Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 198 of 378
Found at i:58368177 original size:49 final size:48
Alignment explanation
Indices: 58368032--58368290 Score: 380
Period size: 49 Copynumber: 5.4 Consensus size: 48
58368022 TACATATATG
* * * * *
58368032 TGTGATAAGGCCGAATGGCCAATGCGATGAATGTGAAAGTGCA-TATG
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATTATA
* *
58368079 TGTGATAAGG-CTGTATGGCCAATGTGATGAATGTGAAAGTGTA-TATA
1 TGTGATAAGGCCT-AATGGCCGATGTGATGAATGTGAAAGTGTATTATA
58368126 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATGTATA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT-TATA
*
58368175 TGTGATAAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT-TATA
*
58368224 TGTGATAAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATATATA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT-TATA
58368273 TGTGATAAGGCCTAATGG
1 TGTGATAAGGCCTAATGG
58368291 TTAATGTAAA
Statistics
Matches: 199, Mismatches: 9, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
46 1 0.01
47 78 0.39
48 2 0.01
49 118 0.59
ACGTcount: A:0.31, C:0.09, G:0.31, T:0.29
Consensus pattern (48 bp):
TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATTATA
Found at i:58373786 original size:25 final size:25
Alignment explanation
Indices: 58373728--58373778 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
58373718 TTTGGATAAA
58373728 TGAAACCAACTTATCCAAAAAATCC
1 TGAAACCAACTTATCCAAAAAATCC
58373753 TGAAACCAACTTATCCAAAAAATCC
1 TGAAACCAACTTATCCAAAAAATCC
58373778 T
1 T
58373779 CGGACCAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.47, C:0.27, G:0.04, T:0.22
Consensus pattern (25 bp):
TGAAACCAACTTATCCAAAAAATCC
Found at i:58375965 original size:27 final size:27
Alignment explanation
Indices: 58375934--58375988 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
58375924 AGTAGCAGAA
*
58375934 CAAACATTATACGCAATCTCTCAGTTT
1 CAAACATTATACGCAATCACTCAGTTT
* *
58375961 CAAACATTATATGCAATCACTCGGTTT
1 CAAACATTATACGCAATCACTCAGTTT
58375988 C
1 C
58375989 TCTCATAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.33, C:0.25, G:0.09, T:0.33
Consensus pattern (27 bp):
CAAACATTATACGCAATCACTCAGTTT
Found at i:58377821 original size:16 final size:18
Alignment explanation
Indices: 58377797--58377833 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
58377787 AATTTTATCA
*
58377797 TTATTAATT-TAAAAT-T
1 TTATAAATTATAAAATGT
58377813 TTATAAATTATAAAATGT
1 TTATAAATTATAAAATGT
58377831 TTA
1 TTA
58377834 AATGAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 8 0.44
17 6 0.33
18 4 0.22
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
TTATAAATTATAAAATGT
Found at i:58387098 original size:8 final size:8
Alignment explanation
Indices: 58387085--58387119 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
58387075 TCAGGAGTGC
58387085 AAGGATGG
1 AAGGATGG
58387093 AAGGATGG
1 AAGGATGG
58387101 AAGGATGG
1 AAGGATGG
*
58387109 AAGGATAG
1 AAGGATGG
58387117 AAG
1 AAG
58387120 AGGAAGGTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.43, C:0.00, G:0.46, T:0.11
Consensus pattern (8 bp):
AAGGATGG
Found at i:58393860 original size:19 final size:19
Alignment explanation
Indices: 58393828--58393879 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
58393818 AAGATGAGTT
*
58393828 ATTAAATAAGATGAACTCA
1 ATTAACTAAGATGAACTCA
*
58393847 ATTAACTAAAATGAACTCA
1 ATTAACTAAGATGAACTCA
58393866 ATTAACTAAGATGA
1 ATTAACTAAGATGA
58393880 GTAATTTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.52, C:0.12, G:0.10, T:0.27
Consensus pattern (19 bp):
ATTAACTAAGATGAACTCA
Found at i:58396118 original size:26 final size:25
Alignment explanation
Indices: 58396067--58396120 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
58396057 AAACTCAATC
*
58396067 TCATTTTTCTTTCTCTCATTCTTTT
1 TCATTTTTCTTTCTCGCATTCTTTT
*
58396092 TCATTTTCTTTTTCTCGCATCTCTTTT
1 TCATTTT-TCTTTCTCGCAT-TCTTTT
58396119 TC
1 TC
58396121 TCTTCTTTCG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.28
26 10 0.40
27 8 0.32
ACGTcount: A:0.07, C:0.26, G:0.02, T:0.65
Consensus pattern (25 bp):
TCATTTTTCTTTCTCGCATTCTTTT
Found at i:58396126 original size:26 final size:26
Alignment explanation
Indices: 58396076--58396128 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
58396066 CTCATTTTTC
* *
58396076 TTTCTCTCATTCTTTTTCATTTTCTT
1 TTTCTCGCATTCTTTTTCATCTTCTT
58396102 TTTCTCGCATCTCTTTTTC-TCTTCTT
1 TTTCTCGCAT-TCTTTTTCATCTTCTT
58396128 T
1 T
58396129 CGATTTCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 16 0.67
27 8 0.33
ACGTcount: A:0.06, C:0.26, G:0.02, T:0.66
Consensus pattern (26 bp):
TTTCTCGCATTCTTTTTCATCTTCTT
Found at i:58398475 original size:17 final size:18
Alignment explanation
Indices: 58398445--58398478 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
58398435 AGCAACTCAT
58398445 TTATTAATCTAAGATGAG
1 TTATTAATCTAAGATGAG
58398463 TTATTAA-CTAAGATGA
1 TTATTAATCTAAGATGA
58398479 ACTCAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.41, C:0.06, G:0.15, T:0.38
Consensus pattern (18 bp):
TTATTAATCTAAGATGAG
Found at i:58398489 original size:19 final size:19
Alignment explanation
Indices: 58398465--58398517 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
58398455 AAGATGAGTT
58398465 ATTAACTAAGATGAACTCA
1 ATTAACTAAGATGAACTCA
58398484 ATTAACTCAA-ATGAACTCA
1 ATTAACT-AAGATGAACTCA
58398503 ATTAACTAAGATGAA
1 ATTAACTAAGATGAA
58398518 TAATTTATTC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
18 2 0.06
19 28 0.88
20 2 0.06
ACGTcount: A:0.49, C:0.15, G:0.09, T:0.26
Consensus pattern (19 bp):
ATTAACTAAGATGAACTCA
Found at i:58399618 original size:12 final size:12
Alignment explanation
Indices: 58399601--58399627 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
58399591 AGTCATGAGC
58399601 CCTTAACTGCAA
1 CCTTAACTGCAA
58399613 CCTTAACTGCAA
1 CCTTAACTGCAA
58399625 CCT
1 CCT
58399628 CAGTCATGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.37, G:0.07, T:0.26
Consensus pattern (12 bp):
CCTTAACTGCAA
Found at i:58403207 original size:30 final size:30
Alignment explanation
Indices: 58403172--58403231 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
58403162 TATTTTATTA
**
58403172 TTAATTTTGTTATTATTTTAAAGGCATTTG
1 TTAATTTAATTATTATTTTAAAGGCATTTG
* *
58403202 TTAATTTAATTATTATTTTAGAGGTATTTG
1 TTAATTTAATTATTATTTTAAAGGCATTTG
58403232 CTTGTTAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.28, C:0.02, G:0.13, T:0.57
Consensus pattern (30 bp):
TTAATTTAATTATTATTTTAAAGGCATTTG
Found at i:58403348 original size:15 final size:15
Alignment explanation
Indices: 58403330--58403380 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 15
58403320 TTTATTTTAG
58403330 TATTTTTTAAATATT
1 TATTTTTTAAATATT
*
58403345 TATTTTTAAAAAATATT
1 TATTTTT--TAAATATT
*
58403362 TA-TTTTTAAA-ACT
1 TATTTTTTAAATATT
58403375 TATTTT
1 TATTTT
58403381 AAAAAGTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
13 4 0.13
14 6 0.20
15 7 0.23
16 4 0.13
17 9 0.30
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (15 bp):
TATTTTTTAAATATT
Found at i:58403379 original size:17 final size:17
Alignment explanation
Indices: 58403338--58403372 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
58403328 AGTATTTTTT
58403338 AAATATTTATTTTTAAA
1 AAATATTTATTTTTAAA
58403355 AAATATTTATTTTTAAA
1 AAATATTTATTTTTAAA
58403372 A
1 A
58403373 CTTATTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
AAATATTTATTTTTAAA
Found at i:58405762 original size:8 final size:9
Alignment explanation
Indices: 58405739--58405790 Score: 50
Period size: 10 Copynumber: 5.2 Consensus size: 9
58405729 TTCATGTATC
58405739 ATTATATTAA
1 ATTAT-TTAA
58405749 ATTATTTAAA
1 ATTATTT-AA
*
58405759 TATTATTTATT
1 -ATTATTTA-A
58405770 ATTATATTAA
1 ATTAT-TTAA
58405780 ATTATTTAA
1 ATTATTTAA
58405789 AT
1 AT
58405791 CTTATTTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
9 8 0.22
10 18 0.50
11 10 0.28
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
ATTATTTAA
Found at i:58405765 original size:11 final size:11
Alignment explanation
Indices: 58405749--58405798 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
58405739 ATTATATTAA
58405749 ATTATTTAAAT
1 ATTATTTAAAT
*
58405760 ATTATTT-ATT
1 ATTATTTAAAT
58405770 ATTATATT-AA-
1 ATTAT-TTAAAT
58405780 ATTATTTAAAT
1 ATTATTTAAAT
*
58405791 CTTATTTA
1 ATTATTTA
58405799 TTATTTTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
9 2 0.06
10 14 0.42
11 17 0.52
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (11 bp):
ATTATTTAAAT
Found at i:58405774 original size:31 final size:31
Alignment explanation
Indices: 58405739--58405819 Score: 128
Period size: 31 Copynumber: 2.6 Consensus size: 31
58405729 TTCATGTATC
58405739 ATTATATTAAATTATTTAAATATTATTTATT
1 ATTATATTAAATTATTTAAATATTATTTATT
*
58405770 ATTATATTAAATTATTTAAATCTTATTTATT
1 ATTATATTAAATTATTTAAATATTATTTATT
* *
58405801 ATTTTATTTAATT-TTTAAA
1 ATTATATTAAATTATTTAAA
58405820 ATAGTTTATG
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
30 6 0.13
31 41 0.87
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (31 bp):
ATTATATTAAATTATTTAAATATTATTTATT
Found at i:58409211 original size:20 final size:20
Alignment explanation
Indices: 58409174--58409211 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
58409164 TTAATAAGTA
*
58409174 AAATTTCTTTTCTATTTTTC
1 AAATTTCTTTGCTATTTTTC
58409194 AAATTTCTTATGCT-TTTT
1 AAATTTCTT-TGCTATTTT
58409212 ATCTTTAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.21, C:0.13, G:0.03, T:0.63
Consensus pattern (20 bp):
AAATTTCTTTGCTATTTTTC
Found at i:58409325 original size:43 final size:43
