Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008845.1 Hibiscus syriacus cultivar Beakdansim tig00112052_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: 591764
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
File 2 of 3
Found at i:307823 original size:36 final size:36
Alignment explanation
Indices: 307765--307838 Score: 121
Period size: 36 Copynumber: 2.1 Consensus size: 36
307755 GCTCATAATG
*
307765 ATGACTATATGTATAATCCTCATACTTGAGATCATT
1 ATGACTATATGCATAATCCTCATACTTGAGATCATT
* *
307801 ATGACTATATGCATGATTCTCATACTTGAGATCATT
1 ATGACTATATGCATAATCCTCATACTTGAGATCATT
307837 AT
1 AT
307839 TATTTCAACA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.39
Consensus pattern (36 bp):
ATGACTATATGCATAATCCTCATACTTGAGATCATT
Found at i:315874 original size:26 final size:25
Alignment explanation
Indices: 315823--315889 Score: 98
Period size: 26 Copynumber: 2.6 Consensus size: 25
315813 ATGCTCGTCC
**
315823 ATCTTCTAGAAGGTGCACTGACTAG
1 ATCTTCTAGAAACTGCACTGACTAG
315848 ATCTTCTAGAAACTGTCACTGACTAG
1 ATCTTCTAGAAACTG-CACTGACTAG
*
315874 ACCTTCTAGAAACTGC
1 ATCTTCTAGAAACTGC
315890 CAGATCAGAC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
25 14 0.37
26 24 0.63
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (25 bp):
ATCTTCTAGAAACTGCACTGACTAG
Found at i:331264 original size:59 final size:58
Alignment explanation
Indices: 331068--331469 Score: 524
Period size: 58 Copynumber: 6.9 Consensus size: 58
331058 TTTCCCGTAT
* * * * * *
331068 GGAAATTCATGCACTTAGAATGAATCTCTTAATGA-TTTGTACACAAAGTACCCAATAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAA-CATTTTGCACACAAAGTGCCCAATAC
* *
331126 GGAAATTCATACACTTAGTATGAATTTCTTAAC-TTTTGCACACGAAGTGCCCAATAT
1 GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTGCACACAAAGTGCCCAATAC
* * * *
331183 GGTAATTCATACACTTACTATGAATTTCTTAACATTTTTTCACACTAAGTGCCCAATAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAACA-TTTTGCACACAAAGTGCCCAATAC
* * *
331242 AGAAATTCATACAATTAGTATGAATTTCTTAACATTTTTCACACAAAGTGCCCAATAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTGCACACAAAGTGCCCAATAC
* *
331300 GGAAATTCATACACATT-GTATGAATTTCTTAATATTTTGCGC-CTAAAGTGCCCAATAC
1 GGAAATTCATACAC-TTAGTATGAATTTCTTAACATTTTGCACAC-AAAGTGCCCAATAC
* * * * *
331358 GGAAAGTCATACACTTAGTATGTATTTCTTAACATTTTTACACACGAAGTGCCCAATAT
1 GGAAATTCATACACTTAGTATGAATTTCTTAACA-TTTTGCACACAAAGTGCCCAATAC
331417 GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACAAAGTGCC
1 GGAAATTCATACACTTAGTATGAATTTCTTAACA-TTTTGCACACAAAGTGCC
331470 ATTTGGTAAT
Statistics
Matches: 302, Mismatches: 34, Indels: 15
0.86 0.10 0.04
Matches are distributed among these distances:
57 53 0.18
58 128 0.42
59 120 0.40
60 1 0.00
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.34
Consensus pattern (58 bp):
GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTGCACACAAAGTGCCCAATAC
Found at i:331424 original size:175 final size:174
Alignment explanation
Indices: 331065--331469 Score: 573
Period size: 175 Copynumber: 2.3 Consensus size: 174
331055 ACATTTCCCG
