Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007725.1 Hibiscus syriacus cultivar Beakdansim tig00109972_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: 3026330
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 14
Found at i:2817190 original size:274 final size:274
Alignment explanation
Indices: 2816695--2817347 Score: 832
Period size: 274 Copynumber: 2.4 Consensus size: 274
2816685 TATTCAATGA
* * * * *
2816695 TTCAACTACTTTTCGATGCTCAATCAATGCACCATTTAAGGTACTTTTCAGAGGTCATTCATTGC
1 TTCAATTACTTTTCGGTGCTCAATCAATGCACCATTTCAGCTACTTTTCAGAAGTCATTCATTGC
* * * *
2816760 AGCAATAATGCA-CTATTTCAGTTTTTTTAAAGCTCATTCAATGTAGAATTCAAGAAACAATTAA
66 AGCAATAATGCATC-ATTTCAGCTTTTTCAGAGCTCATTCAATGCAGAATTCAAGAAACAATTAA
* ** * * * *
2816824 AAAAACGGGTGAAAATAATGGTGTGCTATCATCTTCTGTAACTTTTCAATGATATATCAATTCAA
130 AAAAACGAGTGAAAATAATGGTGCACTATCATCTTCTGCAACTTTTAAATGATATATAAACTCAA
** *
2816889 ATCAGAAACATTTTTTTTGTTGAATTATCACTTCAAATCATAAAAAATGTGTATTTTAACCA-GA
195 ATCAGAAACATTTTTAGTGTTGAATTATCACTTCAAATCATAAAAAATATGTATTTTAACCATG-
*
2816953 CC-AAGTTTTTCACTGT
259 CCGAA-ATTTTCACTGT
* * * *
2816969 TTC-ATATACTTTTTGGTTCTCAATCAATGCACCATTTCAGCTACATTTCAGAAGTCATTCATTA
1 TTCAAT-TACTTTTCGGTGCTCAATCAATGCACCATTTCAGCTACTTTTCAGAAGTCATTCATTG
* ** * *
2817033 CAACAATAATGCATCATTTCAGCTTTTTCAGAGCTCATTCAATGCAGAATTCAATCAACTATTCA
65 CAGCAATAATGCATCATTTCAGCTTTTTCAGAGCTCATTCAATGCAGAATTCAAGAAACAATTAA
* * * *
2817098 GAAAATGAGTGAAAATAGTGGTGCATTATCATCTTCTGCAACTTTTAAATGATATATAAACTCAA
130 AAAAACGAGTGAAAATAATGGTGCACTATCATCTTCTGCAACTTTTAAATGATATATAAACTCAA
*
2817163 ATCAGAAAC-TTTTTCAGTGTTGAATTATCACTTCAAATCATAAAAAATATTTATTTTAACCATG
195 ATCAGAAACATTTTT-AGTGTTGAATTATCACTTCAAATCATAAAAAATATGTATTTTAACCATG
*
2817227 CCGAAATTTTCATTGT
259 CCGAAATTTTCACTGT
* *
2817243 TTCAATTACTTTTCGGTGCTCAATCAATGCACCGTTTCAGCTACTTTTCA-AAGGTCATTCACTG
1 TTCAATTACTTTTCGGTGCTCAATCAATGCACCATTTCAGCTACTTTTCAGAA-GTCATTCATTG
* * *
2817307 CAGTAATAATGCATCATTTCAGCAACTTTTCAGAGGTCATT
65 CAGCAATAATGCATCATTTCAGC--TTTTTCAGAGCTCATT
2817348 TATCGTAGCA
Statistics
Matches: 325, Mismatches: 45, Indels: 16
0.84 0.12 0.04
Matches are distributed among these distances:
273 8 0.02
274 297 0.91
275 6 0.02
276 14 0.04
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (274 bp):
TTCAATTACTTTTCGGTGCTCAATCAATGCACCATTTCAGCTACTTTTCAGAAGTCATTCATTGC
AGCAATAATGCATCATTTCAGCTTTTTCAGAGCTCATTCAATGCAGAATTCAAGAAACAATTAAA
AAAACGAGTGAAAATAATGGTGCACTATCATCTTCTGCAACTTTTAAATGATATATAAACTCAAA
TCAGAAACATTTTTAGTGTTGAATTATCACTTCAAATCATAAAAAATATGTATTTTAACCATGCC
GAAATTTTCACTGT
Found at i:2826910 original size:5 final size:5
Alignment explanation
Indices: 2826895--2826937 Score: 68
Period size: 5 Copynumber: 8.6 Consensus size: 5
2826885 TTTCAGATTA
* *
2826895 GGGAT GAGAT GGGAT GGGAT GGGAT GGGCT GGGAT GGGAT GGG
1 GGGAT GGGAT GGGAT GGGAT GGGAT GGGAT GGGAT GGGAT GGG
2826938 CGGAGCGGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.19, C:0.02, G:0.60, T:0.19
Consensus pattern (5 bp):
GGGAT
Found at i:2827775 original size:14 final size:14
Alignment explanation
Indices: 2827758--2827794 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2827748 AATGAATGAA
2827758 TGGCATGAGTTGTG
1 TGGCATGAGTTGTG
2827772 TGGCATGAGTTGTG
1 TGGCATGAGTTGTG
*
2827786 TGACATGAG
1 TGGCATGAG
2827795 AGTATCCGGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.19, C:0.08, G:0.41, T:0.32
Consensus pattern (14 bp):
TGGCATGAGTTGTG
Found at i:2829022 original size:21 final size:21
Alignment explanation
Indices: 2828998--2829037 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2828988 AATAATTATT
2828998 TTAGTTAA-AAAAATTTAAAAA
1 TTAG-TAAGAAAAATTTAAAAA
*
2829019 TTAGTAAGATAAATTTAAA
1 TTAGTAAGAAAAATTTAAA
2829038 TTTATTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.35
Consensus pattern (21 bp):
TTAGTAAGAAAAATTTAAAAA
Found at i:2829264 original size:18 final size:19
Alignment explanation
Indices: 2829228--2829265 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
2829218 CACGGAATGT
2829228 AAGATTACCAGTAGGAATAA
1 AAGATTACCAG-AGGAATAA
2829248 AAGATTACCAG-GGAATAA
1 AAGATTACCAGAGGAATAA
2829266 GATTACTGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
20 11 0.61
ACGTcount: A:0.50, C:0.11, G:0.21, T:0.18
Consensus pattern (19 bp):
AAGATTACCAGAGGAATAA
Found at i:2829795 original size:20 final size:20
Alignment explanation
Indices: 2829770--2829883 Score: 97
Period size: 20 Copynumber: 5.7 Consensus size: 20
2829760 AATTTGAAAA
2829770 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
2829790 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* ** *
2829810 TTCGCAACACGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
2829830 TTCGCAACT-AGATACTGACT
1 ATCGCAA-TGCGATACTGACT
* * * *
2829850 TTCGCAACGAGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
2829870 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
2829884 TTTCAAAGCG
Statistics
Matches: 78, Mismatches: 12, Indels: 7
0.80 0.12 0.07
Matches are distributed among these distances:
19 2 0.03
20 66 0.85
21 10 0.13
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:2829824 original size:40 final size:40
Alignment explanation
Indices: 2829771--2829883 Score: 117
Period size: 40 Copynumber: 2.8 Consensus size: 40
2829761 ATTTGAAAAA
*
2829771 TCGCAATG-CGATACTGACTATCGCAATGCGATACTGACTT
1 TCGCAACGACGATACT-ACTATCGCAATGCGATACTGACTT
* *
2829811 TCGCAAC-ACGATACTTACTTTCGCAACT-AGATACTGACTT
1 TCGCAACGACGATAC-TACTATCGCAA-TGCGATACTGACTT
*
2829851 TCGCAACGA-GATAATACATAATCGCAATGCGAT
1 TCGCAACGACGATACTAC-T-ATCGCAATGCGAT
2829884 TTTCAAAGCG
Statistics
Matches: 60, Mismatches: 6, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
39 3 0.05
40 45 0.75
41 12 0.20
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.27
Consensus pattern (40 bp):
TCGCAACGACGATACTACTATCGCAATGCGATACTGACTT
Found at i:2830077 original size:22 final size:22
Alignment explanation
Indices: 2830049--2830091 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2830039 CACTCTCTCA
2830049 CCATCTCCGACGAAACCCGTCC
1 CCATCTCCGACGAAACCCGTCC
* *
2830071 CCATCTCCGGCGAAATCCGTC
1 CCATCTCCGACGAAACCCGTC
2830092 TATCTCCATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.47, G:0.16, T:0.16
Consensus pattern (22 bp):
CCATCTCCGACGAAACCCGTCC
Found at i:2830378 original size:20 final size:20
Alignment explanation
Indices: 2830355--2830397 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
2830345 GATAATCAAA
2830355 TTCGCGTTGCGATTGTCATT
1 TTCGCGTTGCGATTGTCATT
* *
2830375 TTCGTGTTGCGATTTTCATT
1 TTCGCGTTGCGATTGTCATT
2830395 TTC
1 TTC
2830398 AGAAACTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.09, C:0.19, G:0.21, T:0.51
Consensus pattern (20 bp):
TTCGCGTTGCGATTGTCATT
Found at i:2832346 original size:19 final size:19
Alignment explanation
Indices: 2832324--2832417 Score: 68
Period size: 19 Copynumber: 5.5 Consensus size: 19
2832314 AATGGCTATT
2832324 GCAATGCGAAATGAAAATC
1 GCAATGCGAAATGAAAATC
2832343 GCAA--CGACAA-G---ATC
1 GCAATGCGA-AATGAAAATC
2832357 GCAATGCGAAATGAAAATC
1 GCAATGCGAAATGAAAATC
2832376 GCAA--CGACAA-G---ATC
1 GCAATGCGA-AATGAAAATC
* *
2832390 ACAACGCGAAATGAAAATC
1 GCAATGCGAAATGAAAATC
2832409 GCAATGCGA
1 GCAATGCGA
2832418 TTTATGTTTC
Statistics
Matches: 58, Mismatches: 3, Indels: 28
0.65 0.03 0.31
Matches are distributed among these distances:
14 13 0.22
15 4 0.07
16 8 0.14
17 8 0.14
18 4 0.07
19 21 0.36
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.12
Consensus pattern (19 bp):
GCAATGCGAAATGAAAATC
Found at i:2832366 original size:33 final size:33
Alignment explanation
Indices: 2832324--2832412 Score: 160
Period size: 33 Copynumber: 2.7 Consensus size: 33
2832314 AATGGCTATT
2832324 GCAATGCGAAATGAAAATCGCAACGACAAGATC
1 GCAATGCGAAATGAAAATCGCAACGACAAGATC
2832357 GCAATGCGAAATGAAAATCGCAACGACAAGATC
1 GCAATGCGAAATGAAAATCGCAACGACAAGATC
* *
2832390 ACAACGCGAAATGAAAATCGCAA
1 GCAATGCGAAATGAAAATCGCAA
2832413 TGCGATTTAT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.11
Consensus pattern (33 bp):
GCAATGCGAAATGAAAATCGCAACGACAAGATC
Found at i:2832461 original size:33 final size:33
Alignment explanation
Indices: 2832424--2832503 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
2832414 GCGATTTATG
* * *
2832424 TTTCGCGTTGCGATTTTGTTGTTGCGATTTTCA
1 TTTCGCATTGCGATCTTGTCGTTGCGATTTTCA
2832457 TTTCGCATTGCGATCTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATCTTGTCGTTGCGATTTTCA
2832490 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
2832504 AGCCATTTCC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTTCGCATTGCGATCTTGTCGTTGCGATTTTCA
Found at i:2832469 original size:19 final size:19
Alignment explanation
Indices: 2832445--2832503 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 19
2832435 GATTTTGTTG
2832445 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2832464 TTGCGA---TC-TTGTCG--
1 TTGCGATTTTCATT-TCGCA
2832478 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2832497 TTGCGAT
1 TTGCGAT
2832504 AGCCATTTCC
Statistics
Matches: 33, Mismatches: 0, Indels: 14
0.70 0.00 0.30
Matches are distributed among these distances:
14 6 0.18
15 2 0.06
16 5 0.15
17 5 0.15
18 2 0.06
19 13 0.39
ACGTcount: A:0.14, C:0.20, G:0.20, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:2832522 original size:20 final size:20
Alignment explanation
Indices: 2832488--2832542 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
2832478 TTGCGATTTT
*
2832488 CATTT-CGCATTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
2832507 CATTTCCGCGTTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
2832527 CATTTCCGCGTTGCGA
1 CATTTCCGCGTTGCGA
2832543 AAGTATGTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 5 0.15
20 29 0.85