Alignment explanation
Indices: 58409277--58409361 Score: 143
Period size: 43 Copynumber: 2.0 Consensus size: 43
58409267 ATTATATTGC
* * *
58409277 TATTACCATAATATAAATGACCTAATTTGATAAGTGCTAAAAT
1 TATTACAATAATATAAATAACCTAAATTGATAAGTGCTAAAAT
58409320 TATTACAATAATATAAATAACCTAAATTGATAAGTGCTAAAA
1 TATTACAATAATATAAATAACCTAAATTGATAAGTGCTAAAA
58409362 GAAACATGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.48, C:0.11, G:0.08, T:0.33
Consensus pattern (43 bp):
TATTACAATAATATAAATAACCTAAATTGATAAGTGCTAAAAT
Found at i:58411792 original size:39 final size:39
Alignment explanation
Indices: 58411738--58411817 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
58411728 TCCGAAATGT
58411738 TTACTCTTTGGTTTTAATATAGAGCACAAGCAAGTCAAC
1 TTACTCTTTGGTTTTAATATAGAGCACAAGCAAGTCAAC
58411777 TTACTCTTTGGTTTTAATATAGAGCACAAGCAAGTCAAC
1 TTACTCTTTGGTTTTAATATAGAGCACAAGCAAGTCAAC
58411816 TT
1 TT
58411818 TATGGGTAAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (39 bp):
TTACTCTTTGGTTTTAATATAGAGCACAAGCAAGTCAAC
Found at i:58415320 original size:23 final size:23
Alignment explanation
Indices: 58415294--58415350 Score: 87
Period size: 26 Copynumber: 2.3 Consensus size: 23
58415284 ACATGAAATT
58415294 CCCATTATGGAACATTTACCTAA
1 CCCATTATGGAACATTTACCTAA
58415317 CCCATTATCATGGAACATTTACCTAA
1 CCCA-T-T-ATGGAACATTTACCTAA
58415343 CCCATTAT
1 CCCATTAT
58415351 CAATTTGTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
23 6 0.19
24 2 0.06
25 2 0.06
26 21 0.68
ACGTcount: A:0.33, C:0.28, G:0.07, T:0.32
Consensus pattern (23 bp):
CCCATTATGGAACATTTACCTAA
Found at i:58415333 original size:26 final size:26
Alignment explanation
Indices: 58415300--58415352 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
58415290 AATTCCCATT
58415300 ATGGAACATTTACCTAACCCATTATC
1 ATGGAACATTTACCTAACCCATTATC
58415326 ATGGAACATTTACCTAACCCATTATC
1 ATGGAACATTTACCTAACCCATTATC
58415352 A
1 A
58415353 ATTTGTATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.36, C:0.26, G:0.08, T:0.30
Consensus pattern (26 bp):
ATGGAACATTTACCTAACCCATTATC
Found at i:58422280 original size:26 final size:26
Alignment explanation
Indices: 58422250--58422357 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
58422240 TGAAATTCCC
58422250 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
58422276 ATCATGGAACATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
58422302 ATCATGAAATATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
58422328 ATTATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
58422354 ATCA
1 ATCA
58422358 ATTTGTATCA
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 74 1.00
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:58431811 original size:30 final size:30
Alignment explanation
Indices: 58431777--58431833 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
58431767 ATTTAATACG
58431777 AACTTTGGAAAAATTACACTTTTGCCCTTA
1 AACTTTGGAAAAATTACACTTTTGCCCTTA
* * *
58431807 AACTTTTGCATAATTACACTTTTGCCC
1 AACTTTGGAAAAATTACACTTTTGCCC
58431834 CTAGGCTCGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.30, C:0.23, G:0.09, T:0.39
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCTTA
Found at i:58436191 original size:21 final size:21
Alignment explanation
Indices: 58436107--58436214 Score: 83
Period size: 21 Copynumber: 5.1 Consensus size: 21
58436097 CCTGATCAAT
*
58436107 ATACGACACAT-AAGTGCCTA
1 ATACGACACATAAAGTGCCTG
* * ** * *
58436127 AAACGATACACGAGGTGCCTA
1 ATACGACACATAAAGTGCCTG
* * *
58436148 ATACGACACACAAGGTGCTTG
1 ATACGACACATAAAGTGCCTG
58436169 ATACGACACATAAAGTGCCTG
1 ATACGACACATAAAGTGCCTG
* *
58436190 ATATATGACACATAAAGTTCCTG
1 --ATACGACACATAAAGTGCCTG
58436213 AT
1 AT
58436215 TGGCAAAGCC
Statistics
Matches: 71, Mismatches: 14, Indels: 5
0.79 0.16 0.06
Matches are distributed among these distances:
20 8 0.11
21 44 0.62
23 19 0.27
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (21 bp):
ATACGACACATAAAGTGCCTG
Found at i:58445523 original size:12 final size:12
Alignment explanation
Indices: 58445506--58445542 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
58445496 TTCAAAAATT
58445506 TAAATCATATCA
1 TAAATCATATCA
58445518 TAAATCATATCA
1 TAAATCATATCA
58445530 TAAATCAT-TCA
1 TAAATCATATCA
58445541 TA
1 TA
58445543 CACATGCATA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 5 0.20
12 20 0.80
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.35
Consensus pattern (12 bp):
TAAATCATATCA
Found at i:58445823 original size:67 final size:66
Alignment explanation
Indices: 58445710--58445909 Score: 294
Period size: 67 Copynumber: 3.0 Consensus size: 66
58445700 ACGGCTGAGA
*
58445710 CACACACCAGTGTAAGCTTCGAACTAGGGCACACGACCGTGCCCCAGCTTGTGTCCTTACCCGTG
1 CACACACCA-TGTAAGCTTCGAACTAGGGCACACGACCGTGTCCCAGCTTGTGTCCTTACCCGTG
58445775 TG
65 TG
* *
58445777 CACACACTCATGTAAGCTTCGAACTAGGGCACACGACCGTATCCCAGCTTGTGTCCTCACCCGTG
1 CACACAC-CATGTAAGCTTCGAACTAGGGCACACGACCGTGTCCCAGCTTGTGTCCTTACCCGTG
58445842 TG
65 TG
* * * * *
58445844 TACACACCCATGTAAGCTTCAAACTA-GGCACACAACCGTGTCCTAGCTTGTATCCTTACCCGTG
1 CACACA-CCATGTAAGCTTCGAACTAGGGCACACGACCGTGTCCCAGCTTGTGTCCTTACCCGTG
58445908 TG
65 TG
58445910 ACTTTTTGAG
Statistics
Matches: 121, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
66 35 0.29
67 83 0.69
68 3 0.02
ACGTcount: A:0.23, C:0.34, G:0.20, T:0.23
Consensus pattern (66 bp):
CACACACCATGTAAGCTTCGAACTAGGGCACACGACCGTGTCCCAGCTTGTGTCCTTACCCGTGT
G
Found at i:58450875 original size:28 final size:28
Alignment explanation
Indices: 58450843--58450941 Score: 112
Period size: 28 Copynumber: 3.5 Consensus size: 28
58450833 GCAATAAGCC
*
58450843 CGCACACTTAGTGCTTAATAGTCGAACT
1 CGCACACTTAGTGCTTAATAATCGAACT
*
58450871 CGCACACTTAGTGC-TATATAATCAAACT
1 CGCACACTTAGTGCTTA-ATAATCGAACT
* * *
58450899 TGCACACTTAGTGCTGT-ATAATTTGAACC
1 CGCACACTTAGTGCT-TAATAA-TCGAACT
58450928 CGCACACTTAGTGC
1 CGCACACTTAGTGC
58450942 CAATTTGTGA
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
27 2 0.03
28 40 0.67
29 17 0.28
30 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTTAATAATCGAACT
Found at i:58454727 original size:40 final size:40
Alignment explanation
Indices: 58454672--58454809 Score: 140
Period size: 40 Copynumber: 3.5 Consensus size: 40
58454662 TGGATGATAA
* *
58454672 CCGGGCTAAGTCCCGAAGGCATTTGCACTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTCGCACGAGTGACTA-TAT
** *
58454712 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTCGCACGAGTGACTATAT
* *
58454752 TCGGGCTATGTCCCGAAGGCATTCG-AGCGAGT-AGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTCGCA-CGAGTGA-CTATAT
* *
58454792 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
58454810 TACTTGGCTT
Statistics
Matches: 83, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
39 15 0.18
40 68 0.82
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTCGCACGAGTGACTATAT
Found at i:58461544 original size:40 final size:40
Alignment explanation
Indices: 58461486--58461687 Score: 273
Period size: 40 Copynumber: 5.0 Consensus size: 40
58461476 TGGATGATAA
* * * *
58461486 CCGGGCTAAGTCCTGAAGGCATTTGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTCGCGCGAGTTACTA-TAT
***
58461526 CCGGGCTAAGTCCCGAAGGCATTCGTTTGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTCGCGCGAGTTACTATAT
*
58461566 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTCGCGCGAGTTACTATAT
*
58461606 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTCGCGCGAGTTACTATAT
* *
58461646 CCGGGCTATGTCCCGAAGGCATTCGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTCGCGCGAGTTA-CTATAT
58461686 CC
1 CC
58461688 AGTTAAATCC
Statistics
Matches: 149, Mismatches: 11, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
39 3 0.02
40 146 0.98
ACGTcount: A:0.22, C:0.25, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTCGCGCGAGTTACTATAT
Found at i:58470237 original size:3 final size:3
Alignment explanation
Indices: 58470229--58470272 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
58470219 TAATGTATAT
58470229 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
58470273 GATGAAAATG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:58471089 original size:25 final size:25
Alignment explanation
Indices: 58471041--58471089 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
58471031 CACAATTGAA
* * *
58471041 ATGAAATGGATTGATTTTGTATATT
1 ATGAAATAGATTGATTATGAATATT
*
58471066 ATGAAATATATTGATTATGAATAT
1 ATGAAATAGATTGATTATGAATAT
58471090 ATGTGTATTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (25 bp):
ATGAAATAGATTGATTATGAATATT
Found at i:58476366 original size:13 final size:13
Alignment explanation
Indices: 58476350--58476378 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
58476340 TAGGTATATG
58476350 TGGTAAAGCCGAA
1 TGGTAAAGCCGAA
58476363 TGGTAAAGCCGAA
1 TGGTAAAGCCGAA
58476376 TGG
1 TGG
58476379 CTAATGTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.34, C:0.14, G:0.34, T:0.17
Consensus pattern (13 bp):
TGGTAAAGCCGAA
Found at i:58476376 original size:61 final size:61
Alignment explanation
Indices: 58476302--58476426 Score: 241
Period size: 61 Copynumber: 2.0 Consensus size: 61
58476292 TAGGTATATG
58476302 TGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATAGGTATATGTGGTAAAGCCGAA
1 TGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATAGGTATATGTGGTAAAGCCGAA
*
58476363 TGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAA
1 TGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATAGGTATATGTGGTAAAGCCGAA
58476424 TGG
1 TGG
58476427 CTAATGTGAA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 63 1.00