* * * * * *
331065 TATGGAAATTCATGCACTTAGAATGAATCTCTTAATGATTTGT-ACACAAAGTACCCAATACGGA
1 TATGGAAATTCATACACTTAGTATGAATTTCTTAA-CATTTTTCACACAAAGTGCCCAATACGGA
* * * * *
331129 AATTCATACACTTAGTATGAATTTCTTAACTTTTGCACACGAAGTGCCCAATATGGTAATTCATA
65 AATTCATACACTTAGTATGAATTTCTTAAATTTTGCACACAAAGTGCCCAATACGGAAAGTCATA
* *
331194 CACTTACTATGAATTTCTTAACATTTTTTCACACTAAGTGCCCAA
130 CACTTACTATGAATTTCTTAACATTTTTACACACGAAGTGCCCAA
** *
331239 TACAGAAATTCATACAATTAGTATGAATTTCTTAACATTTTTCACACAAAGTGCCCAATACGGAA
1 TATGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTCACACAAAGTGCCCAATACGGAA
*
331304 ATTCATACACATT-GTATGAATTTCTTAATATTTTGCGC-CTAAAGTGCCCAATACGGAAAGTCA
66 ATTCATACAC-TTAGTATGAATTTCTTAA-ATTTTGCACAC-AAAGTGCCCAATACGGAAAGTCA
* *
331367 TACACTTAGTATGTATTTCTTAACATTTTTACACACGAAGTGCCCAA
128 TACACTTACTATGAATTTCTTAACATTTTTACACACGAAGTGCCCAA
331414 TATGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACAAAGTGCC
1 TATGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTT-CACACAAAGTGCC
331470 ATTTGGTAAT
Statistics
Matches: 204, Mismatches: 22, Indels: 8
0.87 0.09 0.03
Matches are distributed among these distances:
173 5 0.02
174 76 0.37
175 110 0.54
176 13 0.06
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.34
Consensus pattern (174 bp):
TATGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTCACACAAAGTGCCCAATACGGAA
ATTCATACACTTAGTATGAATTTCTTAAATTTTGCACACAAAGTGCCCAATACGGAAAGTCATAC
ACTTACTATGAATTTCTTAACATTTTTACACACGAAGTGCCCAA
Found at i:331488 original size:59 final size:59
Alignment explanation
Indices: 331068--331469 Score: 532
Period size: 59 Copynumber: 6.9 Consensus size: 59
331058 TTTCCCGTAT
* * * * * *
331068 GGAAATTCATGCACTTAGAATGAATCTCTT-A-ATGATTTGTACACAAAGTACCCAATAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAACAT-TTTTGCACACAAAGTGCCCAATAC
* *
331126 GGAAATTCATACACTTAGTATGAATTTCTTAAC--TTTTGCACACGAAGTGCCCAATAT
1 GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACAAAGTGCCCAATAC
* * * *
331183 GGTAATTCATACACTTACTATGAATTTCTTAACATTTTTTCACACTAAGTGCCCAATAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACAAAGTGCCCAATAC
* *
331242 AGAAATTCATACAATTAGTATGAATTTCTTAACATTTTT-CACACAAAGTGCCCAATAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACAAAGTGCCCAATAC
* *
331300 GGAAATTCATACACATT-GTATGAATTTCTTAATA-TTTTGCGC-CTAAAGTGCCCAATAC
1 GGAAATTCATACAC-TTAGTATGAATTTCTTAACATTTTTGCACAC-AAAGTGCCCAATAC
* * * * *
331358 GGAAAGTCATACACTTAGTATGTATTTCTTAACATTTTTACACACGAAGTGCCCAATAT
1 GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACAAAGTGCCCAATAC
331417 GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACAAAGTGCC
1 GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACAAAGTGCC
331470 ATTTGGTAAT
Statistics
Matches: 301, Mismatches: 33, Indels: 19
0.85 0.09 0.05
Matches are distributed among these distances:
57 57 0.19
58 117 0.39
59 126 0.42
60 1 0.00
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.34
Consensus pattern (59 bp):
GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACAAAGTGCCCAATAC
Found at i:338022 original size:58 final size:57
Alignment explanation
Indices: 337959--338087 Score: 161
Period size: 57 Copynumber: 2.2 Consensus size: 57
337949 TTTCCCATAT
* *
337959 GGAAATTCATACAATTAGTATTAATCTCTTAA-TGATTTTCACACAAAGTGCCCAATAC
1 GGAAATTCATACAATTAGTATGAATCTCTTAACT--TTTGCACACAAAGTGCCCAATAC
* * * * * *
338017 GGAAATTGATACACTTATTATGAATTTCTTAACTTTTGCACACGAAGTGTCCAATAC
1 GGAAATTCATACAATTAGTATGAATCTCTTAACTTTTGCACACAAAGTGCCCAATAC
338074 GGAAATTCATACAA
1 GGAAATTCATACAA
338088 ACATTTTTGC
Statistics
Matches: 60, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
57 32 0.53
58 27 0.45
59 1 0.02
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (57 bp):
GGAAATTCATACAATTAGTATGAATCTCTTAACTTTTGCACACAAAGTGCCCAATAC
Found at i:338120 original size:99 final size:99
Alignment explanation
Indices: 337994--338186 Score: 325
Period size: 99 Copynumber: 1.9 Consensus size: 99
337984 CTCTTAATGA
* *
337994 TTTTCACACAAAGTGCCCAATACGGAAATTGATACACTTATTATGAATTTCTTAAC-TTTTGCAC
1 TTTTCACACAAAGTGCCCAATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTGCAC
* *
338058 ACGAAGTGTCCAATACGGAAATTCATACAAACAT
66 ACGAAGTGCCCAATACGGAAAGTCATACAAACAT
*
338092 TTTTGCACACAAAGTGCCTAATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTGCA
1 TTTT-CACACAAAGTGCCCAATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTGCA
338157 CACGAAGTGCCCAATACGGAAAGTCATACA
65 CACGAAGTGCCCAATACGGAAAGTCATACA
338187 CTTAGTATGA
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
98 4 0.05
99 49 0.56
100 35 0.40
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.30
Consensus pattern (99 bp):
TTTTCACACAAAGTGCCCAATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTGCAC
ACGAAGTGCCCAATACGGAAAGTCATACAAACAT
Found at i:338178 original size:58 final size:58
Alignment explanation
Indices: 338087--338445 Score: 477
Period size: 58 Copynumber: 6.1 Consensus size: 58
338077 AATTCATACA
* * *
338087 AACATTTTTGCACACAAAGTGCCTAATACGGAAATTCATACACTTAGTATGAATTTCTT
1 AACA-TTTTGCACACGAAGTGCCCAATACGGAAAGTCATACACTTAGTATGAATTTCTT
338146 AACATTTTGCACACGAAGTGCCCAATACGGAAAGTCATACACTTAGTATGAATTTCTT
1 AACATTTTGCACACGAAGTGCCCAATACGGAAAGTCATACACTTAGTATGAATTTCTT
* * *
338204 AACATTTTACACACGAAGTGGCCAATACGGAAAGTCATTCACTTAGTATGAATTTCTT
1 AACATTTTGCACACGAAGTGCCCAATACGGAAAGTCATACACTTAGTATGAATTTCTT
* * * * *
338262 AACAATTTTGCACACTAAGTGTCCAATAC-GAAAATCCATACACTTATTTTGAATTTCTT
1 AAC-ATTTTGCACACGAAGTGCCCAATACGGAAAGT-CATACACTTAGTATGAATTTCTT
* * * * *
338321 AACATTTTTCACATGAAGTGCCCAATACGGAAAGCCATACAATTAGTATAAATTTCTT
1 AACATTTTGCACACGAAGTGCCCAATACGGAAAGTCATACACTTAGTATGAATTTCTT
* * * * * *
338379 AACATTTGTACACATGAAGTGCCCAATACAGAAATTCATACACGTAGTATGAATTTATT
1 AACATTT-TGCACACGAAGTGCCCAATACGGAAAGTCATACACTTAGTATGAATTTCTT
338438 AACATTTT
1 AACATTTT
338446 TTCACACAAA
Statistics
Matches: 265, Mismatches: 31, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
58 162 0.61
59 103 0.39
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.32
Consensus pattern (58 bp):
AACATTTTGCACACGAAGTGCCCAATACGGAAAGTCATACACTTAGTATGAATTTCTT