ACGTcount: A:0.16, C:0.29, G:0.24, T:0.31
Consensus pattern (20 bp):
CATTTCCGCGTTGCGATAGC
Found at i:2834599 original size:19 final size:19
Alignment explanation
Indices: 2834572--2834636 Score: 86
Period size: 19 Copynumber: 3.7 Consensus size: 19
2834562 GCAACGAGAG
*
2834572 AATCACAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2834591 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2834610 AATCGCAA--CG--A-GAA
1 AATCGCAATGCGAAATGAA
2834624 AATCGCAATGCGA
1 AATCGCAATGCGA
2834637 TTTTCATTTC
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
14 11 0.26
15 1 0.02
16 2 0.05
17 2 0.05
19 26 0.62
ACGTcount: A:0.48, C:0.18, G:0.20, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:2834687 original size:20 final size:20
Alignment explanation
Indices: 2834662--2834730 Score: 120
Period size: 20 Copynumber: 3.5 Consensus size: 20
2834652 GCGATTCTCT
2834662 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* *
2834682 CGTTGCGATAGCCATTTTCA
1 CGTTGCGATAGTCATTTTCG
2834702 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
2834722 CGTTGCGAT
1 CGTTGCGAT
2834731 TTCCCCGTTG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.16, C:0.22, G:0.25, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:2834688 original size:34 final size:33
Alignment explanation
Indices: 2834643--2834749 Score: 106
Period size: 40 Copynumber: 3.0 Consensus size: 33
2834633 GCGATTTTCA
* *
2834643 TTTCGCATTGCGATTCTCTCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATT-TCACGTTGCGATAGTCAT
2834677 TTTCGCGTTGCGATAGCCATTTTCACGTTGCGATAGTCAT
1 TTTCGCGTTGC----G--A-TTTCACGTTGCGATAGTCAT
*
2834717 TTTCGCGTTGCGATTTCCCCGTTGCGATAGTCA
1 TTTCGCGTTGCGATTT-CACGTTGCGATAGTCA
2834750 AATGAATGTT
Statistics
Matches: 62, Mismatches: 3, Indels: 16
0.77 0.04 0.20
Matches are distributed among these distances:
33 3 0.05
34 26 0.42
36 1 0.02
38 1 0.02
40 29 0.47
41 2 0.03
ACGTcount: A:0.15, C:0.24, G:0.22, T:0.38
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTCACGTTGCGATAGTCAT
Found at i:2835111 original size:20 final size:20
Alignment explanation
Indices: 2835099--2835171 Score: 128
Period size: 20 Copynumber: 3.6 Consensus size: 20
2835089 TCGTTGTGAT
*
2835099 AGTCAGAATCTCGTTGCGAA
1 AGTCAGAATCGCGTTGCGAA
2835119 AGTCAGAATCGCGTTGCGAA
1 AGTCAGAATCGCGTTGCGAA
*
2835139 AGTCAGAATCGCATTGCGAA
1 AGTCAGAATCGCGTTGCGAA
2835159 AGTCAGAATCGCG
1 AGTCAGAATCGCG
2835172 ATTTTTGTGT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.32, C:0.21, G:0.27, T:0.21
Consensus pattern (20 bp):
AGTCAGAATCGCGTTGCGAA
Found at i:2835143 original size:40 final size:40
Alignment explanation
Indices: 2835090--2835171 Score: 128
Period size: 40 Copynumber: 2.0 Consensus size: 40
2835080 TGTATTATCT
* * * *
2835090 CGTTGTGATAGTCAGAATCTCGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGAATCG
2835130 CGTTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGAATCG
2835170 CG
1 CG
2835172 ATTTTTGTGT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (40 bp):
CGTTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGAATCG
Found at i:2835300 original size:22 final size:22
Alignment explanation
Indices: 2835268--2835314 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
2835258 CTCCGGCGAT
2835268 ATCTGTACCTATATCCAACGAC
1 ATCTGTACCTATATCCAACGAC
*
2835290 ATCTGTTCCTATATCCAACGAC
1 ATCTGTACCTATATCCAACGAC
2835312 ATC
1 ATC
2835315 CTTCCTCATC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.30, C:0.32, G:0.09, T:0.30
Consensus pattern (22 bp):
ATCTGTACCTATATCCAACGAC
Found at i:2838450 original size:20 final size:19
Alignment explanation
Indices: 2838422--2838463 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
2838412 CAATCATCTT
*
2838422 AATGTCTATCGCAATGCGGA
1 AATGACTATCGCAATGC-GA
2838442 AATGACTATCGCAATGCGA
1 AATGACTATCGCAATGCGA
2838461 AAT
1 AAT
2838464 AAAAATTGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (19 bp):
AATGACTATCGCAATGCGA
Found at i:2838539 original size:20 final size:19
Alignment explanation
Indices: 2838429--2838579 Score: 80
Period size: 19 Copynumber: 8.6 Consensus size: 19
2838419 CTTAATGTCT
**
2838429 ATCGCAATGCGGAAATGACT
1 ATCGCAATGC-GAAATGAAA
*
2838449 ATCGCAATGCGAAATAAAA
1 ATCGCAATGCGAAATGAAA
* *
2838468 ATTGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
2838482 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
2838501 ACCGCAACGCG--AT---A
1 ATCGCAATGCGAAATGAAA
2838515 ATCGCAATGCGAAATGAAAA
1 ATCGCAATGCGAAATG-AAA
**
2838535 ATCGCAAT--G--A-GGGA
1 ATCGCAATGCGAAATGAAA
*
2838549 ATCGCAAAGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2838568 ATCGCAACGCGA
1 ATCGCAATGCGA
2838580 TTTTAGTTTC
Statistics
Matches: 97, Mismatches: 18, Indels: 33
0.66 0.12 0.22
Matches are distributed among these distances:
14 26 0.27
15 2 0.02
16 6 0.06
17 4 0.04
18 3 0.03
19 37 0.38
20 19 0.20
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2838552 original size:34 final size:33
Alignment explanation
Indices: 2838449--2838576 Score: 175
Period size: 33 Copynumber: 3.8 Consensus size: 33
2838439 GGAAATGACT
* *
2838449 ATCGCAATGCGAAATAAAAATTGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
2838482 ATCGCAATGCGAAATGAAAACCGCAACGCGATA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
2838515 ATCGCAATGCGAAATGAAAAATCGCAATGAGGGA
1 ATCGCAATGCGAAATG-AAAATCGCAACGAGAGA
*
2838549 ATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
2838577 CGATTTTAGT
Statistics
Matches: 82, Mismatches: 12, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
33 55 0.67
34 27 0.33
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:2838561 original size:67 final size:66
Alignment explanation
Indices: 2838449--2838580 Score: 210
Period size: 67 Copynumber: 2.0 Consensus size: 66
2838439 GGAAATGACT
* *
2838449 ATCGCAATGCGAAATAAAAATTGCAACGAGAGAATCGCAATGCGAAATGAAAACCGCAACGCGAT
1 ATCGCAATGCGAAATAAAAATCGCAACGAGAGAATCGCAAAGCGAAATGAAAACCGCAACGCGAT
2838514 A
66 A
* * *
2838515 ATCGCAATGCGAAATGAAAAATCGCAATGAGGGAATCGCAAAGCGAAATGAAAATCGCAACGCGA
1 ATCGCAATGCGAAAT-AAAAATCGCAACGAGAGAATCGCAAAGCGAAATGAAAACCGCAACGCGA
2838580 T
65 T
2838581 TTTAGTTTCG
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
66 15 0.25
67 45 0.75
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.14
Consensus pattern (66 bp):
ATCGCAATGCGAAATAAAAATCGCAACGAGAGAATCGCAAAGCGAAATGAAAACCGCAACGCGAT
A
Found at i:2838598 original size:19 final size:19
Alignment explanation
Indices: 2838576--2838651 Score: 83
Period size: 19 Copynumber: 4.3 Consensus size: 19
2838566 AAATCGCAAC
2838576 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTCA-TTTCGCGTT
*
2838595 GCGA-TTT--TGTCG--TT
1 GCGATTTTCATTTCGCGTT
2838609 GCGATTTTCATTTCGCGTT
1 GCGATTTTCATTTCGCGTT
*
2838628 GCGATTTTCATTTCGCATT
1 GCGATTTTCATTTCGCGTT
2838647 GCGAT
1 GCGAT
2838652 AGTCATTTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
14 6 0.12
15 3 0.06
16 4 0.08
17 4 0.08
18 3 0.06
19 29 0.59
ACGTcount: A:0.12, C:0.18, G:0.24, T:0.46
Consensus pattern (19 bp):
GCGATTTTCATTTCGCGTT
Found at i:2838657 original size:19 final size:19
Alignment explanation
Indices: 2838616--2838659 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
2838606 GTTGCGATTT
* **
2838616 TCATTTCGCGTTGCGATTT
1 TCATTTCGCATTGCGATAG
2838635 TCATTTCGCATTGCGATAG
1 TCATTTCGCATTGCGATAG
2838654 TCATTT
1 TCATTT
2838660 TTGCTTTCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.16, C:0.20, G:0.18, T:0.45
Consensus pattern (19 bp):
TCATTTCGCATTGCGATAG
Found at i:2838777 original size:14 final size:13
Alignment explanation
Indices: 2838758--2838796 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 13
2838748 CATCAATTAA
2838758 ACAAATCAACTTTT
1 ACAAATCAA-TTTT
2838772 ACAAATCATATTTT
1 ACAAATCA-ATTTT
2838786 ACAAATCAATT
1 ACAAATCAATT
2838797 AAACAATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 3 0.12
14 20 0.83
15 1 0.04
ACGTcount: A:0.46, C:0.18, G:0.00, T:0.36
Consensus pattern (13 bp):
ACAAATCAATTTT
Found at i:2842500 original size:19 final size:19
Alignment explanation
Indices: 2842458--2842541 Score: 106
Period size: 19 Copynumber: 4.6 Consensus size: 19
2842448 TTGGTTGAAC
*
2842458 TGAAAATCGCAACGAGAGAA
1 TGAAAATCGCAACGCGA-AA
2842478 TGAAAATCGCAACGCGAAA
1 TGAAAATCGCAACGCGAAA
2842497 TGAAAATCGCAA--CG--A
1 TGAAAATCGCAACGCGAAA
*
2842512 -GATAATCGCAACGCGAAA
1 TGAAAATCGCAACGCGAAA
2842530 TGAAAATCGCAA
1 TGAAAATCGCAA
2842542 TCATTTCGCG
Statistics
Matches: 56, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 24 0.43
20 16 0.29
ACGTcount: A:0.48, C:0.19, G:0.21, T:0.12
Consensus pattern (19 bp):
TGAAAATCGCAACGCGAAA
Found at i:2842569 original size:14 final size:14
Alignment explanation
Indices: 2842550--2842605 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
2842540 AATCATTTCG
2842550 CGTTGCGATTATCT
1 CGTTGCGATTATCT
*
2842564 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TT-A--TCT
2842583 CGTTGCGATTATCT
1 CGTTGCGATTATCT
2842597 CGTTGCGAT
1 CGTTGCGAT
2842606 AGTCATTTCC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 19 0.54
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.12, C:0.21, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTATCT
Found at i:2842584 original size:33 final size:33
Alignment explanation
Indices: 2842542--2842626 Score: 143
Period size: 33 Copynumber: 2.5 Consensus size: 33
2842532 AAAATCGCAA
**
2842542 TCATTTCGCGTTGCGATTATCTCGTTGCGATTT
1 TCATTTCGCGTTGCGATTATCTCGTTGCGATAG
2842575 TCATTTCGCGTTGCGATTATCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTATCTCGTTGCGATAG
2842608 TCATTTCCGCGTTGCGATT
1 TCATTT-CGCGTTGCGATT
2842627 TTCATTCTCG
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
33 37 0.76
34 12 0.24