ACGTcount: A:0.35, C:0.08, G:0.30, T:0.27
Consensus pattern (61 bp):
TGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATAGGTATATGTGGTAAAGCCGAA
Found at i:58476418 original size:48 final size:48
Alignment explanation
Indices: 58476363--58476460 Score: 196
Period size: 48 Copynumber: 2.0 Consensus size: 48
58476353 TAAAGCCGAA
58476363 TGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATG
1 TGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATG
58476411 TGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATG
1 TGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATG
58476459 TG
1 TG
58476461 AAATATGTAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.35, C:0.06, G:0.28, T:0.32
Consensus pattern (48 bp):
TGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATG
Found at i:58476459 original size:26 final size:26
Alignment explanation
Indices: 58476430--58476486 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
58476420 CGAATGGCTA
58476430 ATGTGAAATATGTATGAGATATGTAT
1 ATGTGAAATATGTATGAGATATGTAT
*
58476456 ATGTGAAATATGTATGCGATATGTAT
1 ATGTGAAATATGTATGAGATATGTAT
58476482 ATGTG
1 ATGTG
58476487 GTAAAGCCGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.35, C:0.02, G:0.25, T:0.39
Consensus pattern (26 bp):
ATGTGAAATATGTATGAGATATGTAT
Found at i:58476511 original size:48 final size:48
Alignment explanation
Indices: 58476456--58476715 Score: 439
Period size: 48 Copynumber: 5.4 Consensus size: 48
58476446 AGATATGTAT
*
58476456 ATGTGAAATATGTATGCGATATGTATATGTGGTAAAGCCGAATGGCTA
1 ATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
*
58476504 ATGTGAAATATGTATGGGATATGTATATGTGGTAAAGCCGAATGGCTA
1 ATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
* *
58476552 ATGTGAAATATGTATGGGATATGTATATGTGGTAAAGCCAAATGGCTA
1 ATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
58476600 ATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
1 ATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
* * *
58476648 ATGTGAAATATGTATGAGATACGTATATGTGGTAAAGTCGAAGGGCTA
1 ATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
* *
58476696 GTGTGAAATATGTAGGAGAT
1 ATGTGAAATATGTATGAGAT
58476716 GTGTGTATAT
Statistics
Matches: 203, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 203 1.00
ACGTcount: A:0.35, C:0.06, G:0.28, T:0.31
Consensus pattern (48 bp):
ATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
Found at i:58476580 original size:122 final size:122
Alignment explanation
Indices: 58476363--58476582 Score: 422
Period size: 122 Copynumber: 1.8 Consensus size: 122
58476353 TAAAGCCGAA
58476363 TGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGC
1 TGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGC
58476428 TAATGTGAAATATGTATGAGATATGTATATGTGAAATATGTATGCGATATGTATATG
66 TAATGTGAAATATGTATGAGATATGTATATGTGAAATATGTATGCGATATGTATATG
*
58476485 TGGTAAAGCCGAATGGCTAATGTGAAATATGTATGGGATATGTATATGTGGTAAAGCCGAATGGC
1 TGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGC
*
58476550 TAATGTGAAATATGTATGGGATATGTATATGTG
66 TAATGTGAAATATGTATGAGATATGTATATGTG
58476583 GTAAAGCCAA
Statistics
Matches: 96, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
122 96 1.00
ACGTcount: A:0.34, C:0.06, G:0.28, T:0.32
Consensus pattern (122 bp):
TGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGC
TAATGTGAAATATGTATGAGATATGTATATGTGAAATATGTATGCGATATGTATATG
Found at i:58476964 original size:37 final size:37
Alignment explanation
Indices: 58476856--58476964 Score: 173
Period size: 37 Copynumber: 2.9 Consensus size: 37
58476846 GGAAATATAT
*
58476856 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
*
58476893 TCCGGGTAAGACCCGATGACTACATGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* * *
58476930 TCCGGTTAAGACCCGATAACTTCGTGTGGAGATTT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTT
58476965 CATCTGAGCT
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 66 1.00
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.28
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
Found at i:58490722 original size:46 final size:46
Alignment explanation
Indices: 58490670--58490845 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
58490660 TGGTTGAGCA
58490670 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
58490716 TTCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
58490761 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
58490809 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
58490846 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 62 0.57
47 28 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:58490826 original size:93 final size:93
Alignment explanation
Indices: 58490667--58490838 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
58490657 GGATGGTTGA
* **
58490667 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTTCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
58490732 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
58490760 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
58490825 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
58490839 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:58498271 original size:46 final size:46
Alignment explanation
Indices: 58498221--58498396 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
58498211 TGGTTGAGCA
58498221 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
58498267 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
58498312 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
58498360 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
58498397 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:58498377 original size:93 final size:93
Alignment explanation
Indices: 58498218--58498389 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
58498208 GGATGGTTGA
* *
58498218 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
58498283 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
58498311 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
58498376 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
58498390 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:58505066 original size:46 final size:46
Alignment explanation
Indices: 58505016--58505191 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
58505006 TGGTTGAGCA
58505016 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
58505062 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
58505107 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
58505155 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
58505192 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:58505172 original size:93 final size:93
Alignment explanation
Indices: 58505013--58505184 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
58505003 GGATGGTTGA
* *
58505013 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
58505078 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
58505106 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
58505171 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
58505185 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:58512607 original size:46 final size:46
Alignment explanation
Indices: 58512557--58512732 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
58512547 TGGTTGAGCA
58512557 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
58512603 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
58512648 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
58512696 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
58512733 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:58512713 original size:93 final size:93
Alignment explanation
Indices: 58512554--58512725 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
58512544 GGATGGTTGA
* *
58512554 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
58512619 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
58512647 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
58512712 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
58512726 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:58518161 original size:49 final size:47
Alignment explanation
Indices: 58518053--58518315 Score: 182
Period size: 49 Copynumber: 5.5 Consensus size: 47
58518043 ATACCCGACA
* * * * *
58518053 CCATGTCCTAGACATGGTCTTACACTGGCT-ATTATGTCAAAG-TCGATG
1 CCATGTCCCAGACA-GGTCTTACACTGACTCA-TATATCGAGGCT-GATG
*
58518101 CCATGTCCCAGACAGGTCTTACACTGACTTTCATATATCGAGGCTGATT
1 CCATGTCCCAGACAGGTCTTACACTGAC--TCATATATCGAGGCTGATG
* * * * * *
58518150 CCATGTCCCAGACAGGTGTTACACTGGCTCTCATCTATCAATG-TCCATG
1 CCATGTCCCAGACAGGTCTTACACT-G-ACTCATATATCGAGGCT-GATG
* * * * * *
58518199 CCATGTCCCAGATAGCTCTTACACTGACACACA-A-C-AAGCTGACG
1 CCATGTCCCAGACAGGTCTTACACTGACTCATATATCGAGGCTGATG
* *
58518243 CCATGTCCCAGACAGGTCTTACACT-AGCTCGTATATCTTGAGGCCGATG
1 CCATGTCCCAGACAGGTCTTACACTGA-CTCATATATC--GAGGCTGATG
*
58518292 -CATGTCCCAGACATGTCTTACACT
1 CCATGTCCCAGACAGGTCTTACACT
58518316 AGCTTTCGTC
Statistics
Matches: 169, Mismatches: 32, Indels: 28
0.74 0.14 0.12
Matches are distributed among these distances:
43 1 0.01
44 30 0.18
45 3 0.02
46 2 0.01
47 16 0.09
48 38 0.22
49 75 0.44
50 3 0.02
51 1 0.01
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (47 bp):
CCATGTCCCAGACAGGTCTTACACTGACTCATATATCGAGGCTGATG
Found at i:58518259 original size:93 final size:95
Alignment explanation
Indices: 58518053--58518315 Score: 250
Period size: 93 Copynumber: 2.8 Consensus size: 95
58518043 ATACCCGACA
* * * * *
58518053 CCATGTCCTAGACATGGTCTTACACTGGCTATTATGTCAAAGTCGATGCCATGTCCCAGACAGGT