Found at i:338383 original size:175 final size:176
Alignment explanation
Indices: 338087--338460 Score: 545
Period size: 175 Copynumber: 2.1 Consensus size: 176
338077 AATTCATACA
* *
338087 AACATTTTTGCACACAAAGTGCCTAATACGGAAATTCATACACTTAGTATGAATTTCTTAACATT
1 AACATTTTTGCACACAAAGTGCCTAATACGAAAATCCATACACTTAGTATGAATTTCTTAACATT
* * *
338152 TTGCACACGAAGTGCCCAATACGGAAAGTCATACACTTAGTATGAATTTCTTAACATTT-TACAC
66 TTGCACACGAAGTGCCCAATACGGAAAGCCATACAATTAGTATAAATTTCTTAACATTTGTACAC
* * * * *
338216 ACGAAGTGGCCAATACGGAAAGTCATTCACTTAGTATGAATTTCTT
131 ACGAAGTGCCCAATACAGAAAGTCATACACGTAGTATGAATTTATT
* * * *
338262 AACAATTTTGCACACTAAGTGTCC-AATACGAAAATCCATACACTTATTTTGAATTTCTTAACAT
1 AACATTTTTGCACACAAAGTG-CCTAATACGAAAATCCATACACTTAGTATGAATTTCTTAACAT
* *
338326 TTTTCACATGAAGTGCCCAATACGGAAAGCCATACAATTAGTATAAATTTCTTAACATTTGTACA
65 TTTGCACACGAAGTGCCCAATACGGAAAGCCATACAATTAGTATAAATTTCTTAACATTTGTACA
* *
338391 CATGAAGTGCCCAATACAGAAATTCATACACGTAGTATGAATTTATT
130 CACGAAGTGCCCAATACAGAAAGTCATACACGTAGTATGAATTTATT
* *
338438 AACATTTTTTCACACAAAATGCC
1 AACATTTTTGCACACAAAGTGCC
338461 ATTTGGTAAT
Statistics
Matches: 175, Mismatches: 22, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
175 112 0.64
176 63 0.36
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (176 bp):
AACATTTTTGCACACAAAGTGCCTAATACGAAAATCCATACACTTAGTATGAATTTCTTAACATT
TTGCACACGAAGTGCCCAATACGGAAAGCCATACAATTAGTATAAATTTCTTAACATTTGTACAC
ACGAAGTGCCCAATACAGAAAGTCATACACGTAGTATGAATTTATT
Found at i:338446 original size:117 final size:115
Alignment explanation
Indices: 338087--338452 Score: 482
Period size: 117 Copynumber: 3.1 Consensus size: 115
338077 AATTCATACA
* * *
338087 AACATTTTTGCACACAAAGTGCCTAATACGGAAATTCATACACTTAGTATGAATTTCTTAACATT
1 AACATTTTT-CACACGAAGTGCCCAATACGGAAAGTCATACACTTAGTATGAATTTCTTAACATT
* *
338152 TTGCACACGAAGTGCCCAATACGGAAAGTCATACACTTAGTATGAATTTCTT
65 TTGCACATGAAGTGCCCAATAC-GAAATTCATACACTTAGTATGAATTTCTT
* * *
338204 AACATTTTACACACGAAGTGGCCAATACGGAAAGTCATTCACTTAGTATGAATTTCTTAACAATT
1 AACATTTTTCACACGAAGTGCCCAATACGGAAAGTCATACACTTAGTATGAATTTCTTAAC-ATT
* * * *
338269 TTGCACACT-AAGTGTCCAATACGAAAATCCATACACTTATTTTGAATTTCTT
65 TTGCACA-TGAAGTGCCCAATACG-AAATTCATACACTTAGTATGAATTTCTT
* * * *
338321 AACATTTTTCACATGAAGTGCCCAATACGGAAAGCCATACAATTAGTATAAATTTCTTAACATTT
1 AACATTTTTCACACGAAGTGCCCAATACGGAAAGTCATACACTTAGTATGAATTTCTTAACATTT
* * *
338386 GTACACATGAAGTGCCCAATACAGAAATTCATACACGTAGTATGAATTTATT
66 -TGCACATGAAGTGCCCAATAC-GAAATTCATACACTTAGTATGAATTTCTT
338438 AACATTTTTTCACAC
1 AACA-TTTTTCACAC
338453 AAAATGCCAT
Statistics
Matches: 215, Mismatches: 27, Indels: 13
0.84 0.11 0.05
Matches are distributed among these distances:
116 53 0.25
117 152 0.71
118 10 0.05
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.32
Consensus pattern (115 bp):
AACATTTTTCACACGAAGTGCCCAATACGGAAAGTCATACACTTAGTATGAATTTCTTAACATTT
TGCACATGAAGTGCCCAATACGAAATTCATACACTTAGTATGAATTTCTT
Found at i:341185 original size:23 final size:23
Alignment explanation
Indices: 341158--341218 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 23