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.42
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTATCTCGTTGCGATAG
Found at i:2842631 original size:20 final size:19
Alignment explanation
Indices: 2842564--2842632 Score: 67
Period size: 20 Copynumber: 3.8 Consensus size: 19
2842554 GCGATTATCT
2842564 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
2842583 CGTTGCGA--TT-A--TCT
1 CGTTGCGATTTTCATTTCG
**
2842597 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTTTCATTT-CG
2842617 CGTTGCGATTTTCATT
1 CGTTGCGATTTTCATT
2842633 CTCGAAACTA
Statistics
Matches: 39, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
14 10 0.26
16 2 0.05
17 3 0.08
19 9 0.23
20 15 0.38
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.43
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:2843202 original size:20 final size:20
Alignment explanation
Indices: 2843175--2843268 Score: 125
Period size: 20 Copynumber: 4.7 Consensus size: 20
2843165 CGATAGTCAG
2843175 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * *
2843195 ATTTGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGT
*
2843215 AATTCGCATTGCGATTTACTT
1 -ATTCGCATTGCGATTTACGT
* *
2843236 AATCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
2843256 ATTCGCATTGCGA
1 ATTCGCATTGCGA
2843269 ATTATGAAAA
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
20 45 0.73
21 17 0.27
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:2843225 original size:41 final size:40
Alignment explanation
Indices: 2843175--2843268 Score: 125
Period size: 41 Copynumber: 2.3 Consensus size: 40
2843165 CGATAGTCAG
* * *
2843175 ATTCGCATTGCGATTTACGTATTTGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
* * *
2843215 AATTCGCATTGCGATTTACTTAATCGCGTTGCGATTTACGT
1 -ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
2843256 ATTCGCATTGCGA
1 ATTCGCATTGCGA
2843269 ATTATGAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 13 0.28
41 34 0.72
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.40
Consensus pattern (40 bp):
ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
Found at i:2843309 original size:20 final size:21
Alignment explanation
Indices: 2843152--2843312 Score: 120
Period size: 20 Copynumber: 7.9 Consensus size: 21
2843142 ATGGCGCTAT
2843152 GTAAATCGCATTGCGA--TA-
1 GTAAATCGCATTGCGATTTAC
*
2843170 GTCAGATTCGCATTGCGATTTAC
1 GT-A-AATCGCATTGCGATTTAC
* * *
2843193 GT-ATTTGCATTGCGATTTTC
1 GTAAATCGCATTGCGATTTAC
* *
2843213 CTAATTCGCATTGCGATTTAC
1 GTAAATCGCATTGCGATTTAC
* *
2843234 -TTAATCGCGTTGCGATTTAC
1 GTAAATCGCATTGCGATTTAC
* * *
2843254 GT-ATTCGCATTGCGAATTAT
1 GTAAATCGCATTGCGATTTAC
* ** *
2843274 GAAAATCGCAACGCGA-ATAC
1 GTAAATCGCATTGCGATTTAC
2843294 GTAAATCGCATTGCGATTT
1 GTAAATCGCATTGCGATTT
2843313 TGTATTATCG
Statistics
Matches: 111, Mismatches: 23, Indels: 15
0.74 0.15 0.10
Matches are distributed among these distances:
18 2 0.02
19 1 0.01
20 76 0.68
21 28 0.25
22 2 0.02
23 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (21 bp):
GTAAATCGCATTGCGATTTAC
Found at i:2843323 original size:21 final size:22
Alignment explanation
Indices: 2843298--2843354 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 22
2843288 GAATACGTAA
*
2843298 ATCGCATTGCGATTTTGT-ATT
1 ATCGCATTGCGATTTTGTCAGT
* *
2843319 ATCGCGTTGCGA--TAGTCAGT
1 ATCGCATTGCGATTTTGTCAGT
2843339 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
2843355 CTAAATTCGC
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
19 3 0.11
20 13 0.46
21 11 0.39
22 1 0.04
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.40
Consensus pattern (22 bp):
ATCGCATTGCGATTTTGTCAGT
Found at i:2843365 original size:82 final size:82
Alignment explanation
Indices: 2843218--2843412 Score: 193
Period size: 82 Copynumber: 2.4 Consensus size: 82
2843208 TTTTCCTAAT
*
2843218 TCGCATTGCGATTTACTTAATCGCGTTGCGATTTACGTATTCGCATTGCGAATTATGAAAATCGC
1 TCGCATTGCGATTTACTTAATCGCGTTGCGATTCACGTATTCGCATTGCGAATTATGAAAATCGC
*
2843283 AACGCG-AATACGTAAA
66 AACGCGAAATACGAAAA
** * * * *
2843299 TCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCA-GTA-TCGCATTGCG-ATTTTCTAAAT
1 TCGCATTGCGATTTACT-TAATCGCGTTGCGAT--TCACGTATTCGCATTGCGAATTAT-GAAAA
* **
2843361 TCGCAATGCGAAATTGGAAAA
62 TCGCAACGCGAAATACGAAAA
* *
2843382 TCGCATTGCGATAGTA-ATAATCGCGTTGCGA
1 TCGCATTGCGAT-TTACTTAATCGCGTTGCGA
2843413 ATCTGGAAAC
Statistics
Matches: 93, Mismatches: 15, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
81 19 0.20
82 49 0.53
83 22 0.24
84 3 0.03
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (82 bp):
TCGCATTGCGATTTACTTAATCGCGTTGCGATTCACGTATTCGCATTGCGAATTATGAAAATCGC
AACGCGAAATACGAAAA
Found at i:2847442 original size:48 final size:49
Alignment explanation
Indices: 2847346--2847475 Score: 244
Period size: 48 Copynumber: 2.7 Consensus size: 49
2847336 CCCCAGAAAC
*
2847346 CAATAAGAGAAAATCAATAAACAACTCAAACCCCAAAAAAATGAATGAA
1 CAATAAGAGAATATCAATAAACAACTCAAACCCCAAAAAAATGAATGAA
2847395 CAATAAGAGAATATCAATAAACAA-TCAAACCCCAAAAAAATGAATGAA
1 CAATAAGAGAATATCAATAAACAACTCAAACCCCAAAAAAATGAATGAA
2847443 CAATAAGAGAATATCAATAAACAACTCAAACCC
1 CAATAAGAGAATATCAATAAACAACTCAAACCC
2847476 GAGAAACCAA
Statistics
Matches: 79, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
48 48 0.61
49 31 0.39
ACGTcount: A:0.59, C:0.19, G:0.08, T:0.14
Consensus pattern (49 bp):
CAATAAGAGAATATCAATAAACAACTCAAACCCCAAAAAAATGAATGAA
Found at i:2848299 original size:24 final size:23
Alignment explanation
Indices: 2848259--2848304 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
2848249 TTGTGATTTT
*
2848259 TTTTAATTTTTTAATTAGTTTATA
1 TTTTAATTTTATAATTA-TTTATA
2848283 TTTTAA-TTTATATATTATTTAT
1 TTTTAATTTTATA-ATTATTTAT
2848305 TTAATTAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (23 bp):
TTTTAATTTTATAATTATTTATA
Found at i:2848712 original size:29 final size:29
Alignment explanation
Indices: 2848667--2848724 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
2848657 GTGTTGGCCG
*
2848667 TAGGTCGCCATGCCTTCCGGGCGACCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
* *
2848696 TAGGTCGCCATGTCTTCCCGGCGAGCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
2848725 AAGAGATTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.14, C:0.36, G:0.28, T:0.22
Consensus pattern (29 bp):
TAGGTCGCCATGCCTTCCCGGCGACCTAC
Found at i:2848786 original size:14 final size:14
Alignment explanation
Indices: 2848767--2848799 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
2848757 CGCTGGGCAT
2848767 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
2848781 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
2848795 ACGAG
1 CCGAG
2848800 CTATGCGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.39, G:0.30, T:0.06
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:2848833 original size:33 final size:33
Alignment explanation
Indices: 2848781--2848861 Score: 110
Period size: 33 Copynumber: 2.5 Consensus size: 33
2848771 GGCCATCCGA
* * * *
2848781 CCGAGGCCATCCGAACGAGCTATGCGAGGGCAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
2848814 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
2848847 CCGAGGG-AAGCCGAG
1 CCGAGGGCAA-CCGAG
2848862 AGAGGGTAGG
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
32 2 0.05
33 41 0.95
ACGTcount: A:0.26, C:0.27, G:0.38, T:0.09
Consensus pattern (33 bp):
CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
Found at i:2848915 original size:29 final size:29
Alignment explanation
Indices: 2848869--2848924 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
2848859 GAGAGAGGGT
*
2848869 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGGGCATGGCGACCTACA
* *
2848898 AGGTTGCCCGGAGGGCATTGCGACCTA
1 AGGTCGCCCGGAGGGCATGGCGACCTA
2848925 TGTGTTGGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.20, C:0.29, G:0.36, T:0.16
Consensus pattern (29 bp):
AGGTCGCCCGGAGGGCATGGCGACCTACA
Found at i:2850385 original size:23 final size:23
Alignment explanation
Indices: 2850359--2850403 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2850349 AAACGAACTT
*
2850359 AATAAATGAACATAAACAAATAC
1 AATAAACGAACATAAACAAATAC
*
2850382 AATAAACGAACATAAACGAATA
1 AATAAACGAACATAAACAAATA
2850404 ACACAAACAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.64, C:0.13, G:0.07, T:0.16
Consensus pattern (23 bp):
AATAAACGAACATAAACAAATAC
Found at i:2850411 original size:23 final size:23
Alignment explanation
Indices: 2850366--2850411 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
2850356 CTTAATAAAT
*
2850366 GAACATAAACAAATACAATAAAC
1 GAACATAAACAAATACAACAAAC
*
2850389 GAACATAAACGAATA-ACACAAAC
1 GAACATAAACAAATACA-ACAAAC
2850412 ACAAAAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 1 0.05
23 19 0.95
ACGTcount: A:0.63, C:0.20, G:0.07, T:0.11
Consensus pattern (23 bp):
GAACATAAACAAATACAACAAAC
Found at i:2850899 original size:16 final size:16
Alignment explanation
Indices: 2850878--2850913 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
2850868 TCATTTACAA
2850878 CCCTAAGAATTAGTAG
1 CCCTAAGAATTAGTAG
*
2850894 CCCTAAGAATTAGTCG
1 CCCTAAGAATTAGTAG
2850910 CCCT
1 CCCT
2850914 GCTTGTCGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.25
Consensus pattern (16 bp):
CCCTAAGAATTAGTAG
Found at i:2851095 original size:35 final size:36
Alignment explanation
Indices: 2851022--2851106 Score: 127
Period size: 35 Copynumber: 2.4 Consensus size: 36
2851012 TTTGTTCTAC
*
2851022 CTTCTGGGTTGCAAATTAGAAAAAAAAGAATCTATG
1 CTTCTGAGTTGCAAATTAGAAAAAAAAGAATCTATG
* * *
2851058 CTTCTGAGTTGCAAATTAG-AAGAAACGAATCTGTG
1 CTTCTGAGTTGCAAATTAGAAAAAAAAGAATCTATG
2851093 CTTCTGAGTTGCAA
1 CTTCTGAGTTGCAA
2851107 TTACACAGAA
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
35 27 0.60
36 18 0.40
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.29