1 CCATGTCCCAGACA-GGTCTTACACTGGCTCTTATATCAAAGTCCATGCCATGTCCCAGACAGCT
* * * **
58518118 CTTACACTGACTTTCATATATCGAGGCTGATT
65 CTTACACTGAC-TACACATATCGAAGCTGACG
* * * *
58518150 CCATGTCCCAGACAGGTGTTACACTGGCTCTCATCTATCAATGTCCATGCCATGTCCCAGATAGC
1 CCATGTCCCAGACAGGTCTTACACTGGCTCT--TATATCAAAGTCCATGCCATGTCCCAGACAGC
58518215 TCTTACACTGAC-ACACA-A-C-AAGCTGACG
64 TCTTACACTGACTACACATATCGAAGCTGACG
* * ** *
58518243 CCATGTCCCAGACAGGTCTTACACTAGCTCGTATATCTTGAGGCCGATG-CATGTCCCAGACATG
1 CCATGTCCCAGACAGGTCTTACACTGGCTCTTATATC-AAAGTCC-ATGCCATGTCCCAGACA-G
58518307 -TCTTACACT
63 CTCTTACACT
58518316 AGCTTTCGTC
Statistics
Matches: 138, Mismatches: 23, Indels: 15
0.78 0.13 0.09
Matches are distributed among these distances:
91 5 0.04
92 24 0.17
93 38 0.28
94 1 0.01
95 1 0.01
96 18 0.13
97 13 0.09
98 38 0.28
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (95 bp):
CCATGTCCCAGACAGGTCTTACACTGGCTCTTATATCAAAGTCCATGCCATGTCCCAGACAGCTC
TTACACTGACTACACATATCGAAGCTGACG
Found at i:58518300 original size:48 final size:46
Alignment explanation
Indices: 58518244--58518361 Score: 148
Period size: 46 Copynumber: 2.5 Consensus size: 46
58518234 AAGCTGACGC
* ** *
58518244 CATGTCCCAGACAGGTCTTACACTAGCTCGTAT-ATCTTGAGGCCGATG
1 CATGTCCCAGACATGTCTTACACTAGCT--T-TCATCTCAAGACCGATG
* *
58518292 CATGTCCCAGACATGTCTTACACTAGCTTTCGTCTCAATACCGATG
1 CATGTCCCAGACATGTCTTACACTAGCTTTCATCTCAAGACCGATG
58518338 CATGTCCCAGACATGTCTTACACT
1 CATGTCCCAGACATGTCTTACACT
58518362 GGCACACATA
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
45 1 0.02
46 35 0.56
48 27 0.43
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.29
Consensus pattern (46 bp):
CATGTCCCAGACATGTCTTACACTAGCTTTCATCTCAAGACCGATG
Found at i:58527181 original size:40 final size:40
Alignment explanation
Indices: 58527088--58527304 Score: 305
Period size: 40 Copynumber: 5.5 Consensus size: 40
58527078 AAGCCAAGTA
* * *
58527088 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTC-AATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* * *
58527126 CCTTCGGGACATAGCCCGGATATCGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
58527166 CCTTCGAGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
58527206 CCTTTGGGACTTAGCCCGGATATAGTAACTCGTACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
58527246 CCTTCGGGACTTAGCCCGGATGTAATAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
58527286 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
58527305 TTATCATCCA
Statistics
Matches: 160, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
38 12 0.08
39 16 0.10
40 132 0.82
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:58528616 original size:12 final size:12
Alignment explanation
Indices: 58528599--58528623 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
58528589 ACATGAGAGC
58528599 TTTTTTTTTTCT
1 TTTTTTTTTTCT
58528611 TTTTTTTTTTCT
1 TTTTTTTTTTCT
58528623 T
1 T
58528624 CTAGGTACGG
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:0.08, G:0.00, T:0.92
Consensus pattern (12 bp):
TTTTTTTTTTCT
Found at i:58529287 original size:42 final size:42
Alignment explanation
Indices: 58529203--58529288 Score: 118
Period size: 42 Copynumber: 2.0 Consensus size: 42
58529193 TATGTGATTT
* *
58529203 ATATTGAAATGGAAAAAACGAGAAATGAATATGAGATGAGAA
1 ATATTGAAATGGAAAAAACGAGAAATGAATATAAGATAAGAA
* * * *
58529245 ATATTGAAATGGAAAATATGAGAAATGATTGTAAGATAAGAA
1 ATATTGAAATGGAAAAAACGAGAAATGAATATAAGATAAGAA
58529287 AT
1 AT
58529289 GAAATATGGA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.53, C:0.01, G:0.22, T:0.23
Consensus pattern (42 bp):
ATATTGAAATGGAAAAAACGAGAAATGAATATAAGATAAGAA
Found at i:58532635 original size:14 final size:14
Alignment explanation
Indices: 58532618--58532645 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
58532608 AATTGAGAAA
58532618 GAAAAAGAAGAGAT
1 GAAAAAGAAGAGAT
58532632 GAAAAAGAAGAGAT
1 GAAAAAGAAGAGAT
58532646 AGAAGAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.29, T:0.07
Consensus pattern (14 bp):
GAAAAAGAAGAGAT
Found at i:58533432 original size:13 final size:13
Alignment explanation
Indices: 58533416--58533440 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
58533406 AAGATGCAGA
58533416 GGGTAGATTATGG
1 GGGTAGATTATGG
58533429 GGGTAGATTATG
1 GGGTAGATTATG
58533441 TGTCACACAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.44, T:0.32
Consensus pattern (13 bp):
GGGTAGATTATGG
Found at i:58540614 original size:20 final size:20
Alignment explanation
Indices: 58540591--58540632 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
58540581 AGCTTGTCTG
*
58540591 CAATTATGGTGGCTTGACCA
1 CAATTATGGTGGCTTAACCA
58540611 CAATTATGGTGGCTTAACCA
1 CAATTATGGTGGCTTAACCA
58540631 CA
1 CA
58540633 TACATCTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (20 bp):
CAATTATGGTGGCTTAACCA
Found at i:58567504 original size:39 final size:39
Alignment explanation
Indices: 58567449--58567646 Score: 182
Period size: 39 Copynumber: 5.0 Consensus size: 39
58567439 GTTCGATTTT
* * * *
58567449 CAAATACTCAAATTCCTATTGGAAACCCAACTTTGTATC
1 CAAATACTCAAATTCCTAGTGAAAACCCAAATTTGTAAC
* **
58567488 CAAATACTCAACTTCCTAGTGAAAAAACATAATTTTGTAAC
1 CAAATACTCAAATTCCTAGTGAAAACCCA-AA-TTTGTAAC
* * * * * *
58567529 CAAATACTCAAAGTCCTAATGAAAATCCAACTTCGTGAC
1 CAAATACTCAAATTCCTAGTGAAAACCCAAATTTGTAAC
* **
58567568 CAAATACTCAAATTCCTAGCGAAATAACATAAATTTGTAAC
1 CAAATACTCAAATTCCTAGTG-AA-AACCCAAATTTGTAAC
* *
58567609 CAAATACTCAAATACCTA-TTAGAAACCCAAATTTGTAA
1 CAAATACTCAAATTCCTAGTGA-AAACCCAAATTTGTAA
58567647 ATTCTTTAAA
Statistics
Matches: 125, Mismatches: 29, Indels: 10
0.76 0.18 0.06
Matches are distributed among these distances:
39 62 0.50
40 5 0.04
41 58 0.46
ACGTcount: A:0.43, C:0.22, G:0.08, T:0.27
Consensus pattern (39 bp):
CAAATACTCAAATTCCTAGTGAAAACCCAAATTTGTAAC
Found at i:58567537 original size:41 final size:41
Alignment explanation
Indices: 58567449--58567626 Score: 166
Period size: 41 Copynumber: 4.4 Consensus size: 41
58567439 GTTCGATTTT
* * ** * *
58567449 CAAATACTCAAATTCCTATTG--GAAACCCAACTTTGTATC
1 CAAATACTCAAATTCCTAGTGAAAAAACATAAATTTGTAAC
* *
58567488 CAAATACTCAACTTCCTAGTGAAAAAACATAATTTTGTAAC
1 CAAATACTCAAATTCCTAGTGAAAAAACATAAATTTGTAAC
* * * * * * *
58567529 CAAATACTCAAAGTCCTAATG-AAAATC-CAACTTCGTGAC
1 CAAATACTCAAATTCCTAGTGAAAAAACATAAATTTGTAAC
* *
58567568 CAAATACTCAAATTCCTAGCGAAATAACATAAATTTGTAAC
1 CAAATACTCAAATTCCTAGTGAAAAAACATAAATTTGTAAC
*
58567609 CAAATACTCAAATACCTA
1 CAAATACTCAAATTCCTA
58567627 TTAGAAACCC
Statistics
Matches: 110, Mismatches: 25, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
39 45 0.41
40 9 0.08
41 56 0.51
ACGTcount: A:0.43, C:0.23, G:0.07, T:0.27
Consensus pattern (41 bp):
CAAATACTCAAATTCCTAGTGAAAAAACATAAATTTGTAAC
Found at i:58567559 original size:80 final size:80
Alignment explanation
Indices: 58567449--58567620 Score: 247
Period size: 80 Copynumber: 2.1 Consensus size: 80
58567439 GTTCGATTTT
* * * * * *
58567449 CAAATACTCAAATTCCTATTGGAAACCCAACTTTGT-ATCCAAATACTCAACTTCCTAGTGAAAA
1 CAAATACTCAAAGTCCTAATGAAAACCCAACTTCGTGA-CCAAATACTCAAATTCCTAGCGAAAA
*
58567513 AACATAATTTTGTAAC
65 AACATAAATTTGTAAC
* *
58567529 CAAATACTCAAAGTCCTAATGAAAATCCAACTTCGTGACCAAATACTCAAATTCCTAGCGAAATA
1 CAAATACTCAAAGTCCTAATGAAAACCCAACTTCGTGACCAAATACTCAAATTCCTAGCGAAAAA
58567594 ACATAAATTTGTAAC
66 ACATAAATTTGTAAC
58567609 CAAATACTCAAA
1 CAAATACTCAAA
58567621 TACCTATTAG
Statistics
Matches: 82, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
80 81 0.99
81 1 0.01
ACGTcount: A:0.43, C:0.23, G:0.08, T:0.27
Consensus pattern (80 bp):
CAAATACTCAAAGTCCTAATGAAAACCCAACTTCGTGACCAAATACTCAAATTCCTAGCGAAAAA
ACATAAATTTGTAAC
Found at i:58569648 original size:39 final size:41
Alignment explanation
Indices: 58569598--58569678 Score: 114
Period size: 41 Copynumber: 2.0 Consensus size: 41
58569588 TGAATCAAAG
58569598 TTAATTGGTTCAGGTAA-C-AAAGA-AACAAAAAAGAATTAA
1 TTAATTGGTTCAGGTAACCAAAAGATAA-AAAAAAGAATTAA
* *
58569637 TTAATTGGTTCATGTAACCAAAAGATAAAAAAAAGAGTTAA
1 TTAATTGGTTCAGGTAACCAAAAGATAAAAAAAAGAATTAA
58569678 T
1 T
58569679 GGTTTCAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
39 16 0.43
40 1 0.03
41 18 0.49
42 2 0.05
ACGTcount: A:0.52, C:0.07, G:0.15, T:0.26
Consensus pattern (41 bp):
TTAATTGGTTCAGGTAACCAAAAGATAAAAAAAAGAATTAA
Found at i:58571838 original size:20 final size:20
Alignment explanation
Indices: 58571815--58571862 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
58571805 TTTTTGCTTC
58571815 TTTTTGTCCTAAAACTAACA
1 TTTTTGTCCTAAAACTAACA
* ** *
58571835 TTTTTTTGTTAAAACTAACT
1 TTTTTGTCCTAAAACTAACA
58571855 TTTTTGTC
1 TTTTTGTC
58571863 AAAACACCCA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.27, C:0.15, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTTGTCCTAAAACTAACA
Found at i:58571859 original size:18 final size:19
Alignment explanation
Indices: 58571824--58571867 Score: 63
Period size: 18 Copynumber: 2.3 Consensus size: 19
58571814 CTTTTTGTCC
58571824 TAAAACTAACATTTTTTTGT
1 TAAAACTAACA-TTTTTTGT
58571844 TAAAACTAAC-TTTTTTGT
1 TAAAACTAACATTTTTTGT
*
58571862 CAAAAC
1 TAAAAC
58571868 ACCCAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 13 0.57
20 10 0.43
ACGTcount: A:0.39, C:0.14, G:0.05, T:0.43
Consensus pattern (19 bp):
TAAAACTAACATTTTTTGT
Found at i:58573151 original size:18 final size:18
Alignment explanation
Indices: 58573124--58573166 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
58573114 TTAGTGAAAA
* *
58573124 TGGGCTCACATGCCCGTG
1 TGGGCCCACACGCCCGTG
*
58573142 TGGGCCCACACGCTCGTG
1 TGGGCCCACACGCCCGTG
58573160 T-GGCCCA
1 TGGGCCCA
