTAAG-AAAAAGGTAATATTTTAGATT-CAACCGA-A
2450182 AAAAATATTA
1 AAAAATATTA
2450192 TGCTTCTTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
40 11 0.25
41 21 0.48
42 12 0.27
ACGTcount: A:0.51, C:0.09, G:0.10, T:0.30
Consensus pattern (41 bp):
AAAAATATTAAGAAAAAGGTAATATTTTAGATTCAACCGAA
Found at i:2453527 original size:17 final size:18
Alignment explanation
Indices: 2453493--2453532 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
2453483 ATATTTCACT
* *
2453493 AATAGAGGAAATATTACA
1 AATAGAGGAAAGAATACA
2453511 AATAGA-GAAAGAATACA
1 AATAGAGGAAAGAATACA
2453528 AATAG
1 AATAG
2453533 CCTTTAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.60, C:0.05, G:0.17, T:0.17
Consensus pattern (18 bp):
AATAGAGGAAAGAATACA
Done.