Consensus pattern (36 bp):
CTTCTGAGTTGCAAATTAGAAAAAAAAGAATCTATG
Found at i:2856374 original size:15 final size:14
Alignment explanation
Indices: 2856338--2856376 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 14
2856328 TTAATTTTAT
2856338 AAAAAAATTTAAAA
1 AAAAAAATTTAAAA
2856352 AAATAAAATTTATAAA
1 AAA-AAAATTTA-AAA
2856368 ATAAAAAAT
1 A-AAAAAAT
2856377 CGATGGAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 3 0.14
15 8 0.36
16 9 0.41
17 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AAAAAAATTTAAAA
Found at i:2870261 original size:2 final size:2
Alignment explanation
Indices: 2870254--2870290 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2870244 TTTATTTTTA
2870254 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 A
2870291 ATTTAATTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2871041 original size:2 final size:2
Alignment explanation
Indices: 2871034--2871061 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2871024 TTTTCTTAAA
2871034 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
2871062 TATCTTCAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2874333 original size:21 final size:21
Alignment explanation
Indices: 2874307--2874404 Score: 71
Period size: 21 Copynumber: 4.7 Consensus size: 21
2874297 ATTTTCATAT
*
2874307 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
2874328 TCGCAATGC-AGACTTGGACTA
1 TCGCAATGCGA-ACTTCGACTA
* *
2874349 TCACAATGCGAA-TAT-GTA-AA
1 TCGCAATGCGAACT-TCG-ACTA
*
2874369 TCGCAATGCGATA-ATCGACTA
1 TCGCAATGCGA-ACTTCGACTA
*
2874390 TCGTAATGCGAACTT
1 TCGCAATGCGAACTT
2874405 GGACGTGTCG
Statistics
Matches: 60, Mismatches: 9, Indels: 16
0.71 0.11 0.19
Matches are distributed among these distances:
20 17 0.28
21 42 0.70
22 1 0.02
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.24
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:2874455 original size:5 final size:5
Alignment explanation
Indices: 2874446--2874481 Score: 56
Period size: 5 Copynumber: 7.4 Consensus size: 5
2874436 CAACCCGACC
*
2874446 CGAGA TGAGA CGAGA CGAGA CGAGA CGAGA CG-GA CG
1 CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CG
2874482 GCGGCGGCGA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
4 4 0.14
5 25 0.86
ACGTcount: A:0.36, C:0.19, G:0.42, T:0.03
Consensus pattern (5 bp):
CGAGA
Found at i:2875128 original size:21 final size:21
Alignment explanation
Indices: 2875104--2875240 Score: 138
Period size: 21 Copynumber: 6.6 Consensus size: 21
2875094 TTTGGAATAA
**
2875104 ATCGCAACACGAACTTCGACT
1 ATCGCAATGCGAACTTCGACT
* *
2875125 ATCGTAATGCGAACTTGGACT
1 ATCGCAATGCGAACTTCGACT
*
2875146 ATCGCAATGCGAA-TAT-GTA-A
1 ATCGCAATGCGAACT-TCG-ACT
*
2875166 ATCGCAATGCGATA-GTCGACT
1 ATCGCAATGCGA-ACTTCGACT
*
2875187 ATCGCAATGCGAACTTGGACT
1 ATCGCAATGCGAACTTCGACT
*
2875208 ATCGCAACGCGAACTTCGACT
1 ATCGCAATGCGAACTTCGACT
*
2875229 ATCGCATTGCGA
1 ATCGCAATGCGA
2875241 TTTACATATT
Statistics
Matches: 96, Mismatches: 14, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
20 17 0.18
21 79 0.82
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (21 bp):
ATCGCAATGCGAACTTCGACT
Found at i:2875275 original size:21 final size:21
Alignment explanation
Indices: 2875249--2875385 Score: 197
Period size: 21 Copynumber: 6.6 Consensus size: 21
2875239 GATTTACATA
2875249 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
2875270 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
*
2875291 TTCGCGTTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* *
2875312 TTCGCATTGCGAT-TTACATA-
1 TTCGCATTGCGATAGTCCA-AG
2875332 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
2875353 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
*
2875374 TTCGCGTTGCGA
1 TTCGCATTGCGA
2875386 ATCTGGAAAC
Statistics
Matches: 103, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
20 17 0.17
21 86 0.83
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.31
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:2875275 original size:41 final size:41
Alignment explanation
Indices: 2875230--2875365 Score: 213
Period size: 41 Copynumber: 3.3 Consensus size: 41
2875220 ACTTCGACTA
2875230 TCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGT
* *
2875271 TCGCATTGCGATAGT-CGA-AGTTCGCGTTGCGATAGTCCAAGT
1 TCGCATTGCGAT-TTAC-ATA-TTCGCATTGCGATAGTCCAAGT
2875313 TCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGT
2875354 TCGCATTGCGAT
1 TCGCATTGCGAT
2875366 AGTCGAAGTT
Statistics
Matches: 86, Mismatches: 4, Indels: 10
0.86 0.04 0.10
Matches are distributed among these distances:
41 49 0.57
42 37 0.43
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.32
Consensus pattern (41 bp):
TCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGT
Found at i:2875275 original size:83 final size:83
Alignment explanation
Indices: 2875113--2875364 Score: 237
Period size: 83 Copynumber: 3.0 Consensus size: 83
2875103 AATCGCAACA
* * * * *
2875113 CGAACTTCGACTATCGTAATGCGAACTTGGACTATCGCAATGCGAATATGTA-A-A-TCGCAATG
1 CGAACTTGGACTATCGCAATGCGAACTTCGACTATCGCATTGCG-AT-T-TACATATTCGCATTG
* * *
2875175 CGATAGT-CGACTATCGCAATG
63 CGATAGTCCAAGT-TCGCATTG
*
2875196 CGAACTTGGACTATCGCAACGCGAACTTCGACTATCGCATTGCGATTTACATATTCGCATTGCGA
1 CGAACTTGGACTATCGCAATGCGAACTTCGACTATCGCATTGCGATTTACATATTCGCATTGCGA
2875261 TAGTCCAAGTTCGCATTG
66 TAGTCCAAGTTCGCATTG
* * * * ** * * * *
2875279 CGATAGTCGAAGT-TCGCGTTGCGATAGTCCAAGT-TCGCATTGCGATTTACATATTCGCATTGC
1 CGA-ACTTGGACTATCGCAATGCGA-ACTTCGACTATCGCATTGCGATTTACATATTCGCATTGC
2875342 GATAGTCCAAGTTCGCATTG
64 GATAGTCCAAGTTCGCATTG
2875362 CGA
1 CGA
2875365 TAGTCGAAGT
Statistics
Matches: 143, Mismatches: 20, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
80 2 0.01
81 2 0.01
82 3 0.02
83 123 0.86
84 13 0.09
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (83 bp):
CGAACTTGGACTATCGCAATGCGAACTTCGACTATCGCATTGCGATTTACATATTCGCATTGCGA
TAGTCCAAGTTCGCATTG
Found at i:2875369 original size:83 final size:83
Alignment explanation
Indices: 2875230--2875385 Score: 312
Period size: 83 Copynumber: 1.9 Consensus size: 83
2875220 ACTTCGACTA
2875230 TCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGAAGTTCG
1 TCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGAAGTTCG
2875295 CGTTGCGATAGTCCAAGT
66 CGTTGCGATAGTCCAAGT
2875313 TCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGAAGTTCG
1 TCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGAAGTTCG
2875378 CGTTGCGA
66 CGTTGCGA
2875386 ATCTGGAAAC
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 73 1.00
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.31
Consensus pattern (83 bp):
TCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGAAGTTCG
CGTTGCGATAGTCCAAGT
Found at i:2875645 original size:31 final size:31
Alignment explanation
Indices: 2875610--2875678 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
2875600 TATATAGTAT
* *
2875610 ATAAATTATCAGTTTTGGTATGTTTTAGCAC
1 ATAAACTATCAGTCTTGGTATGTTTTAGCAC
* *
2875641 ATAAACTATCAGTCTTGGTTTGTTTTAGTAC
1 ATAAACTATCAGTCTTGGTATGTTTTAGCAC
2875672 ATAAACT
1 ATAAACT
2875679 TTTAATTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.43
Consensus pattern (31 bp):
ATAAACTATCAGTCTTGGTATGTTTTAGCAC
Found at i:2876570 original size:135 final size:135
Alignment explanation
Indices: 2876400--2876670 Score: 452
Period size: 135 Copynumber: 2.0 Consensus size: 135
2876390 ATGAATTAGC
* * * *
2876400 TCTGAATGTGACATGCTGTTTGATAATGGTTCTGAATCATTTAGAATACACTTCTATGCTGAATC
1 TCTGAATGTGACATGATGTTTGATAATGGCTCTGAATCATTCAAAATACACTTCTATGCTGAATC
2876465 ATTCAGCACTATTTTACTGAATCAGTCAGCACTGAATCATTCAGAGGTGCGAAACAAACGCTCTG
66 ATTCAGCACTATTTTACTGAATCAGTCAGCACTGAATCATTCAGAGGTGCGAAACAAACGCTCTG
2876530 AATGT
131 AATGT
* *
2876535 TCTGAATGTGACATGATGTTTGATAATGGCTCTGAATCATTCAAAATATACTTCTATGCTTAATC
1 TCTGAATGTGACATGATGTTTGATAATGGCTCTGAATCATTCAAAATACACTTCTATGCTGAATC
* * * *
2876600 ATTTAGCACTATTTTGCTGAATCAGTCAGCACTGAATCATTTAGATGTGCGAAACAAACGCTCTG
66 ATTCAGCACTATTTTACTGAATCAGTCAGCACTGAATCATTCAGAGGTGCGAAACAAACGCTCTG
2876665 AATGT
131 AATGT
2876670 T
1 T
2876671 GAACGGTTCA
Statistics
Matches: 126, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
135 126 1.00
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Consensus pattern (135 bp):
TCTGAATGTGACATGATGTTTGATAATGGCTCTGAATCATTCAAAATACACTTCTATGCTGAATC
ATTCAGCACTATTTTACTGAATCAGTCAGCACTGAATCATTCAGAGGTGCGAAACAAACGCTCTG
AATGT
Found at i:2877012 original size:38 final size:38
Alignment explanation
Indices: 2876934--2877013 Score: 92
Period size: 39 Copynumber: 2.1 Consensus size: 38
2876924 ATCAATTTGG
* *
2876934 AAAATATTATATATTTTCTTTAAAAAATTTAAATTCAT
1 AAAATATTATATATTTTCTTTAAAAAATTAAAAATCAT
* *
2876972 AAAAT-TTATATAATTTTTTTTTACAAAATTAAAAAT-AT
1 AAAATATTATAT-A-TTTTCTTTAAAAAATTAAAAATCAT
2877010 AAAA
1 AAAA
2877014 AGGTTTAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
37 6 0.17
38 12 0.33
39 18 0.50
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (38 bp):
AAAATATTATATATTTTCTTTAAAAAATTAAAAATCAT
Found at i:2878670 original size:21 final size:20
Alignment explanation
Indices: 2878640--2878679 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
2878630 TATTTTTTTA
2878640 ATTATTTTAAT-AATAAAAGT
1 ATTATTTTAATGAA-AAAAGT
2878660 ATTATTTTTAATGAAAAAAG
1 ATTA-TTTTAATGAAAAAAG
2878680 AAAAAAACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 12 0.67
22 2 0.11
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.42
Consensus pattern (20 bp):
ATTATTTTAATGAAAAAAGT
Found at i:2879880 original size:20 final size:20
Alignment explanation
Indices: 2879855--2879893 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2879845 AGAAGACTGG
*
2879855 TGGATGAAGTCGGACTCGAA
1 TGGATGAAGTCGAACTCGAA