341148 AACTATGTGG
* *
341158 TCCTTCGAGATAGTTCTAAGTGC
1 TCCTTCGAGACAATTCTAAGTGC
* * *
341181 TCCTTCGGGACAATTCTACGTGG
1 TCCTTCGAGACAATTCTAAGTGC
*
341204 TCCTTCGAGAAAATT
1 TCCTTCGAGACAATT
341219 TTCTACACGG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (23 bp):
TCCTTCGAGACAATTCTAAGTGC
Found at i:345322 original size:20 final size:20
Alignment explanation
Indices: 345297--345370 Score: 96
Period size: 20 Copynumber: 3.7 Consensus size: 20
345287 TGCATCCTTC
*
345297 GTGCATGGATGCACAGTATG
1 GTGCATCGATGCACAGTATG
345317 GTGCATCGATGCACA-TCATG
1 GTGCATCGATGCACAGT-ATG
* * *
345337 ATGCATCGATGCACAGGAGG
1 GTGCATCGATGCACAGTATG
345357 GTGCATCGATGCAC
1 GTGCATCGATGCAC
345371 TAATTGCATT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 1 0.02
20 46 0.98
ACGTcount: A:0.26, C:0.22, G:0.31, T:0.22
Consensus pattern (20 bp):
GTGCATCGATGCACAGTATG
Found at i:345412 original size:94 final size:98
Alignment explanation
Indices: 345297--345474 Score: 249
Period size: 94 Copynumber: 1.9 Consensus size: 98
345287 TGCATCCTTC
* *
345297 GTGCATGGATGCACAGTATGGTGCATCGATGCAC-A-T-CATGATGCATCGATGCACAG-GAGGG
1 GTGCATGGATGCACAGCATGGTGCATCGATGCACTAGTGCA-GATGCATCGATGCACAGCCAGGG
345358 TGCATCGATGCACTA-ATTGCATTCGGTGTTTGA
65 TGCATCGATGCACTACATTGCATTCGGTGTTTGA
* * * *
345391 GTGCATGGATGCACTGCATGGTGCATTGATGCACTAGTGCAGATGCATGGATGCACTGCCAGGGT
1 GTGCATGGATGCACAGCATGGTGCATCGATGCACTAGTGCAGATGCATCGATGCACAGCCAGGGT
*
345456 GCATGGATGCACTACATTG
66 GCATCGATGCACTACATTG
345475 GTGCATGGAT
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
94 31 0.43
95 1 0.01
96 16 0.22
97 20 0.28
98 4 0.06
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.26
Consensus pattern (98 bp):
GTGCATGGATGCACAGCATGGTGCATCGATGCACTAGTGCAGATGCATCGATGCACAGCCAGGGT
GCATCGATGCACTACATTGCATTCGGTGTTTGA
Found at i:345477 original size:21 final size:20
Alignment explanation
Indices: 345391--345489 Score: 92
Period size: 21 Copynumber: 4.8 Consensus size: 20
345381 CGGTGTTTGA
*
345391 GTGCATGGATGCACTGCATG
1 GTGCATGGATGCACTACATG
*
345411 GTGCATTGATGCACTAGTGCA-G
1 GTGCATGGATGCACTA---CATG
* * *
345433 ATGCATGGATGCACTGCCAGG
1 GTGCATGGATGCACT-ACATG
345454 GTGCATGGATGCACTACATTG
1 GTGCATGGATGCACTACA-TG
*
345475 GTGCATGGATTCACT
1 GTGCATGGATGCACT
345490 TTGACACCCT
Statistics
Matches: 64, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
20 18 0.28
21 30 0.47
22 14 0.22
23 2 0.03
ACGTcount: A:0.22, C:0.20, G:0.31, T:0.26
Consensus pattern (20 bp):
GTGCATGGATGCACTACATG
Found at i:345480 original size:42 final size:40
Alignment explanation
Indices: 345391--345489 Score: 110
Period size: 42 Copynumber: 2.4 Consensus size: 40
345381 CGGTGTTTGA
* *
345391 GTGCATGGATGCACTGCATGGTGCATTGATGCACTAGTGCAG
1 GTGCATGGATGCACTGCAGGGTGCATGGATGCACTA--GCAG
*
345433 ATGCATGGATGCACTGCCAGGGTGCATGGATGCACTA-CATTG
1 GTGCATGGATGCACTG-CAGGGTGCATGGATGCACTAGCA--G
*
345475 GTGCATGGATTCACT
1 GTGCATGGATGCACT
345490 TTGACACCCT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
40 2 0.04
42 29 0.59