58573167 TGTGGGCCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.12, C:0.37, G:0.33, T:0.19
Consensus pattern (18 bp):
TGGGCCCACACGCCCGTG
Found at i:58573165 original size:27 final size:27
Alignment explanation
Indices: 58573135--58573194 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
58573125 GGGCTCACAT
* *
58573135 GCCCGTGTGGGCCCACACGCTCGTGTG
1 GCCCATGTGGGCCCACACACTCGTGTG
58573162 GCCCATGTGGGCCCACACACTCGTGTG
1 GCCCATGTGGGCCCACACACTCGTGTG
58573189 GCCCAT
1 GCCCAT
58573195 ATGACCCAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.12, C:0.38, G:0.32, T:0.18
Consensus pattern (27 bp):
GCCCATGTGGGCCCACACACTCGTGTG
Found at i:58575799 original size:25 final size:25
Alignment explanation
Indices: 58575771--58575835 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
58575761 TCAATTCATA
*
58575771 TAATGGGAAGCTCAT-GTGAGCCAT
1 TAATGGGAAGCTCATAGAGAGCCAT
* *
58575795 GTAATAGGAAGCT-TTAGAGAGCCAT
1 -TAATGGGAAGCTCATAGAGAGCCAT
*
58575820 TAACGGGAAGCTCATA
1 TAATGGGAAGCTCATA
58575836 CGAGCTAATA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
24 11 0.34
25 21 0.66
ACGTcount: A:0.34, C:0.15, G:0.28, T:0.23
Consensus pattern (25 bp):
TAATGGGAAGCTCATAGAGAGCCAT
Found at i:58577411 original size:24 final size:22
Alignment explanation
Indices: 58577369--58577426 Score: 59
Period size: 24 Copynumber: 2.6 Consensus size: 22
58577359 ATTAATTTTT
58577369 TAAA-AAAA-TATAAAAATT-A
1 TAAATAAAATTATAAAAATTAA
58577388 TAGAATAAAATTATAAAATTATTAA
1 TA-AATAAAATTATAAAA--ATTAA
*
58577413 TAAATAAATTTATA
1 TAAATAAAATTATA
58577427 TATTTTTATA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
19 2 0.06
20 2 0.06
21 4 0.12
22 7 0.22
24 14 0.44
25 3 0.09
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (22 bp):
TAAATAAAATTATAAAAATTAA
Found at i:58577436 original size:8 final size:8
Alignment explanation
Indices: 58577420--58577511 Score: 60
Period size: 8 Copynumber: 10.6 Consensus size: 8
58577410 TAATAAATAA
*
58577420 ATTTATAT
1 ATTTTTAT
58577428 ATTTTTAT
1 ATTTTTAT
58577436 AATTTTTAT
1 -ATTTTTAT
* *
58577445 GCTTCTTAAAT
1 -ATT-TT-TAT
* *
58577456 AATTTTAA
1 ATTTTTAT
58577464 AATTTTTTAT
1 A-TTT-TTAT
58577474 ATTTTTAT
1 ATTTTTAT
58577482 ATTTTTGA-
1 ATTTTT-AT
58577490 ATTTTTAT
1 ATTTTTAT
58577498 ATTTTATAT
1 ATTTT-TAT
58577507 ATTTT
1 ATTTT
58577512 AAAATATTAA
Statistics
Matches: 66, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
7 1 0.02
8 30 0.45
9 26 0.39
10 7 0.11
11 2 0.03
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (8 bp):
ATTTTTAT
Found at i:58577442 original size:9 final size:9
Alignment explanation
Indices: 58577421--58577511 Score: 50
Period size: 9 Copynumber: 10.2 Consensus size: 9
58577411 AATAAATAAA
58577421 TTTATATATT
1 TTTATA-ATT
58577431 TTTATAATT
1 TTTATAATT
**
58577440 TTTATGCTT
1 TTTATAATT
*
58577449 CTTA-AATAAT
1 TTTATAAT--T
*
58577459 TTTAAAATT
1 TTTATAATT
58577468 TTT-TATATT
1 TTTATA-ATT
58577477 TTTAT-ATT
1 TTTATAATT
*
58577485 TTT-GAATT
1 TTTATAATT
58577493 TTTAT-A-T
1 TTTATAATT
58577500 TTTATATATT
1 TTTATA-ATT
58577510 TT
1 TT
58577512 AAAATATTAA
Statistics
Matches: 62, Mismatches: 9, Indels: 20
0.68 0.10 0.22
Matches are distributed among these distances:
7 6 0.10
8 15 0.24
9 24 0.39
10 14 0.23
11 3 0.05
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (9 bp):
TTTATAATT
Found at i:58577512 original size:9 final size:8
Alignment explanation
Indices: 58577467--58577511 Score: 65
Period size: 8 Copynumber: 5.5 Consensus size: 8
58577457 ATTTTAAAAT
58577467 TTTTTATA
1 TTTTTATA
58577475 TTTTTATA
1 TTTTTATA
58577483 TTTTTGA-A
1 TTTTT-ATA
58577491 TTTTTATA
1 TTTTTATA
58577499 TTTTATATA
1 TTTT-TATA
58577508 TTTT
1 TTTT
58577512 AAAATATTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
7 1 0.03
8 24 0.71
9 9 0.26
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (8 bp):
TTTTTATA
Found at i:58580069 original size:16 final size:16
Alignment explanation
Indices: 58580048--58580111 Score: 53
Period size: 16 Copynumber: 4.0 Consensus size: 16
58580038 TTTTATTTTA
58580048 TTATGTAATTTATTTG
1 TTATGTAATTTATTTG
* *
58580064 TTATGT-GTTT-TTAGG
1 TTATGTAATTTATT-TG
*
58580079 TTGAT-TAGATTTATTTT
1 TT-ATGTA-ATTTATTTG
58580096 TTATGTAATTTATTTG
1 TTATGTAATTTATTTG
58580112 GCATGTTATT
Statistics
Matches: 36, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
14 2 0.06
15 7 0.19
16 18 0.50
17 7 0.19
18 2 0.06
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (16 bp):
TTATGTAATTTATTTG
Found at i:58590635 original size:34 final size:34
Alignment explanation
Indices: 58590597--58590673 Score: 93
Period size: 34 Copynumber: 2.3 Consensus size: 34
58590587 ACATAATTAT
* *
58590597 ATATGTATAGTTTGGTATAATCGAA-AGTGAATAC
1 ATATGTATAGTTTGATATAACCGAAGA-TGAATAC
* *
58590631 ATATGTATGGTTTGATATAACCGAAGATGAATAT
1 ATATGTATAGTTTGATATAACCGAAGATGAATAC
*
58590665 ATATATATA
1 ATATGTATA
58590674 CATTTGTTTG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
34 35 0.97
35 1 0.03
ACGTcount: A:0.40, C:0.05, G:0.18, T:0.36
Consensus pattern (34 bp):
ATATGTATAGTTTGATATAACCGAAGATGAATAC
Found at i:58591186 original size:3 final size:3
Alignment explanation
Indices: 58591178--58591207 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
58591168 ATGCTTGAAG
58591178 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
58591208 AGAGATTGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:58597760 original size:34 final size:34
Alignment explanation
Indices: 58597722--58597798 Score: 93
Period size: 34 Copynumber: 2.3 Consensus size: 34
58597712 ACATAATTAT
* *
58597722 ATATGTATAGTTTGGTATAATCGAA-AGTGAATAC
1 ATATGTATAGTTTGATATAACCGAAGA-TGAATAC
* *
58597756 ATATGTATGGTTTGATATAACCGAAGATGAATAT
1 ATATGTATAGTTTGATATAACCGAAGATGAATAC
*
58597790 ATATATATA
1 ATATGTATA
58597799 TACATTTGTT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
34 35 0.97
35 1 0.03
ACGTcount: A:0.40, C:0.05, G:0.18, T:0.36
Consensus pattern (34 bp):
ATATGTATAGTTTGATATAACCGAAGATGAATAC
Found at i:58598000 original size:59 final size:61
Alignment explanation
Indices: 58597869--58598004 Score: 161
Period size: 59 Copynumber: 2.3 Consensus size: 61
58597859 TAAGCTTGAG
* * *
58597869 ATGAGCACTAAGTGTGCGAAGTGAAATTGGTACTGAGTACTAAGTGTACGAAATTGATCAT
1 ATGAGCACTAAGTGTGCAAAGTGAAATTGATACTGAGTACTAAGTGTACGAAATCGATCAT
* * * * * * *
58597930 TTG-GCATTAAGTGTGCAAATTG-AATTTATACTGAGTACTAAGTGTACGAGATCGGTTA-
1 ATGAGCACTAAGTGTGCAAAGTGAAATTGATACTGAGTACTAAGTGTACGAAATCGATCAT
58597988 ATGAGCACTAAGTGTGC
1 ATGAGCACTAAGTGTGC
58598005 GAGTTTATCT
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
58 2 0.03
59 42 0.68
60 16 0.26
61 2 0.03
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (61 bp):
ATGAGCACTAAGTGTGCAAAGTGAAATTGATACTGAGTACTAAGTGTACGAAATCGATCAT
Found at i:58603715 original size:26 final size:28
Alignment explanation
Indices: 58603675--58603726 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
58603665 GGAATTTAAA
58603675 AAAAGAACAGGTGAAACA-AAAAAAATG
1 AAAAGAACAGGTGAAACAGAAAAAAATG
* *
58603702 AAAAG-ACAGTTGAAATAGAAAAAAA
1 AAAAGAACAGGTGAAACAGAAAAAAA
58603727 AAAGAATTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 10 0.45
27 12 0.55
ACGTcount: A:0.67, C:0.06, G:0.17, T:0.10
Consensus pattern (28 bp):
AAAAGAACAGGTGAAACAGAAAAAAATG
Found at i:58605557 original size:40 final size:39
Alignment explanation
Indices: 58605513--58605731 Score: 217
Period size: 40 Copynumber: 5.5 Consensus size: 39
58605503 GCTCGATTGT
* * *
58605513 CTTCGGGACATAGCCCGGTTATAGTAATTCACACAATTGC
1 CTTCGGGACATAGCCCGGTT-TAGTAACTCGCACAAATGC
58605553 CTTCGGGA-ATTAGCCCGGATTTAGTAACTCGCACAAATGC
1 CTTCGGGACA-TAGCCCGG-TTTAGTAACTCGCACAAATGC
* * * *
58605593 CTTCGGGACTTAACCCGATTTTGGTAACTCGCACAAATGC
1 CTTCGGGACATAGCCCG-GTTTAGTAACTCGCACAAATGC
* * *
58605633 CTTCGGGACTTAACCCGGTTTTGGTAACTCGCACAAATGC
1 CTTCGGGACATAGCCCGG-TTTAGTAACTCGCACAAATGC
* * * *
58605673 CTTCGGGA-ATTGACCCGGATTTAGTCACTTAGCACAAAAGC
1 CTTCGGGACATAG-CCCGG-TTTAGTAAC-TCGCACAAATGC
*
58605714 CTTCGGGACTTAGCCCGG
1 CTTCGGGACATAGCCCGG
58605732 ACATCATTCG
Statistics
Matches: 153, Mismatches: 18, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
39 2 0.01
40 124 0.81
41 25 0.16
42 2 0.01
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.26
Consensus pattern (39 bp):
CTTCGGGACATAGCCCGGTTTAGTAACTCGCACAAATGC
Found at i:58605628 original size:80 final size:81
Alignment explanation
Indices: 58605544--58605732 Score: 256
Period size: 80 Copynumber: 2.3 Consensus size: 81
58605534 TAGTAATTCA
* * *
58605544 CACAATTGCCTTCGGGAATTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCC
1 CACAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGGAATTAACCC
* *
58605609 -GATTTTGGTAAC-TCG
66 GGA-TTTAGTAACTTAG
* * * *
58605624 CACAAATGCCTTCGGGACTTAACCCGGTTTTGGTAACTCGCACAAATGCCTTCGGGAATTGACCC
1 CACAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGGAATTAACCC
*
58605689 GGATTTAGTCACTTAG
66 GGATTTAGTAACTTAG
*
58605705 CACAAAAGCCTTCGGGACTTAGCCCGGA
1 CACAAATGCCTTCGGGACTTAGCCCGGA
58605733 CATCATTCGA
Statistics
Matches: 94, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
80 65 0.69
81 29 0.31
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (81 bp):
CACAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGGAATTAACCC
GGATTTAGTAACTTAG
Found at i:58614397 original size:22 final size:22
Alignment explanation
Indices: 58614347--58614405 Score: 77
Period size: 20 Copynumber: 2.8 Consensus size: 22
58614337 ATGTCCAAGT
** *
58614347 AAAGGAGGCACATGCCCATGTG
1 AAAGGAGGCACACACCCATGAG
58614369 AAA--AGGCACACACCCATGAG
1 AAAGGAGGCACACACCCATGAG