*
2879875 TGGATGGAGTCGAACTCGA
1 TGGATGAAGTCGAACTCGA
2879894 GGTCTGATAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.15, G:0.36, T:0.21
Consensus pattern (20 bp):
TGGATGAAGTCGAACTCGAA
Found at i:2884120 original size:24 final size:25
Alignment explanation
Indices: 2884072--2884124 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 25
2884062 AAATCAACAT
2884072 ACAATTCGATTCAACAAAAATATTC
1 ACAATTCGATTCAACAAAAATATTC
* *
2884097 ACAATTTGATTTAAC-AAAATATTC
1 ACAATTCGATTCAACAAAAATATTC
2884121 ACAA
1 ACAA
2884125 CCTGACTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 13 0.50
25 13 0.50
ACGTcount: A:0.49, C:0.17, G:0.04, T:0.30
Consensus pattern (25 bp):
ACAATTCGATTCAACAAAAATATTC
Found at i:2885843 original size:17 final size:17
Alignment explanation
Indices: 2885816--2885854 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
2885806 AATTTACAAT
2885816 TAATT-TAAATAATATC
1 TAATTATAAATAATATC
2885832 TAATTATAAATAATATC
1 TAATTATAAATAATATC
2885849 TAATTA
1 TAATTA
2885855 ATTTAATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTATAAATAATATC
Found at i:2892248 original size:37 final size:37
Alignment explanation
Indices: 2892195--2892268 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
2892185 TCTTTTTCCA
*
2892195 CCTCCCATTATAATTATTATAACTATTAGGATTAATT
1 CCTCCCATTATAATTATTATAACTATTAGGATAAATT
*
2892232 CCTCCCATTATTATTATTATAACTATTAGGATAAATT
1 CCTCCCATTATAATTATTATAACTATTAGGATAAATT
2892269 ACACGTTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.35, C:0.16, G:0.05, T:0.43
Consensus pattern (37 bp):
CCTCCCATTATAATTATTATAACTATTAGGATAAATT
Found at i:2892407 original size:23 final size:23
Alignment explanation
Indices: 2892381--2892427 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
2892371 TACCCCATTC
* * *
2892381 AAAATTTAACATTAAGTTTTAAA
1 AAAATTAAAAATTAAGTATTAAA
*
2892404 AAAATTAAAAATTTAGTATTAAA
1 AAAATTAAAAATTAAGTATTAAA
2892427 A
1 A
2892428 CAGATCATAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.36
Consensus pattern (23 bp):
AAAATTAAAAATTAAGTATTAAA
Found at i:2896368 original size:38 final size:38
Alignment explanation
Indices: 2896317--2896399 Score: 130
Period size: 38 Copynumber: 2.2 Consensus size: 38
2896307 TAGTTAATTT
* *
2896317 GACTCGAATTGAGAAGCATATCACCTTCATAGTAACTC
1 GACTCGAACTGAGAAGCATATCACCTTCACAGTAACTC
* *
2896355 GACTCGAACTGAGAAGCATATCACCTTGACATTAACTC
1 GACTCGAACTGAGAAGCATATCACCTTCACAGTAACTC
2896393 GACTCGA
1 GACTCGA
2896400 GTTTTGAGAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (38 bp):
GACTCGAACTGAGAAGCATATCACCTTCACAGTAACTC
Found at i:2897066 original size:20 final size:21
Alignment explanation
Indices: 2897041--2897092 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
2897031 TTTTCCCAAT
*
2897041 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
2897061 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
2897082 TCGCAATGCGA
1 TCGCAATGCGA
2897093 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:2897155 original size:122 final size:122
Alignment explanation
Indices: 2897022--2897259 Score: 358
Period size: 122 Copynumber: 2.0 Consensus size: 122
2897012 GTCTACAGTG
*
2897022 TCGTTGCGATTTTCCCAATTCGCAATGCGAATAAGTAAATCGCAACGCGAATT-GGGAAAATCGC
1 TCGTTGCGATTTTCACAATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTAGGG-AAATCGC
*
2897086 AATGCG-ATAC-TGACTATCGCAATGCG-ATACTTACTATCGCAATGCGATTTACGTATTC
65 AATGCGAATACGT-A-AATCGCAATGCGAAT-CTTACTATCGCAATGCGATTTACGTATTC
* * *
2897144 TCGTTGCGATTTTCATAATTCGCAATGCGAATACGTAAATCGCAATGCGAATTAGGGAAATCGCA
1 TCGTTGCGATTTTCACAATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTAGGGAAATCGCA
*
2897209 ATGCGAATACGTAAATCGCAATGCGAATCTTACTATCGCATTGCGATTTAC
66 ATGCGAATACGTAAATCGCAATGCGAATCTTACTATCGCAATGCGATTTAC
2897260 ATAGCGCCAT
Statistics
Matches: 106, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
122 95 0.90
123 10 0.09
124 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (122 bp):
TCGTTGCGATTTTCACAATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTAGGGAAATCGCA
ATGCGAATACGTAAATCGCAATGCGAATCTTACTATCGCAATGCGATTTACGTATTC
Found at i:2897193 original size:41 final size:41
Alignment explanation
Indices: 2897026--2897234 Score: 126
Period size: 41 Copynumber: 5.1 Consensus size: 41
2897016 ACAGTGTCGT
** * *
2897026 TGCGATTTTCCCAATTCGCAATGCGAATAAGTAAATCGCAA
1 TGCGATTTTCATAAATCGCAATGCGAATACGTAAATCGCAA
* *** *
2897067 CGCGAATTGGGA-AAATCGCAATGCG-ATAC-TGACTATCGCAA
1 TGCG-ATTTTCATAAATCGCAATGCGAATACGT-A-AATCGCAA
* * * * **
2897108 TGCGATACTT-ACT--ATCGCAATGCGATTTACGT-ATTCTCGT
1 TGCGAT-TTTCA-TAAATCGCAATGCGA-ATACGTAAATCGCAA
*
2897148 TGCGATTTTCATAATTCGCAATGCGAATACGTAAATCGCAA
1 TGCGATTTTCATAAATCGCAATGCGAATACGTAAATCGCAA
* ****
2897189 TGCGAATTAGGGAAATCGCAATGCGAATACGTAAATCGCAA
1 TGCGATTTTCATAAATCGCAATGCGAATACGTAAATCGCAA
2897230 TGCGA
1 TGCGA
2897235 ATCTTACTAT
Statistics
Matches: 124, Mismatches: 31, Indels: 26
0.69 0.17 0.14
Matches are distributed among these distances:
39 4 0.03
40 33 0.27
41 80 0.65
42 6 0.05
43 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.26
Consensus pattern (41 bp):
TGCGATTTTCATAAATCGCAATGCGAATACGTAAATCGCAA
Found at i:2897248 original size:20 final size:20
Alignment explanation
Indices: 2897041--2897236 Score: 130
Period size: 20 Copynumber: 9.7 Consensus size: 20
2897031 TTTTCCCAAT
*
2897041 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
2897061 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
2897082 TCGCAATGCG-ATAC-TGACTA
1 TCGCAATGCGAATACGT-A-AA
* *
2897102 TCGCAATGCG-ATACTTACTA
1 TCGCAATGCGAATACGTA-AA
* *
2897122 TCGCAATGCGATTTACGT-AT
1 TCGCAATGCGA-ATACGTAAA
* ** * * * *
2897142 TCTCGTTGCGATTTTCATAAT
1 TCGCAATGCGA-ATACGTAAA
2897163 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
2897183 TCGCAATGCGAATTAGGGAAA
1 TCGCAATGCGAA-TACGTAAA
2897204 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
2897224 TCGCAATGCGAAT
1 TCGCAATGCGAAT
2897237 CTTACTATCG
Statistics
Matches: 139, Mismatches: 29, Indels: 16
0.76 0.16 0.09
Matches are distributed among these distances:
19 2 0.01
20 90 0.65
21 43 0.31
22 4 0.03
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.26
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:2897802 original size:20 final size:20
Alignment explanation
Indices: 2897777--2897825 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
2897767 GAGAATGAAA
2897777 ATCGCAACGCGGAAATAACT
1 ATCGCAACGCGGAAATAACT
2897797 ATCGCAACGCGGAAATAACT
1 ATCGCAACGCGGAAATAACT
2897817 ATCGCAACG
1 ATCGCAACG
2897826 AGAGAATCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.39, C:0.27, G:0.20, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGGAAATAACT
Found at i:2897857 original size:19 final size:19
Alignment explanation
Indices: 2897774--2897874 Score: 68
Period size: 20 Copynumber: 5.5 Consensus size: 19
2897764 TTCGAGAATG
2897774 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
2897794 ACTATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
** *
2897814 ACTATCGCAA--CG--A-G
1 AAAATCGCAACGCGAAATA
* *
2897828 AGAATCACAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
2897847 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
2897866 AAAATCGCA
1 AAAATCGCA
2897875 TTACGATTTT
Statistics
Matches: 65, Mismatches: 11, Indels: 11
0.75 0.13 0.13
Matches are distributed among these distances:
14 7 0.11
15 1 0.02
16 2 0.03
17 1 0.02
18 2 0.03
19 24 0.37
20 28 0.43
ACGTcount: A:0.47, C:0.25, G:0.18, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:2897940 original size:20 final size:20
Alignment explanation
Indices: 2897906--2897963 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 20
2897896 GCGATTCTCT
2897906 CGTTGCGA-TAGTCATTTCCG
1 CGTTGCGATTA-TCATTTCCG
*
2897926 CGTTGCGATTATCATTAT-CT
1 CGTTGCGATTATCATT-TCCG
*
2897946 CGTTGCGATTTTCATTTC
1 CGTTGCGATTATCATTTC
2897964 AACCAAATGA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
19 1 0.03
20 29 0.88
21 3 0.09
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTATCATTTCCG
Found at i:2900132 original size:42 final size:40
Alignment explanation
Indices: 2900061--2900174 Score: 102
Period size: 42 Copynumber: 2.7 Consensus size: 40
2900051 GCTTGACATC
* * * * *
2900061 CCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATT
1 CCTCGAGAGTCC-CTCCCACCGTTCAAGAGGCCACTATCA-T
*
2900103 CCTCGAGAGTCCTCTCCCACCGTTCAAGAGGCCACTGTCAT
1 CCTCGAGAGTCC-CTCCCACCGTTCAAGAGGCCACTATCAT
* * *
2900144 CGTTGAAGAAGTCCCTCCCACCATTCAAGAG
1 CCTCG-AG-AGTCCCTCCCACCGTTCAAGAG
2900175 CCCGATTCAC
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.07
42 51 0.85
43 5 0.08
ACGTcount: A:0.24, C:0.35, G:0.18, T:0.23
Consensus pattern (40 bp):
CCTCGAGAGTCCCTCCCACCGTTCAAGAGGCCACTATCAT
Found at i:2901550 original size:14 final size:14
Alignment explanation
Indices: 2901531--2901566 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2901521 ATTGTTTAAT
2901531 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
2901545 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
2901559 TGATTTGT
1 TGATTTGT
2901567 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:2901727 original size:19 final size:19
Alignment explanation
Indices: 2901705--2901748 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
2901695 GCAACGATAG
2901705 AATCGCAACGCA-AAATTAA
1 AATCGCAACG-AGAAATTAA
*
2901724 AATCGTAACGAGAAATTAA
1 AATCGCAACGAGAAATTAA
*
2901743 ATTCGC
1 AATCGC
2901749 GTTGCGATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 1 0.05
19 20 0.95
ACGTcount: A:0.48, C:0.18, G:0.14, T:0.20
Consensus pattern (19 bp):
AATCGCAACGAGAAATTAA
Found at i:2901794 original size:33 final size:33
Alignment explanation
Indices: 2901752--2901874 Score: 178