43 18 0.37
ACGTcount: A:0.22, C:0.20, G:0.31, T:0.26
Consensus pattern (40 bp):
GTGCATGGATGCACTGCAGGGTGCATGGATGCACTAGCAG
Found at i:345917 original size:108 final size:109
Alignment explanation
Indices: 345782--346000 Score: 413
Period size: 108 Copynumber: 2.0 Consensus size: 109
345772 GCTCCCCCTT
345782 TTTCATTAAGAAATTGATTTTTTCAAACCAAACTTCTCCCCCTTTTTGTTATATCAAAAATAATT
1 TTTCATTAAGAAATTGATTTTTTCAAACCAAACTTCTCCCCCTTTTTGTTATATCAAAAATAATT
*
345847 CAAAATAACATTGGAGAGTAAGTAGTAA-TTGAAATTTTGAAAA
66 CAAAATAACATTGGAGAGTAAGTAGTAATTTGAAATTTTAAAAA
345890 TTTCATTAAGAAATTGATTTTTTCAAACCAAACTTCTCCCCCTTTTTGTTATATCAAAAATAATT
1 TTTCATTAAGAAATTGATTTTTTCAAACCAAACTTCTCCCCCTTTTTGTTATATCAAAAATAATT
345955 CAAAATAACATTGGAGAGTAAGTAGTAATTTTGAAATTTTAAAAA
66 CAAAATAACATTGGAGAGTAAGTAGTAA-TTTGAAATTTTAAAAA
346000 T
1 T
346001 CATTTGAAAA
Statistics
Matches: 108, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
108 93 0.86
110 15 0.14
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.38
Consensus pattern (109 bp):
TTTCATTAAGAAATTGATTTTTTCAAACCAAACTTCTCCCCCTTTTTGTTATATCAAAAATAATT
CAAAATAACATTGGAGAGTAAGTAGTAATTTGAAATTTTAAAAA
Found at i:348996 original size:20 final size:20
Alignment explanation
Indices: 348906--348996 Score: 101
Period size: 20 Copynumber: 4.5 Consensus size: 20
348896 TGTAGCCTTC
* *
348906 GTGCATGGATACACAGCAGG
1 GTGCATCGATGCACAGCAGG
**
348926 GTGCATCGATGCTTAGCAGG
1 GTGCATCGATGCACAGCAGG
* * *
348946 GTGCATCGATGCAAAACATG
1 GTGCATCGATGCACAGCAGG
* *
348966 ATGCATCGATGCACAGGAGG
1 GTGCATCGATGCACAGCAGG
348986 GTGCATCGATG
1 GTGCATCGATG
348997 TACTAATTGC
Statistics
Matches: 57, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 57 1.00
ACGTcount: A:0.27, C:0.20, G:0.33, T:0.20
Consensus pattern (20 bp):
GTGCATCGATGCACAGCAGG
Found at i:349090 original size:21 final size:21
Alignment explanation
Indices: 349061--349118 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
349051 CACTAGTGCA
* *
349061 GGTGTATGGATGCACTGCCGG
1 GGTGCATGGATGCACTGCAGG
349082 GGTGCATGGATGCACTGCAGG
1 GGTGCATGGATGCACTGCAGG
349103 GGTGCATGGATGCACT
1 GGTGCATGGATGCACT
349119 TTGACATCCT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.17, C:0.19, G:0.41, T:0.22
Consensus pattern (21 bp):
GGTGCATGGATGCACTGCAGG
Found at i:350071 original size:44 final size:44
Alignment explanation
Indices: 350016--350190 Score: 262
Period size: 44 Copynumber: 4.0 Consensus size: 44
350006 ATACCATGAG
* *
350016 TGGCACCTTTCTACCAATAATGCA-TCGTTATGCATTTTCATTTA
1 TGGCACATTTCTGCCAATAATGCACT-GTTATGCATTTTCATTTA
*
350060 TGGCACATTTCTGCCAATAATTCACTGTTATGCATTTTCATTTA
1 TGGCACATTTCTGCCAATAATGCACTGTTATGCATTTTCATTTA
* * * *
350104 TGGCACATTGCTGCCAGTAATGCACCGTTATGCATTTTCATTAA
1 TGGCACATTTCTGCCAATAATGCACTGTTATGCATTTTCATTTA
*
350148 TGGCACATTTCTGCCAATAATGCACTGCTATGCATTTTCATTT
1 TGGCACATTTCTGCCAATAATGCACTGTTATGCATTTTCATTT
350191 TTTTCGGTAA
Statistics
Matches: 117, Mismatches: 13, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
44 116 0.99
45 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (44 bp):