58614389 AAAGGAGGCACACACCC
1 AAAGGAGGCACACACCC
58614406 GTGTGTTCCA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 17 0.53
22 15 0.47
ACGTcount: A:0.39, C:0.29, G:0.25, T:0.07
Consensus pattern (22 bp):
AAAGGAGGCACACACCCATGAG
Found at i:58614511 original size:21 final size:21
Alignment explanation
Indices: 58614472--58614540 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
58614462 CAGGATCAAC
* *
58614472 CGTGTGAAAGTCGGACACAGT
1 CGTGTGAAAGTCTGTCACAGT
*
58614493 CGTGTGAAAGTCTGTCACA-C
1 CGTGTGAAAGTCTGTCACAGT
*
58614513 CTGTGTGAAAATCTGTCAC-GCT
1 C-GTGTGAAAGTCTGTCACAG-T
58614535 CGTGTG
1 CGTGTG
58614541 CCCATAGGAC
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
20 1 0.03
21 38 0.95
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26
Consensus pattern (21 bp):
CGTGTGAAAGTCTGTCACAGT
Found at i:58618056 original size:10 final size:10
Alignment explanation
Indices: 58618041--58618068 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
58618031 ATTTTGTAAA
58618041 GTAATTTTTG
1 GTAATTTTTG
58618051 GTAATTTTTG
1 GTAATTTTTG
58618061 GTAATTTT
1 GTAATTTT
58618069 AATGTTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.21, C:0.00, G:0.18, T:0.61
Consensus pattern (10 bp):
GTAATTTTTG
Found at i:58619210 original size:48 final size:48
Alignment explanation
Indices: 58619149--58619639 Score: 847
Period size: 48 Copynumber: 10.2 Consensus size: 48
58619139 ATATACACAC
* * *
58619149 ATCTCCTACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
58619197 ATCTCATATATATTTCACATTAGCCATTCGCCTTTACCACATATACAT
1 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
* *
58619245 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
* * *
58619293 ATCTCATACATATTTCACATTAGCCGTTCGGCTTTACCACATGTACAT
1 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
* *
58619341 ATCTCATATATATTTCACAGTAGCCGTTCGGCTTTACCACATATACAT
1 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
58619389 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
58619437 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
58619485 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCATATATACAT
1 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
58619533 ATCTCATATATATTTTACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
* *
58619581 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
58619629 ATCTCATATAT
1 ATCTCATATAT
58619640 TTCACAATCT
Statistics
Matches: 421, Mismatches: 22, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 421 1.00
ACGTcount: A:0.31, C:0.26, G:0.07, T:0.36
Consensus pattern (48 bp):
ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
Found at i:58619656 original size:113 final size:113
Alignment explanation
Indices: 58619533--58619752 Score: 404
Period size: 113 Copynumber: 1.9 Consensus size: 113
58619523 ATATATACAT
* *
58619533 ATCTCATATATATTTTACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCA
1 ATCTCATATATATTTCACATTAGCCATTCAGCTTTACCACATATACATATCTCATACATATTTCA
58619598 CACTAGCCATTCGGCTTTACCACATATACATATCTCATATATTTCACA
66 CACTAGCCATTCGGCTTTACCACATATACATATCTCATATATTTCACA
*
58619646 ATCTCATATATATTTCACATTAGCCATTCAGCTTTACCACATATACATATCTCATATATATTTCA
1 ATCTCATATATATTTCACATTAGCCATTCAGCTTTACCACATATACATATCTCATACATATTTCA
*
58619711 CATTAGCCATTCGGCTTTACCACATATACATATCTCATATAT
66 CACTAGCCATTCGGCTTTACCACATATACATATCTCATATAT
58619753 CAATTTCAGC
Statistics
Matches: 103, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
113 103 1.00
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.38
Consensus pattern (113 bp):
ATCTCATATATATTTCACATTAGCCATTCAGCTTTACCACATATACATATCTCATACATATTTCA
CACTAGCCATTCGGCTTTACCACATATACATATCTCATATATTTCACA
Found at i:58619659 original size:65 final size:65
Alignment explanation
Indices: 58619581--58619704 Score: 221
Period size: 65 Copynumber: 1.9 Consensus size: 65
58619571 ACATATACAT
*
58619581 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATATATTTCACA
1 ATCTCATACATATTTCACACTAGCCATTCAGCTTTACCACATATACATATCTCATATATTTCACA
* *
58619646 ATCTCATATATATTTCACATTAGCCATTCAGCTTTACCACATATACATATCTCATATAT
1 ATCTCATACATATTTCACACTAGCCATTCAGCTTTACCACATATACATATCTCATATAT
58619705 ATTTCACATT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 56 1.00
ACGTcount: A:0.33, C:0.26, G:0.04, T:0.37
Consensus pattern (65 bp):
ATCTCATACATATTTCACACTAGCCATTCAGCTTTACCACATATACATATCTCATATATTTCACA
Found at i:58619702 original size:48 final size:48
Alignment explanation
Indices: 58619646--58619752 Score: 205
Period size: 48 Copynumber: 2.2 Consensus size: 48
58619636 ATATTTCACA
58619646 ATCTCATATATATTTCACATTAGCCATTCAGCTTTACCACATATACAT
1 ATCTCATATATATTTCACATTAGCCATTCAGCTTTACCACATATACAT
*
58619694 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATATATATTTCACATTAGCCATTCAGCTTTACCACATATACAT
58619742 ATCTCATATAT
1 ATCTCATATAT
58619753 CAATTTCAGC
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 58 1.00
ACGTcount: A:0.33, C:0.24, G:0.05, T:0.38
Consensus pattern (48 bp):
ATCTCATATATATTTCACATTAGCCATTCAGCTTTACCACATATACAT
Found at i:58622903 original size:19 final size:19
Alignment explanation
Indices: 58622879--58622915 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
58622869 ATTTTGATGT
58622879 TGTGGTATG-ATAGTTTAAA
1 TGTGGTATGTAT-GTTTAAA
58622898 TGTGGTATGTATGTTTAA
1 TGTGGTATGTATGTTTAA
58622916 TTCGATGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (19 bp):
TGTGGTATGTATGTTTAAA
Found at i:58624759 original size:21 final size:21
Alignment explanation
Indices: 58624733--58624779 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
58624723 AAAAAGTTAT
* *
58624733 GAGAGAAAGATATAGGGATGA
1 GAGAGAAAGATAGAGGGACGA
58624754 GAGAGAAAGATAGAGGGACGA
1 GAGAGAAAGATAGAGGGACGA
58624775 GAGAG
1 GAGAG
58624780 GGAAAGTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.47, C:0.02, G:0.43, T:0.09
Consensus pattern (21 bp):
GAGAGAAAGATAGAGGGACGA
Found at i:58625675 original size:34 final size:35
Alignment explanation
Indices: 58625632--58625697 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
58625622 AATTCATGCC
58625632 GATATTTTAAT-AAAATAAAGTATTTAAACTAGAT
1 GATATTTTAATCAAAATAAAGTATTTAAACTAGAT
* *
58625666 GATATTTTAATCAAATTAAATTATTTAAACTA
1 GATATTTTAATCAAAATAAAGTATTTAAACTA
58625698 ATTAATGACA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 11 0.38
35 18 0.62
ACGTcount: A:0.48, C:0.05, G:0.06, T:0.41
Consensus pattern (35 bp):
GATATTTTAATCAAAATAAAGTATTTAAACTAGAT
Found at i:58626864 original size:2 final size:2
Alignment explanation
Indices: 58626857--58626894 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
58626847 TCATGCAAGC
58626857 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
58626895 AAACTTAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:58629490 original size:2 final size:2
Alignment explanation
Indices: 58629483--58629517 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
58629473 GATAAAATAG
58629483 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 A
58629518 AGACATAAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:58629698 original size:12 final size:12
Alignment explanation
Indices: 58629681--58629705 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
58629671 CTAAAGTAAC
58629681 TGATAAGTTACT
1 TGATAAGTTACT
58629693 TGATAAGTTACT
1 TGATAAGTTACT
58629705 T
1 T
58629706 TTCGTTATAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (12 bp):
TGATAAGTTACT
Found at i:58637403 original size:49 final size:50
Alignment explanation
Indices: 58637337--58637465 Score: 145
Period size: 50 Copynumber: 2.6 Consensus size: 50
58637327 TCAAGTCGAT
* *
58637337 GCCATGTCCCACACATGGTCTTACATTGACTATCGAAATC-GAG-GCTGAC
1 GCCATGTCCCAAACATGGTCTTACATTGACTATC-AAATCTCAGTGCTGAC
* * * * * * *
58637386 GCCATGTGCCAAACATGGTCTTACACTGGCTCTCACATCTCCGTGCTGAT
1 GCCATGTCCCAAACATGGTCTTACATTGACTATCAAATCTCAGTGCTGAC
*
58637436 GCCATGTCCCAGACATGGTCTTACATTGAC
1 GCCATGTCCCAAACATGGTCTTACATTGAC
58637466 ACATCTCCTA
Statistics
Matches: 65, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
48 4 0.06
49 30 0.46
50 31 0.48
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.26
Consensus pattern (50 bp):
GCCATGTCCCAAACATGGTCTTACATTGACTATCAAATCTCAGTGCTGAC
Found at i:58637516 original size:46 final size:47
Alignment explanation
Indices: 58637284--58637552 Score: 182
Period size: 46 Copynumber: 5.7 Consensus size: 47
58637274 AGGGTGTAAT
*
58637284 GCCGATGTCATGTCCCAGACATGGTCTTACACTGGC-T-CATC-CATCAA
1 GCCGATG-CATGTCCCAGACATGGTCTTACACTGGCTTACATCTC--CTA
* * * * ** *
58637331 GTCGATGCCATGTCCCACACATGGTCTTACATTGAC-TATCGAAAT-CGA
1 GCCGATG-CATGTCCCAGACATGGTCTTACACTGGCTTA-C-ATCTCCTA
* * * *
58637379 GGCTGACGCCATGTGCCAAACATGGTCTTACACTGGCTCTCACATCTCCGT-
1 -GCCGATG-CATGTCCCAGACATGGTCTTACACTGGCT-T-ACATCTCC-TA
* * *
58637430 GCTGATGCCATGTCCCAGACATGGTCTTACATTGAC--ACATCTCCTA
1 GCCGATG-CATGTCCCAGACATGGTCTTACACTGGCTTACATCTCCTA
* *
58637476 GCCGATGCATGTCCCAGACAT-GTTTTACACTGGCTTACATCT-CGA
1 GCCGATGCATGTCCCAGACATGGTCTTACACTGGCTTACATCTCCTA
*
58637521 GGCCGATGCATGTCCCAGATAT-GTCTTACACT
1 -GCCGATGCATGTCCCAGACATGGTCTTACACT
58637553 AGCTCTCGTC
Statistics
Matches: 178, Mismatches: 30, Indels: 29
0.75 0.13 0.12
Matches are distributed among these distances:
44 10 0.06
45 17 0.10
46 49 0.28
47 32 0.18
48 2 0.01
49 30 0.17
50 34 0.19
51 3 0.02
52 1 0.01
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (47 bp):
GCCGATGCATGTCCCAGACATGGTCTTACACTGGCTTACATCTCCTA
Found at i:58640827 original size:45 final size:45
Alignment explanation
Indices: 58640728--58640999 Score: 320
Period size: 45 Copynumber: 6.1 Consensus size: 45