Period size: 33 Copynumber: 3.7 Consensus size: 33
2901742 AATTCGCGTT
2901752 GCGATTTTCATTTCGCATTGCGATTCACTCGTA
1 GCGATTTTCATTTCGCATTGCGATTCACTCGTA
* *
2901785 GCGATTTTCATTTCGCATTGCGAAAT-AC-CATA
1 GCGATTTTCATTTCGCATTGCG-ATTCACTCGTA
* *
2901817 TGCGATTTTCATTTCGCATTGCGATTCTCTCGTT
1 -GCGATTTTCATTTCGCATTGCGATTCACTCGTA
2901851 GCGATTTTCATTTCGCATTGCGAT
1 GCGATTTTCATTTCGCATTGCGAT
2901875 AGTAATTTCC
Statistics
Matches: 80, Mismatches: 6, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
32 5 0.06
33 71 0.89
34 4 0.05
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.41
Consensus pattern (33 bp):
GCGATTTTCATTTCGCATTGCGATTCACTCGTA
Found at i:2904182 original size:12 final size:12
Alignment explanation
Indices: 2904165--2904189 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2904155 TCTTCGGGGA
2904165 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2904177 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2904189 C
1 C
2904190 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:2904398 original size:24 final size:24
Alignment explanation
Indices: 2904364--2904417 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2904354 CTGAAACATC
*
2904364 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
*
2904388 ATCAAAGTCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
2904412 ATCAAA
1 ATCAAA
2904418 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:2904431 original size:24 final size:24
Alignment explanation
Indices: 2904364--2904431 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
2904354 CTGAAACATC
* * * *
2904364 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAGTCCGAATACTGACCAAG
* *
2904388 ATCAAAGTCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
2904412 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
2904432 TAGTACTCAC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.25
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:2905431 original size:19 final size:18
Alignment explanation
Indices: 2905407--2905503 Score: 75
Period size: 19 Copynumber: 5.6 Consensus size: 18
2905397 TCATTTGACC
2905407 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
2905426 ATCGCAA-CG--AT-AGA
1 ATCGCAAGCGAAATGAAA
2905440 ATCGCAACGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
**
2905459 ATCGCAA-CG--A-GGGA
1 ATCGCAAGCGAAATGAAA
2905473 ATCGCAAAGCGAAATGAAA
1 ATCGC-AAGCGAAATGAAA
2905492 ATCGCAACGCGA
1 ATCGCAA-GCGA
2905504 TTTTAGTTTC
Statistics
Matches: 61, Mismatches: 6, Indels: 22
0.69 0.07 0.25
Matches are distributed among these distances:
14 16 0.26
15 5 0.08
16 4 0.07
17 4 0.07
18 5 0.08
19 27 0.44
ACGTcount: A:0.44, C:0.21, G:0.24, T:0.11
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:2905452 original size:33 final size:33
Alignment explanation
Indices: 2905407--2905500 Score: 152
Period size: 33 Copynumber: 2.8 Consensus size: 33
2905397 TCATTTGACC
* *
2905407 ATCGCAATGCGAAATGAAAATCGCAACGATAGA
1 ATCGCAAAGCGAAATGAAAATCGCAACGAGAGA
* *
2905440 ATCGCAACGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAAAGCGAAATGAAAATCGCAACGAGAGA
2905473 ATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAAAGCGAAATGAAAATCGCAACG
2905501 CGATTTTAGT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.12
Consensus pattern (33 bp):
ATCGCAAAGCGAAATGAAAATCGCAACGAGAGA
Found at i:2905522 original size:19 final size:19
Alignment explanation
Indices: 2905500--2905557 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
2905490 AAATCGCAAC
2905500 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
2905519 GCGATTTT-G--T--CGTT
1 GCGATTTTAGTTTCGCGTT
2905533 GCGATTTTCA-TTTCGCGTT
1 GCGATTTT-AGTTTCGCGTT
2905552 GCGATT
1 GCGATT
2905558 CTCTCGTTGC
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
14 12 0.36
16 1 0.03
17 1 0.03
18 1 0.03
19 18 0.55
ACGTcount: A:0.10, C:0.17, G:0.26, T:0.47
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:2905547 original size:33 final size:33
Alignment explanation
Indices: 2905500--2905655 Score: 224
Period size: 33 Copynumber: 4.7 Consensus size: 33
2905490 AAATCGCAAC
* *
2905500 GCGATTTT-AGTTTCGCGTTGCGATTTTGTCGTT
1 GCGATTTTCA-TTTCGCGTTGCGATTCTCTCGTT
2905533 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
*
2905566 GCGATTTTCATTTCGCATTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
*
2905599 GCGATTTTCATTTCGCATTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
** *
2905632 GCGATAGTCAGTTTCGTGTTGCGA
1 GCGATTTTCA-TTTCGCGTTGCGA
2905656 CATGCTGTTT
Statistics
Matches: 114, Mismatches: 7, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
33 102 0.89
34 12 0.11
ACGTcount: A:0.12, C:0.21, G:0.23, T:0.44
Consensus pattern (33 bp):
GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
Found at i:2905567 original size:14 final size:14
Alignment explanation
Indices: 2905548--2905636 Score: 70
Period size: 14 Copynumber: 5.6 Consensus size: 14
2905538 TTTCATTTCG
2905548 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2905562 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
2905579 CGCATTGCGATTCTCT
1 CG--TTGCGATTCTCT
*
2905595 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
2905612 CGCATTGCGATTCTCT
1 CG--TTGCGATTCTCT
2905628 CGTTGCGAT
1 CGTTGCGAT
2905637 AGTCAGTTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 20
0.72 0.05 0.24
Matches are distributed among these distances:
14 21 0.34
16 14 0.23
17 14 0.23
19 12 0.20
ACGTcount: A:0.11, C:0.25, G:0.20, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2905588 original size:19 final size:18
Alignment explanation
Indices: 2905531--2905623 Score: 85
Period size: 19 Copynumber: 5.4 Consensus size: 18
2905521 GATTTTGTCG
2905531 TTGCGATTTTCATTTCGC
1 TTGCGATTTTCATTTCGC
*
2905549 GTTGCGA--TTC-TCTCG-
1 -TTGCGATTTTCATTTCGC
2905564 TTGCGATTTTCATTTCGC
1 TTGCGATTTTCATTTCGC
*
2905582 ATTGCGA--TTC-TCTCG-
1 -TTGCGATTTTCATTTCGC
2905597 TTGCGATTTTCATTTCGC
1 TTGCGATTTTCATTTCGC
2905615 ATTGCGATT
1 -TTGCGATT
2905624 CTCTCGTTGC
Statistics
Matches: 60, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
14 12 0.20
16 14 0.23
17 14 0.23
19 20 0.33
ACGTcount: A:0.12, C:0.23, G:0.19, T:0.46
Consensus pattern (18 bp):
TTGCGATTTTCATTTCGC
Found at i:2907659 original size:20 final size:20
Alignment explanation
Indices: 2907636--2907703 Score: 84
Period size: 20 Copynumber: 3.5 Consensus size: 20
2907626 GAAACTTAAA
2907636 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
2907656 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGAAAATGACT
* **
2907676 ATCGCAATGC-AAAATGAAA
1 ATCGCAACGCGAAAATGACT
2907695 ATCGCAACG
1 ATCGCAACG
2907704 ACAAAATCAC
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 13 0.32
20 27 0.68
ACGTcount: A:0.40, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:2907709 original size:14 final size:14
Alignment explanation
Indices: 2907692--2907812 Score: 80
Period size: 14 Copynumber: 7.7 Consensus size: 14
2907682 ATGCAAAATG
2907692 AAAATCGCAACGAC
1 AAAATCGCAACGAC
* *
2907706 AAAATCACAAAGCGAAATG
1 AAAATCGC-AA-CG--A-C
2907725 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
2907739 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
*
2907755 ATGAAATTGCAACGAC
1 A--AAATCGCAACGAC
*
2907771 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
2907787 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
2907803 AAAATCGCAA
1 AAAATCGCAA
2907813 TGCGAAACAC
Statistics
Matches: 84, Mismatches: 10, Indels: 26
0.70 0.08 0.22
Matches are distributed among these distances:
14 34 0.40
15 3 0.04
16 18 0.21
17 2 0.02
18 20 0.24
19 7 0.08
ACGTcount: A:0.50, C:0.22, G:0.17, T:0.11
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:2907772 original size:32 final size:33
Alignment explanation
Indices: 2907676--2907819 Score: 229
Period size: 32 Copynumber: 4.4 Consensus size: 33
2907666 GGAAATGGCT
*
2907676 ATCGCAATGCAAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
2907709 ATCACAAAGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
2907742 ATCGCAATGCGAAATG-AAATTGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
2907774 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
2907806 ATCGCAATGCGAAA
1 ATCGCAATGCGAAA
2907820 CACAAATCGC
Statistics
Matches: 102, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
32 58 0.57
33 44 0.43
ACGTcount: A:0.49, C:0.22, G:0.17, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:2907887 original size:33 final size:33
Alignment explanation
Indices: 2907831--2907922 Score: 148
Period size: 33 Copynumber: 2.8 Consensus size: 33
2907821 ACAAATCGCA
* *
2907831 TTGCAATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
2907864 TTGCGATTATCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
2907897 TTGCGATTTTCATTTCGCTTTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
2907923 AGCCATTTTC
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.13, C:0.18, G:0.21, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:2907888 original size:19 final size:17
Alignment explanation
Indices: 2907838--2907922 Score: 65
Period size: 14 Copynumber: 5.1 Consensus size: 17
2907828 GCATTGCAAT
2907838 TTTCATTTCGCGTTGCGA
1 TTTCATTTCGC-TTGCGA
*
2907856 TTT--TGTCG-TTGCGA
1 TTTCATTTCGCTTGCGA
2907870 TTATCATTTCGCATTGCGA
1 TT-TCATTTCGC-TTGCGA
*
2907889 TTT--TGTCG-TTGCGA
1 TTTCATTTCGCTTGCGA
2907903 TTTTCATTTCGCTTTGCGA
1 -TTTCATTTCGC-TTGCGA
2907922 T
1 T
2907923 AGCCATTTTC
Statistics
Matches: 53, Mismatches: 4, Indels: 20
0.69 0.05 0.26
Matches are distributed among these distances:
14 14 0.26
15 4 0.08
16 8 0.15
17 8 0.15
18 5 0.09
19 14 0.26
ACGTcount: A:0.12, C:0.19, G:0.21, T:0.48
Consensus pattern (17 bp):
TTTCATTTCGCTTGCGA