TGGCACATTTCTGCCAATAATGCACTGTTATGCATTTTCATTTA
Found at i:357367 original size:54 final size:54
Alignment explanation
Indices: 357251--357559 Score: 336
Period size: 54 Copynumber: 5.7 Consensus size: 54
357241 ACAATATGGT
* * * ** ** *
357251 AATTCATGAACTCATTATGAATTGCATGGGGTTGCACACTTAGTGCCAATACGGA
1 AATTCATAAACTTATTATGAATTTC-TTAGGTTGCACACACAGTGCCAATACAGA
* * * *
357306 AATTCATAAACTTATTATGAATTTATTAGGTTGCAAACACAG-GACCAAAACATA
1 AATTCATAAACTTATTATGAATTTCTTAGGTTGCACACACAGTG-CCAATACAGA
* * *
357360 AATTCATAAACATATTATGAATTTCTTAGGCTGCACACACAGTGCCAATACGGA
1 AATTCATAAACTTATTATGAATTTCTTAGGTTGCACACACAGTGCCAATACAGA
* * * * * **
357414 AATTCATAAATTTATTATGGATTTCATAGGTTGCACACACAGTGTCGATACATC
1 AATTCATAAACTTATTATGAATTTCTTAGGTTGCACACACAGTGCCAATACAGA
*
357468 AATTCAT-AACTTATTATGAATTTCTTAGGTTGCATACACAGTGCCAATACAGA
1 AATTCATAAACTTATTATGAATTTCTTAGGTTGCACACACAGTGCCAATACAGA
* * *
357521 AACTAATAAA-TATATTATGAATTTCTTAAGTTGCACACA
1 AATTCATAAACT-TATTATGAATTTCTTAGGTTGCACACA
357560 AACTGATCAT
Statistics
Matches: 209, Mismatches: 41, Indels: 9
0.81 0.16 0.03
Matches are distributed among these distances:
53 45 0.22
54 142 0.68
55 22 0.11
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (54 bp):
AATTCATAAACTTATTATGAATTTCTTAGGTTGCACACACAGTGCCAATACAGA
Found at i:357531 original size:107 final size:108
Alignment explanation
Indices: 357251--357559 Score: 363
Period size: 107 Copynumber: 2.9 Consensus size: 108
357241 ACAATATGGT
* * * ** **
357251 AATTCATGAACTCATTATGAATTGCATGGGGTTGCACACTTAGTGCCAATACGGAAATTCATAAA
1 AATTCATAAACTTATTATGAATTTC-TTAGGTTGCACACACAGTGCCAATACGGAAATTCATAAA
* *
357316 CTTATTATGAATTT-ATTAGGTTGCAAACACAGGACCAAAACATA
65 TTTATTATGAATTTCA-TAGGTTGCACACACAGGACCAAAACATA
* *
357360 AATTCATAAACATATTATGAATTTCTTAGGCTGCACACACAGTGCCAATACGGAAATTCATAAAT
1 AATTCATAAACTTATTATGAATTTCTTAGGTTGCACACACAGTGCCAATACGGAAATTCATAAAT
* * * * *
357425 TTATTATGGATTTCATAGGTTGCACACACAGTG-TCGATACATC
66 TTATTATGAATTTCATAGGTTGCACACACAG-GACCAAAACATA
* * * *
357468 AATTCAT-AACTTATTATGAATTTCTTAGGTTGCATACACAGTGCCAATACAGAAACTAATAAAT
1 AATTCATAAACTTATTATGAATTTCTTAGGTTGCACACACAGTGCCAATACGGAAATTCATAAAT
* * *
357532 ATATTATGAATTTCTTAAGTTGCACACA
66 TTATTATGAATTTCATAGGTTGCACACA
357560 AACTGATCAT
Statistics
Matches: 172, Mismatches: 26, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
107 75 0.44
108 74 0.43
109 23 0.13
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (108 bp):
AATTCATAAACTTATTATGAATTTCTTAGGTTGCACACACAGTGCCAATACGGAAATTCATAAAT
TTATTATGAATTTCATAGGTTGCACACACAGGACCAAAACATA
Found at i:358656 original size:11 final size:11
Alignment explanation
Indices: 358640--358666 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
358630 TTCCCCCTTT
358640 TCCCTCTTAAA
1 TCCCTCTTAAA
358651 TCCCTCTTAAA
1 TCCCTCTTAAA
358662 TCCCT
1 TCCCT
358667 AATAAGGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.22, C:0.41, G:0.00, T:0.37
Consensus pattern (11 bp):
TCCCTCTTAAA
Found at i:364428 original size:54 final size:53
Alignment explanation