58640718 TTTTCTCAAA
* * * * *
58640728 TCACCAGCATT-TCGCCTACTAGGCTC-GAGGCCCG-ATATCAT-
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAACATC
* * **
58640769 TCCACCGGCATTATAGCCTGTTAGGCTCGAAA-GCCTGAATAGTATC
1 T-CACCGGCATTATAGCCTGCTAGGCTC-AAAGGCCCGAATAACATC
* * *
58640815 TCACCGGTATTATAGGCTGCTAGGCTCAAAGGCCCGAATAATATC
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAACATC
*
58640860 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAACATT
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAACATC
* * * *
58640905 TCACTGGCATTATAGCCTGCTAGGCTCAAAAGCCTGAATAACATT
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAACATC
* *
58640950 TCACCGGCATTATAGCCTGTTAGGCTCAAAGGCCCGAATAACATT
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAACATC
58640995 TCACC
1 TCACC
58641000 ACTTCTTTCC
Statistics
Matches: 200, Mismatches: 24, Indels: 10
0.85 0.10 0.04
Matches are distributed among these distances:
41 1 0.00
42 9 0.05
43 12 0.06
44 7 0.04
45 170 0.85
46 1 0.00
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.25
Consensus pattern (45 bp):
TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAACATC
Found at i:58640929 original size:135 final size:132
Alignment explanation
Indices: 58640728--58641000 Score: 366
Period size: 135 Copynumber: 2.0 Consensus size: 132
58640718 TTTTCTCAAA
* * * *
58640728 TCACCAGCATTTCGCCTACTAGGCTCGAGGCCCGATATCATTCCACCGGCATTATAGCCTGTTAG
1 TCACCAGCATTTAGCCTACTAGGCTCAAGGCCCGATAACATTCCACCGGCATTATAGCCTGCTAG
* ** * * *
58640793 GCTCGAAAGCCTGAATAGTATCTCACCGGTATTATAGGCTGCTAGGCTCAAAGGCCCGAATAATA
66 GCTCAAAAGCCTGAATAACATCTCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAACA
58640858 TC
131 TC
* * * *
58640860 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAACATTTCACTGGCATTATAGCCTGC
1 TCACCAGCATT-TAGCCTACTAGGCTC-AAGGCCCG-ATAACATTCCACCGGCATTATAGCCTGC
* *
58640925 TAGGCTCAAAAGCCTGAATAACATTTCACCGGCATTATAGCCTGTTAGGCTCAAAGGCCCGAATA
63 TAGGCTCAAAAGCCTGAATAACATCTCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATA
*
58640990 ACATT
128 ACATC
58640995 TCACCA
1 TCACCA
58641001 CTTCTTTCCC
Statistics
Matches: 120, Mismatches: 18, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
132 10 0.08
133 13 0.11
134 7 0.06
135 90 0.75
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.25
Consensus pattern (132 bp):
TCACCAGCATTTAGCCTACTAGGCTCAAGGCCCGATAACATTCCACCGGCATTATAGCCTGCTAG
GCTCAAAAGCCTGAATAACATCTCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAACA
TC
Found at i:58648494 original size:29 final size:29
Alignment explanation
Indices: 58648437--58648494 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
58648427 TCTCCAAATT
*
58648437 ATATATATTATATTACTCAATCCCGTCAA
1 ATATATATTATATTACTCAATCCCATCAA
* *
58648466 ATATTTATTATATTACTCAATCTCATCAA
1 ATATATATTATATTACTCAATCCCATCAA
58648495 CATGTGACTA
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:0.38, C:0.19, G:0.02, T:0.41
Consensus pattern (29 bp):
ATATATATTATATTACTCAATCCCATCAA
Found at i:58660703 original size:11 final size:11
Alignment explanation
Indices: 58660683--58660744 Score: 54
Period size: 11 Copynumber: 5.4 Consensus size: 11
58660673 GAGACTGTAG
58660683 AAAAAG-AAAA
1 AAAAAGAAAAA
58660693 AAAAAGAAAAA
1 AAAAAGAAAAA
58660704 AAAGAGAGAGAAAA
1 AAA-A-AGA-AAAA
*
58660718 GAAAAAGAAAAC
1 -AAAAAGAAAAA
**
58660730 AAAATTAAAAA
1 AAAAAGAAAAA
58660741 AAAA
1 AAAA
58660745 GTTGAGAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
10 6 0.14
11 19 0.44
12 4 0.09
13 6 0.14
14 5 0.12
15 3 0.07
ACGTcount: A:0.82, C:0.02, G:0.13, T:0.03
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:58662309 original size:16 final size:16
Alignment explanation
Indices: 58662288--58662319 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
58662278 TTAATTAATC
58662288 ACTTGGATGCTAAGTT
1 ACTTGGATGCTAAGTT
*
58662304 ACTTGGATGCTGAGTT
1 ACTTGGATGCTAAGTT
58662320 GCTTTGATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.12, G:0.28, T:0.38
Consensus pattern (16 bp):
ACTTGGATGCTAAGTT
Found at i:58665830 original size:33 final size:33
Alignment explanation
Indices: 58665788--58665853 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
58665778 TTTTGTGAAA
58665788 GGATTTTTCATGAAACCACCTAAAATGGACCTT
1 GGATTTTTCATGAAACCACCTAAAATGGACCTT
58665821 GGATTTTTCATGAAACCACCTAAAATGGACCTT
1 GGATTTTTCATGAAACCACCTAAAATGGACCTT
58665854 TTTGTAAAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.30
Consensus pattern (33 bp):
GGATTTTTCATGAAACCACCTAAAATGGACCTT
Found at i:58666697 original size:48 final size:48
Alignment explanation
Indices: 58666620--58666998 Score: 345
Period size: 48 Copynumber: 7.9 Consensus size: 48
58666610 GGTTATGTGG
* * *
58666620 GAGCCAGTGTAAGACCATGT-TTGGA-ATGGCATTGGCATTGTTATGA
1 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGTTATGA
* * *** *
58666666 GAGCTAGTGTAAGACTATGTCTGGGACATGGCATCGGCCTCAATATGC
1 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGTTATGA
* * * * *
58666714 GAGCCAGTGTAAGACCATGTTTGGAACATGGCACCGGCATTGCTAT-A
1 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGTTATGA
* * * * *
58666761 TGTGTTAGTGTAAGACCATGTCTGAGACATGGCATCAGCACTGATGTATGA
1 -GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTG-T-TATGA
* *** *
58666812 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCCATATGC
1 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGTTATGA
* * * *
58666860 GAGCTAGTGTAAGACAATGTTTGGAACATGGCATTGGCATTGTTAT-A
1 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGTTATGA
* ** *
58666907 TGTG-TCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACCGATGTATGG
1 -GAGCT-AGTGTAAGACCATGTCTGGGACATGGCATCGGCATTG-T-TATGA
** *
58666958 GAGCTAGTGTAAGACCATGTCCAGGACATGGCATCAGCATT
1 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATT
58666999 TTACCCTTTT
Statistics
Matches: 259, Mismatches: 62, Indels: 20
0.76 0.18 0.06
Matches are distributed among these distances:
46 18 0.07
47 5 0.02
48 160 0.62
49 1 0.00
50 73 0.28
51 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.26
Consensus pattern (48 bp):
GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGTTATGA
Found at i:58666872 original size:98 final size:98
Alignment explanation
Indices: 58666620--58666996 Score: 346
Period size: 98 Copynumber: 3.9 Consensus size: 98
58666610 GGTTATGTGG
* * * * *
58666620 GAGCCAGTGTAAGACCATGT-TTGGA-ATGGCATTGGCA-TTGTTATGAGAGCTAGTGTAAGACT
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACTCGATATG-GAGCTAGTGTAAGACC
* * * *
58666682 ATGTCTGGGACATGGCATCGGC-CTCA-ATATGC
65 ATGTCTGAGACATGGCATCAGCACTGATATATGA
* * * * * * *
58666714 GAGCCAGTGTAAGACCATGTTTGGAACATGGCACCGGCATTGCTATAT-GTGTTAGTGTAAGACC
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACT-CGATATGGAGCTAGTGTAAGACC
*
58666778 ATGTCTGAGACATGGCATCAGCACTGATGTATGA
65 ATGTCTGAGACATGGCATCAGCACTGATATATGA
* * *
58666812 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC-CTCCATATGCGAGCTAGTGTAAGACA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACTCGATATG-GAGCTAGTGTAAGACC
* ** * *
58666876 ATGTTTG-GAACATGGCATTGGCATTGTTATAT--
65 ATGTCTGAG-ACATGGCATCAGCACTGATATATGA
* *
58666908 GTGTCAGTGTAAGACCATGTCTGGGACATGGCATCGGCAC-CGATGTATGGGAGCTAGTGTAAGA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACTCGA--TAT-GGAGCTAGTGTAAGA
*
58666972 CCATGTC-CAGGACATGGCATCAGCA
63 CCATGTCTGA-GACATGGCATCAGCA
58666997 TTTTACCCTT
Statistics
Matches: 229, Mismatches: 39, Indels: 26
0.78 0.13 0.09
Matches are distributed among these distances:
94 20 0.09
95 3 0.01
96 85 0.37
97 7 0.03
98 112 0.49
99 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (98 bp):
GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACTCGATATGGAGCTAGTGTAAGACCA
TGTCTGAGACATGGCATCAGCACTGATATATGA
Found at i:58666880 original size:146 final size:145
Alignment explanation
Indices: 58666624--58666992 Score: 555
Period size: 146 Copynumber: 2.6 Consensus size: 145
58666614 ATGTGGGAGC
* * * *
58666624 CAGTGTAAGACCATGTTTGGA-ATGGCATTGGCATTG-T-TATGAGAGCTAGTGTAAGACTATGT
1 CAGTGTAAGACCATGTCTGGACATGGCATCGGCACTGATGTATGAGAGCTAGTGTAAGACCATGT
*
58666686 CTGGGACATGGCATCGGCCTCAATATGCGAGCCAGTGTAAGACCATGTTTGGAACATGGCACCGG
66 CTGGGACATGGCATCGGCCTCAATATGCGAGCCAGTGTAAGACAATGTTTGGAACATGGCACCGG
58666751 CATTGCTATATGTGT
131 CATTGCTATATGTGT
* *
58666766 TAGTGTAAGACCATGTCTGAGACATGGCATCAGCACTGATGTATGAGAGCTAGTGTAAGACCATG
1 CAGTGTAAGACCATGTCTG-GACATGGCATCGGCACTGATGTATGAGAGCTAGTGTAAGACCATG
* * **
58666831 TCTGGGACATGGCATCGGCCTCCATATGCGAGCTAGTGTAAGACAATGTTTGGAACATGGCATTG
65 TCTGGGACATGGCATCGGCCTCAATATGCGAGCCAGTGTAAGACAATGTTTGGAACATGGCACCG
*
58666896 GCATTGTTATATGTGT
130 GCATTGCTATATGTGT
* *
58666912 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACCGATGTATGGGAGCTAGTGTAAGACCATG
1 CAGTGTAAGACCATGTCT-GGACATGGCATCGGCACTGATGTATGAGAGCTAGTGTAAGACCATG
**
58666977 TCCAGGACATGGCATC
65 TCTGGGACATGGCATC
58666993 AGCATTTTAC
Statistics
Matches: 204, Mismatches: 18, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
142 17 0.08
143 2 0.01
144 12 0.06
145 1 0.00
146 171 0.84
147 1 0.00
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.27
Consensus pattern (145 bp):
CAGTGTAAGACCATGTCTGGACATGGCATCGGCACTGATGTATGAGAGCTAGTGTAAGACCATGT
CTGGGACATGGCATCGGCCTCAATATGCGAGCCAGTGTAAGACAATGTTTGGAACATGGCACCGG
CATTGCTATATGTGT
Found at i:58669164 original size:14 final size:14
Alignment explanation
Indices: 58669145--58669171 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
58669135 ATCCCACCCC
58669145 AATCAGATACAGAA
1 AATCAGATACAGAA
58669159 AATCAGATACAGA
1 AATCAGATACAGA
58669172 TTTATCAGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.15, G:0.15, T:0.15