Found at i:2907934 original size:20 final size:20
Alignment explanation
Indices: 2907909--2907961 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
2907899 GCGATTTTCA
*
2907909 TTTCGCTTTGCGATAGCCAT
1 TTTCGCGTTGCGATAGCCAT
*
2907929 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGCCAT
*
2907949 TTTCGTGTTGCGA
1 TTTCGCGTTGCGA
2907962 AAGTAAACTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.13, C:0.21, G:0.25, T:0.42
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGCCAT
Found at i:2909837 original size:20 final size:20
Alignment explanation
Indices: 2909789--2909847 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
2909779 AATAGTTTCT
** *
2909789 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
2909809 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
2909829 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
2909848 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:2910128 original size:20 final size:21
Alignment explanation
Indices: 2910103--2910142 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
2910093 TATGAGAGAT
2910103 GGAGATA-GACGGATTTCGCC
1 GGAGATAGGACGGATTTCGCC
2910123 GGAGATAGGGACGGATTTCG
1 GGAGATA-GGACGGATTTCG
2910143 TTGGAGATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
22 11 0.61
ACGTcount: A:0.25, C:0.15, G:0.40, T:0.20
Consensus pattern (21 bp):
GGAGATAGGACGGATTTCGCC
Found at i:2910148 original size:22 final size:20
Alignment explanation
Indices: 2910102--2910150 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 20
2910092 CTATGAGAGA
2910102 TGGAGATAGACGGATTTCGC
1 TGGAGATAGACGGATTTCGC
* *
2910122 CGGAGATAGGGACGGATTTCGT
1 TGGAGATA--GACGGATTTCGC
2910144 TGGAGAT
1 TGGAGAT
2910151 GGGTGAGAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 7 0.29
22 17 0.71
ACGTcount: A:0.24, C:0.12, G:0.39, T:0.24
Consensus pattern (20 bp):
TGGAGATAGACGGATTTCGC
Found at i:2910430 original size:20 final size:20
Alignment explanation
Indices: 2910321--2910435 Score: 90
Period size: 20 Copynumber: 5.7 Consensus size: 20
2910311 CGCTTTGAAA
*
2910321 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
2910342 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
*
2910362 ATCGCATTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
2910382 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
2910403 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
*
2910423 ATCACATTGCGAT
1 ATCGCATTGCGAT
2910436 TTTCCCAATT
Statistics
Matches: 74, Mismatches: 16, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
19 5 0.07
20 44 0.59
21 23 0.31
22 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:2910546 original size:21 final size:21
Alignment explanation
Indices: 2910506--2910546 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2910496 ACTGTAGACA
** *
2910506 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACT
2910527 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
2910547 GCGAATTTGC
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:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACT
Found at i:2918910 original size:20 final size:20
Alignment explanation
Indices: 2918882--2918921 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2918872 CATCGTGATT
*
2918882 ATTTTATAACAATTTGATAA
1 ATTTAATAACAATTTGATAA
* *
2918902 ATTTAATAACTATTTTATAA
1 ATTTAATAACAATTTGATAA
2918922 CTTTTAAAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (20 bp):
ATTTAATAACAATTTGATAA
Found at i:2929814 original size:19 final size:19
Alignment explanation
Indices: 2929786--2929822 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2929776 AAAAACGTGT
2929786 TGTTGAGATAGTGAAAAAG
1 TGTTGAGATAGTGAAAAAG
*
2929805 TGTTGCGATAGTGAAAAA
1 TGTTGAGATAGTGAAAAA
2929823 TCCAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.03, G:0.30, T:0.27
Consensus pattern (19 bp):
TGTTGAGATAGTGAAAAAG
Found at i:2930245 original size:21 final size:21
Alignment explanation
Indices: 2930221--2930290 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
2930211 ATTTTTCAAA
2930221 ATCGCAACGCGAACTTTGACT
1 ATCGCAACGCGAACTTTGACT
**
2930242 ATCGCAA--CGAA-TTTGAAAA
1 ATCGCAACGCGAACTTTG-ACT
* *
2930261 ATCGCAACGTGAACTTGGACT
1 ATCGCAACGCGAACTTTGACT
2930282 ATCGCAACG
1 ATCGCAACG
2930291 AATTTGGACT
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
18 4 0.10
19 12 0.31
21 20 0.51
22 3 0.08
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.21
Consensus pattern (21 bp):
ATCGCAACGCGAACTTTGACT
Found at i:2930275 original size:40 final size:40
Alignment explanation
Indices: 2930218--2930296 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 40
2930208 GCGATTTTTC
*
2930218 AAAATCGCAACGCGAACTTTGACTATCGCAACGAATTTGA
1 AAAATCGCAACGCGAACTTGGACTATCGCAACGAATTTGA
*
2930258 AAAATCGCAACGTGAACTTGGACTATCGCAACGAATTTG
1 AAAATCGCAACGCGAACTTGGACTATCGCAACGAATTTG
2930297 GACTAACGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.23
Consensus pattern (40 bp):
AAAATCGCAACGCGAACTTGGACTATCGCAACGAATTTGA
Found at i:2930299 original size:19 final size:19
Alignment explanation
Indices: 2930238--2930301 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
2930228 CGCGAACTTT
2930238 GACTATCGCAACGAATTTG
1 GACTATCGCAACGAATTTG
* ** *
2930257 AAAAATCGCAACGTGAACTTG
1 GACTATCGCAAC--GAATTTG
2930278 GACTATCGCAACGAATTTG
1 GACTATCGCAACGAATTTG
2930297 GACTA
1 GACTA
2930302 ACGTAAATTT
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
19 20 0.57
21 15 0.43
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.23
Consensus pattern (19 bp):
GACTATCGCAACGAATTTG
Found at i:2930498 original size:19 final size:19
Alignment explanation
Indices: 2930466--2930532 Score: 116
Period size: 19 Copynumber: 3.5 Consensus size: 19
2930456 GGAAACTGAT
2930466 TTGCGATATTAGAGATCGCG
1 TTGCGAT-TTAGAGATCGCG
2930486 TTGCGATTTAGAGATCGCG
1 TTGCGATTTAGAGATCGCG
*
2930505 TTGCGATTTAGAGATCGCA
1 TTGCGATTTAGAGATCGCG
2930524 TTGCGATTT
1 TTGCGATTT
2930533 TGTTGGTCAT
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
19 39 0.85
20 7 0.15
ACGTcount: A:0.22, C:0.15, G:0.28, T:0.34
Consensus pattern (19 bp):
TTGCGATTTAGAGATCGCG
Found at i:2937463 original size:17 final size:17
Alignment explanation
Indices: 2937430--2937463 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2937420 AATGAATAAT
*
2937430 TTTAAAATATTAGAATA
1 TTTAAAATATTAAAATA
*
2937447 TTTAAAATTTTAAAATA
1 TTTAAAATATTAAAATA
2937464 GATAAAAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
TTTAAAATATTAAAATA
Found at i:2941554 original size:21 final size:20
Alignment explanation
Indices: 2941468--2941625 Score: 86
Period size: 20 Copynumber: 7.8 Consensus size: 20
2941458 AAATAACCAA
**
2941468 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
2941487 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
** *
2941507 CAAAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
2941527 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
2941548 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* * **
2941569 CAAATTCACATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
2941589 CAAGAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
2941610 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
2941626 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 44 0.42
21 44 0.42
ACGTcount: A:0.40, C:0.25, G:0.16, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:2941654 original size:20 final size:20
Alignment explanation
Indices: 2941593--2941821 Score: 212
Period size: 20 Copynumber: 11.4 Consensus size: 20
2941583 GATTTTCAAG
* ** *
2941593 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
2941613 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
* *
2941633 AATCGTAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
2941653 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2941673 AATAGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2941693 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2941713 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2941733 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
2941753 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
2941773 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
2941793 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
2941813 AATCACAAC
1 AATCGCAAC
2941822 ACTGAAATTT
Statistics
Matches: 171, Mismatches: 32, Indels: 12
0.80 0.15 0.06
Matches are distributed among these distances:
19 2 0.01
20 167 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:2942553 original size:24 final size:24
Alignment explanation
Indices: 2942514--2942560 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2942504 AAATTTGGTC
2942514 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
2942538 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
2942561 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:2942752 original size:12 final size:12
Alignment explanation
Indices: 2942735--2942759 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2942725 ATATAATCCT
2942735 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2942747 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2942759 G
1 G
2942760 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:2945149 original size:72 final size:72
Alignment explanation
Indices: 2945056--2945289 Score: 295
Period size: 72 Copynumber: 3.3 Consensus size: 72
2945046 GCAACGAGAG
2945056 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
2945121 AAATGAA
66 AAATGAA
* * *
2945128 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
2945193 AAATGAA
66 AAATGAA
* * * * * *
2945200 AATCGCAACGAGAGAATCG-CAATGCGAA-ATGAAAATCGCAATGC-GAAATGAAAATCGCAA--
1 AATCGCAATGCGA-AAT-GAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATG
*
2945260 CG--A-GAG
64 CGAAATGAA
2945266 AATCGCAATGCGGAAATGAAAATC
1 AATCGCAATGC-GAAATGAAAATC
2945290 GCAATGCGAA
Statistics
Matches: 141, Mismatches: 17, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
65 1 0.01
66 17 0.12
67 3 0.02
69 2 0.01
71 16 0.11
72 93 0.66
73 8 0.06
74 1 0.01
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.14
Consensus pattern (72 bp):
AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
AAATGAA
Found at i:2945177 original size:53 final size:52
Alignment explanation
Indices: 2945042--2945311 Score: 415
Period size: 53 Copynumber: 5.1 Consensus size: 52
2945032 CGGAAATTAC
*
2945042 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAA--C--AA-GAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
2945089 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C-G--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
2945147 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
2945200 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
2945252 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
2945305 AATCGCA
1 AATCGCA
2945312 TTGCGATTCT
Statistics
Matches: 207, Mismatches: 3, Indels: 20
0.90 0.01 0.09
Matches are distributed among these distances:
47 8 0.04
49 1 0.00
50 1 0.00
52 66 0.32
53 115 0.56
55 2 0.01
56 1 0.00
57 2 0.01
58 11 0.05
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.13
Consensus pattern (52 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:2945317 original size:72 final size:68
Alignment explanation
Indices: 2945023--2945316 Score: 276
Period size: 72 Copynumber: 4.2 Consensus size: 68
2945013 GCATTTGACT
** * * *
2945023 ATCGCAACACGGAAATTACAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAAC-AAG
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAAG
2945087 AAA
66 AAA
*
2945090 ATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 ATCGCAATGCGGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAA
*
2945155 CG-AGAGA
61 CGAAGAAA
* * * * *
2945162 ATCGCAATGCGGAAATGAAAATCGCAATGCGA-AAT-GAAAAT-CGCAACGAGAGAATCGCAATG
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCG-CAATGCGAAATGA-A-AATCGCAA--
2945224 CGAAATGAAA
61 CG-AA-GAAA
2945234 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAA--CG
2945298 AAATGAAA
63 -AA-GAAA
*
2945306 ATCGCATTGCG
1 ATCGCAATGCG
2945317 ATTCTCTCGT
Statistics
Matches: 189, Mismatches: 19, Indels: 32
0.79 0.08 0.13
Matches are distributed among these distances:
65 7 0.04
66 7 0.04
67 33 0.17
69 4 0.02
70 1 0.01
71 21 0.11
72 108 0.57
73 3 0.02
74 5 0.03
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.14
Consensus pattern (68 bp):
ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAAG
AAA
Found at i:2945331 original size:105 final size:105
Alignment explanation
Indices: 2945042--2945311 Score: 426
Period size: 105 Copynumber: 2.6 Consensus size: 105
2945032 CGGAAATTAC
*
2945042 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCCCAA--C--AA-GAAAATCGCAATGCG
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--C-
*
2945101 GAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
63 G--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
2945147 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAG
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAG
2945212 AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
66 AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
2945252 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCA
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCA
2945312 TTGCGATTCT
Statistics
Matches: 157, Mismatches: 2, Indels: 12
0.92 0.01 0.07
Matches are distributed among these distances:
105 125 0.80
106 16 0.10
108 2 0.01
109 1 0.01
110 2 0.01
111 11 0.07
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.13
Consensus pattern (105 bp):
AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAG
AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:2945351 original size:53 final size:52
Alignment explanation
Indices: 2945288--2945403 Score: 151
Period size: 53 Copynumber: 2.2 Consensus size: 52
2945278 GAAATGAAAA
* *
2945288 TCGCAATGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTACGATTTTCATT
** ** **
2945340 TCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTACGATTTTCATT
1 T-CGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTACGATTTTCATT
2945393 TCGCATTGCGA
1 TCGCATTGCGA
2945404 TTTTCATTTC
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
52 11 0.20
53 44 0.80
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.39
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTACGATTTTCATT
Found at i:2945366 original size:19 final size:19
Alignment explanation
Indices: 2945326--2945413 Score: 114
Period size: 19 Copynumber: 4.8 Consensus size: 19
2945316 GATTCTCTCG
2945326 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
2945346 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2945365 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
*
2945379 TTACGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2945398 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
2945414 AACATAATGC
Statistics
Matches: 59, Mismatches: 4, Indels: 11
0.80 0.05 0.15
Matches are distributed among these distances:
14 5 0.08
16 7 0.12
17 7 0.12
19 25 0.42
20 15 0.25
ACGTcount: A:0.15, C:0.23, G:0.15, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:2945523 original size:14 final size:14
Alignment explanation
Indices: 2945504--2945540 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2945494 CATCAATTAC
2945504 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2945518 ACAAATCATCTTTT
1 ACAAATCAACTTTT
2945532 ACAAATCAA
1 ACAAATCAA
2945541 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2947503 original size:19 final size:19
Alignment explanation
Indices: 2947461--2947619 Score: 175
Period size: 19 Copynumber: 8.6 Consensus size: 19
2947451 TAGTTTACTT
* *
2947461 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
2947481 TCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAATGAAAA
* **
2947500 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
**
2947519 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
2947538 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2947557 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
2947571 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
2947590 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2947609 TCGCAATGCGA
1 TCGCAACGCGA
2947620 TTTTGGTTTC
Statistics
Matches: 120, Mismatches: 14, Indels: 11
0.83 0.10 0.08
Matches are distributed among these distances:
14 8 0.07
16 5 0.04
17 5 0.04
19 90 0.75
20 12 0.10
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:2947595 original size:52 final size:55
Alignment explanation
Indices: 2947461--2947614 Score: 197
Period size: 52 Copynumber: 2.8 Consensus size: 55
2947451 TAGTTTACTT
* * *
2947461 TCGCAACACGAAACTTAAAATCGCAACGCGAAATGAGAATCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAAC-CAAAATCGCAACGCGAAATGAAAATCGCAAC-AG-AACCAAAA
*
2947519 TCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAATCGCAAC-G-A-CAGAA
1 TCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAATCGCAACAGAACCAAAA
* **
2947571 TCGCAATGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAA
1 TCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAATCGCAA
2947615 TGCGATTTTG
Statistics
Matches: 89, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
52 45 0.51
53 1 0.01
55 1 0.01
57 29 0.33
58 13 0.15
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (55 bp):
TCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAATCGCAACAGAACCAAAA
Found at i:2947650 original size:14 final size:14
Alignment explanation
Indices: 2947631--2947689 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
2947621 TTTGGTTTCG
2947631 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
2947645 CGTTGCGATTTTGGTTT
1 CGTTGCGATTTT-G--T
*
2947662 CGCGTTGCGATTCTGT
1 --CGTTGCGATTTTGT
2947678 CGTTGCGATTTT
1 CGTTGCGATTTT
2947690 CATTTCGCGT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 23 0.61
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.29
ACGTcount: A:0.07, C:0.17, G:0.29, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:2947657 original size:33 final size:33
Alignment explanation
Indices: 2947615--2947738 Score: 185
Period size: 33 Copynumber: 3.7 Consensus size: 33
2947605 AAAATCGCAA
*
2947615 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
2947648 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
** *
2947681 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
* *
2947714 TGCGATTTTAAGTTTCGTGTTGCGA
1 TGCGATTTT-GGTTTCGCGTTGCGA
2947739 AAGTAAACTA
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
33 71 0.86
34 12 0.14
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:2947669 original size:19 final size:18
Alignment explanation
Indices: 2947615--2947706 Score: 83
Period size: 19 Copynumber: 5.4 Consensus size: 18
2947605 AAAATCGCAA
2947615 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
2947634 TGCGATTTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
2947648 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
2947667 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
2947681 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
2947700 TGCGATT
1 TGCGATT
2947707 CTCTCGTTGC
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
14 23 0.38
15 1 0.02
16 2 0.03
17 2 0.03
18 2 0.03
19 30 0.50
ACGTcount: A:0.08, C:0.17, G:0.28, T:0.47
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Done.