Consensus pattern (14 bp):
AATCAGATACAGAA
Found at i:58671881 original size:42 final size:42
Alignment explanation
Indices: 58671834--58671970 Score: 148
Period size: 42 Copynumber: 3.3 Consensus size: 42
58671824 TGTGTTATCA
* * *
58671834 TGTAAGACCATATCTGAGATATGGCGTTGATATGAGATTTCG
1 TGTAAGACCATATCTGGGATATGGCATCGATATGAGATTTCG
** * *
58671876 TGTAAGACCACGTCTGGGACATGGCATCGAAATGAGATTTCG
1 TGTAAGACCATATCTGGGATATGGCATCGATATGAGATTTCG
* * * * ** *
58671918 TATAAGATCATATTTGGGATATGGCATCGATGTGAGATCCCA
1 TGTAAGACCATATCTGGGATATGGCATCGATATGAGATTTCG
58671960 TGTAAGACCAT
1 TGTAAGACCAT
58671971 GTCTAGGACA
Statistics
Matches: 75, Mismatches: 20, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
42 75 1.00
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (42 bp):
TGTAAGACCATATCTGGGATATGGCATCGATATGAGATTTCG
Found at i:58674429 original size:2 final size:2
Alignment explanation
Indices: 58674422--58674464 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
58674412 ACATAAGAGA
58674422 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
58674464 A
1 A
58674465 GCACTTAGAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:58675952 original size:2 final size:2
Alignment explanation
Indices: 58675945--58675969 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
58675935 CATGTAGTTA
58675945 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 A
58675970 CATGTATGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:58690233 original size:11 final size:12
Alignment explanation
Indices: 58690201--58690233 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
58690191 GAGCTATAGC
58690201 AAACTTAATTAT
1 AAACTTAATTAT
*
58690213 AAACTGAATTA-
1 AAACTTAATTAT
58690224 AAACTTAATT
1 AAACTTAATT
58690234 TATTAGAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.52, C:0.09, G:0.03, T:0.36
Consensus pattern (12 bp):
AAACTTAATTAT
Found at i:58690301 original size:20 final size:21
Alignment explanation
Indices: 58690264--58690311 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
58690254 GAGCTGAATC
*
58690264 GAGCTGAATTCTAGCTCAAAT
1 GAGCTGAATTCGAGCTCAAAT
*
58690285 GAGCTGAA-TCGAGCTCAAGT
1 GAGCTGAATTCGAGCTCAAAT
58690305 GAGCTGA
1 GAGCTGA
58690312 TGGGAGCTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 17 0.68
21 8 0.32
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.23
Consensus pattern (21 bp):
GAGCTGAATTCGAGCTCAAAT
Found at i:58691362 original size:21 final size:21
Alignment explanation
Indices: 58691315--58691366 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
58691305 CTCTTTTTCT
* **
58691315 TTTCTCTTTCAATTTCTTTTC
1 TTTCTTTTTCAATTTCTTGCC
* *
58691336 TCTCTTTTTCATTTTCTTGCC
1 TTTCTTTTTCAATTTCTTGCC
58691357 TTTCTTTTTC
1 TTTCTTTTTC
58691367 CACTCTCATT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.06, C:0.25, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTCTTTTTCAATTTCTTGCC
Found at i:58693477 original size:25 final size:24
Alignment explanation
Indices: 58693425--58693478 Score: 67
Period size: 22 Copynumber: 2.3 Consensus size: 24
58693415 GAACTTGATC
58693425 ACTTCACTTTTTTTTTTTTATAAT
1 ACTTCACTTTTTTTTTTTTATAAT
* *
58693449 --TTCATTTTTTTTCTTTTTTTAAT
1 ACTTCACTTTTTTT-TTTTTATAAT
58693472 ACTTCAC
1 ACTTCAC
58693479 AATATCACTA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
22 11 0.46
23 9 0.38
25 4 0.17
ACGTcount: A:0.19, C:0.15, G:0.00, T:0.67
Consensus pattern (24 bp):
ACTTCACTTTTTTTTTTTTATAAT
Found at i:58697811 original size:11 final size:12
Alignment explanation
Indices: 58697779--58697811 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
58697769 GAGCTATAGC
58697779 AAACTTAATTAT
1 AAACTTAATTAT
*
58697791 AAACTGAATTA-
1 AAACTTAATTAT
58697802 AAACTTAATT
1 AAACTTAATT
58697812 TATTAGAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.52, C:0.09, G:0.03, T:0.36
Consensus pattern (12 bp):
AAACTTAATTAT
Found at i:58697879 original size:20 final size:21
Alignment explanation
Indices: 58697843--58697889 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
58697833 AGTTGAATCA
*
58697843 AGCTGAATTCTAGCTCAAATG
1 AGCTGAATTCGAGCTCAAATG
*
58697864 AGCTGAA-TCGAGCTCAAGTG
1 AGCTGAATTCGAGCTCAAATG
58697884 AGCTGA
1 AGCTGA
58697890 TGGGAGCTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.23
Consensus pattern (21 bp):
AGCTGAATTCGAGCTCAAATG
Found at i:58699286 original size:35 final size:35
Alignment explanation
Indices: 58699240--58699330 Score: 103
Period size: 35 Copynumber: 2.6 Consensus size: 35
58699230 TACTTTCTGT
58699240 TTGGTGTGTTTCGGAGGGATTAGCTCTTT-TGAGCA
1 TTGGTGTGTTTCGGAGGGATTAGCT-TTTATGAGCA
* ** *
58699275 TTGGTGTGTTTCAGTTGGACTAGCTTTTATGAGCA
1 TTGGTGTGTTTCGGAGGGATTAGCTTTTATGAGCA
* * *
58699310 ATGGTATGTTTTGGAGGGATT
1 TTGGTGTGTTTCGGAGGGATT
58699331 GGCCCGTGTG
Statistics
Matches: 44, Mismatches: 11, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
34 3 0.07
35 41 0.93
ACGTcount: A:0.16, C:0.09, G:0.33, T:0.42
Consensus pattern (35 bp):
TTGGTGTGTTTCGGAGGGATTAGCTTTTATGAGCA
Found at i:58701213 original size:27 final size:27
Alignment explanation
Indices: 58701180--58701254 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 27
58701170 ATCTCAACGA
**
58701180 GACGTTAAACACGGAGTAGTCTGGCAG
1 GACGTTAAACACGGAGTAGTCTGAAAG
* * *
58701207 GATGTTAAACATGGGGTAGTCTGAAAG
1 GACGTTAAACACGGAGTAGTCTGAAAG
58701234 GACGTTAAACAC-GAGATAGTC
1 GACGTTAAACACGGAG-TAGTC
58701255 CGATGGGATG
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
26 2 0.05
27 37 0.95
ACGTcount: A:0.33, C:0.15, G:0.31, T:0.21
Consensus pattern (27 bp):
GACGTTAAACACGGAGTAGTCTGAAAG
Found at i:58703733 original size:40 final size:40
Alignment explanation
Indices: 58703677--58703864 Score: 270
Period size: 40 Copynumber: 4.7 Consensus size: 40
58703667 ATAACCACAA
* *
58703677 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
* * *
58703717 CCACAAATGCCTTCGGGTCTTAGCCCGGATATAACAACTC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
58703757 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
* *
58703797 GCACAAATGCCTTCGGGTCTTAACCCGGATATAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAT-AGCAACTC
* * *
58703837 GCATAAATGCCTTCGGGGCTTAGCCCGG
1 GCACAAATGCCTTCGGGTCTTAACCCGG
58703865 GTATCATTCA
Statistics
Matches: 134, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
40 132 0.99
41 2 0.01
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.23
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
Found at i:58703794 original size:80 final size:79
Alignment explanation
Indices: 58703657--58703864 Score: 301
Period size: 80 Copynumber: 2.6 Consensus size: 79
58703647 TCTTTGGAAT
* * *
58703657 TTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCCCAC
1 TTAGCCCGGATATAA-CACTAGCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTCCCAC
58703721 AAATGCCTTCGGGTC
65 AAATGCCTTCGGGTC
* *
58703736 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTCGCAC
1 TTAGCCCGGATATAAC-ACTAGCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTCCCAC
58703801 AAATGCCTTCGGGTC
65 AAATGCCTTCGGGTC
* * * *
58703816 TTAACCCGGATATAATCACTAGCATAAATGCCTTCGGGGCTTAGCCCGG
1 TTAGCCCGGATATAA-CACTAGCACAAATGCCTTCGGGTCTTAACCCGG
58703865 GTATCATTCA
Statistics
Matches: 116, Mismatches: 10, Indels: 5
0.89 0.08 0.04
Matches are distributed among these distances:
79 5 0.04
80 110 0.95
81 1 0.01
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (79 bp):
TTAGCCCGGATATAACACTAGCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTCCCACA
AATGCCTTCGGGTC
Found at i:58704624 original size:2 final size:2
Alignment explanation
Indices: 58704617--58704650 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
58704607 ATGTGCAAAC
58704617 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
58704651 GCTAGAGCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58708940 original size:3 final size:3
Alignment explanation
Indices: 58708932--58708967 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
58708922 ATTAACAAAC
58708932 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
58708968 TAAGGAAGTC
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:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:58711120 original size:11 final size:11
Alignment explanation
Indices: 58711097--58711134 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
58711087 AGCTTCTTCA
58711097 TTTTGTTTGTTT
1 TTTTGTTT-TTT
58711109 TTTCT-TTTTTT
1 TTT-TGTTTTTT
58711120 TTTTGTTTTTT
1 TTTTGTTTTTT
58711131 TTTT
1 TTTT
58711135 TTGGGGGGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 1 0.04
11 16 0.67
12 6 0.25
13 1 0.04
ACGTcount: A:0.00, C:0.03, G:0.08, T:0.89
Consensus pattern (11 bp):
TTTTGTTTTTT
Found at i:58711123 original size:12 final size:12
Alignment explanation
Indices: 58711106--58711135 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
58711096 ATTTTGTTTG
58711106 TTTTTTCTTTTT
1 TTTTTTCTTTTT
*
58711118 TTTTTTGTTTTT
1 TTTTTTCTTTTT
58711130 TTTTTT
1 TTTTTT
58711136 TGGGGGGGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.03, G:0.03, T:0.93
Consensus pattern (12 bp):
TTTTTTCTTTTT
Found at i:58711124 original size:19 final size:18
Alignment explanation
Indices: 58711097--58711136 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
58711087 AGCTTCTTCA
58711097 TTTTGTTTGTTTTTTCTTT
1 TTTTGTTTGTTTTTT-TTT
*
58711116 TTTTTTTTGTTTTTTTTT
1 TTTTGTTTGTTTTTTTTT
58711134 TTT
1 TTT
58711137 GGGGGGGGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.00, C:0.03, G:0.07, T:0.90
Consensus pattern (18 bp):
TTTTGTTTGTTTTTTTTT
Done.