Indices: 364366--364624 Score: 326
Period size: 54 Copynumber: 4.8 Consensus size: 53
364356 TGCTAATAAA
*
364366 AAAATTCATAAACTTATTATGAATTTCTTCGGTTGCACACACAGAGCCAATAC
1 AAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACACAGAGCCAATAC
*
364419 ACAAATTCATAAACATATTATGAATTTCTTAGGTTGCACACACAGTA-CCAATAC
1 A-AAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACACAG-AGCCAATAC
* *
364473 GAAAATTCATAAACTTATTATGAATTTCTTAGTTTGCACACACAGTGCCAATAC
1 -AAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACACAGAGCCAATAC
* * * * *
364527 ATAAATTTATAAACTCT-TTTTGAATTTCTTAGGTTGCACACACAGTGTCAATATG
1 A-AAATTCATAAACT-TATTATGAATTTCTTAGGTTGCACACACAGAGCCAATA-C
* * *
364582 GATATTCATAAA-TATGTTATGAATTTCTTAGGTTGCACACACA
1 AAAATTCATAAACT-TATTATGAATTTCTTAGGTTGCACACACA
364625 ATGCTCATTC
Statistics
Matches: 183, Mismatches: 15, Indels: 15
0.86 0.07 0.07
Matches are distributed among these distances:
53 4 0.02
54 176 0.96
55 3 0.02
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.34
Consensus pattern (53 bp):
AAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACACAGAGCCAATAC
Found at i:364497 original size:108 final size:108
Alignment explanation
Indices: 364366--364624 Score: 369
Period size: 108 Copynumber: 2.4 Consensus size: 108
364356 TGCTAATAAA
*
364366 AAAATTCATAAACTTATTATGAATTTCTTCGGTTGCACACACAGAGCCAATACACAAATTCATAA
1 AAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACACAGAGCCAATACACAAATTCATAA
364431 ACAT-ATTATGAATTTCTTAGGTTGCACACACAGTACCAATACG
66 AC-TCATTATGAATTTCTTAGGTTGCACACACAGTACCAATACG
* * * *
364474 AAAATTCATAAACTTATTATGAATTTCTTAGTTTGCACACACAGTGCCAATACATAAATTTATAA
1 AAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACACAGAGCCAATACACAAATTCATAA
* * ** *
364539 ACTCTTTTTGAATTTCTTAGGTTGCACACACAGTGTCAATATG
66 ACTCATTATGAATTTCTTAGGTTGCACACACAGTACCAATACG
* * *
364582 GATATTCATAAA-TATGTTATGAATTTCTTAGGTTGCACACACA
1 AAAATTCATAAACT-TATTATGAATTTCTTAGGTTGCACACACA
364625 ATGCTCATTC
Statistics
Matches: 135, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
107 2 0.01
108 133 0.99
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.34
Consensus pattern (108 bp):
AAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACACAGAGCCAATACACAAATTCATAA
ACTCATTATGAATTTCTTAGGTTGCACACACAGTACCAATACG
Found at i:365944 original size:44 final size:44
Alignment explanation
Indices: 365881--365980 Score: 164
Period size: 44 Copynumber: 2.3 Consensus size: 44
365871 ATTACAATGA
*
365881 ATTTTCATTTATGACACATTTATGCCAATAATGCACCATTATGC
1 ATTTTCATTTATGACACATTTATGCCAAGAATGCACCATTATGC
* * *
365925 ATTTTCATTTATGGCACATTTATGGCAAGAATGCACCGTTATGC
1 ATTTTCATTTATGACACATTTATGCCAAGAATGCACCATTATGC
365969 ATTTTCATTTAT
1 ATTTTCATTTAT
365981 TCCACCCTTA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 52 1.00
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (44 bp):
ATTTTCATTTATGACACATTTATGCCAAGAATGCACCATTATGC
Found at i:366008 original size:19 final size:19
Alignment explanation
Indices: 365984--366021 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
365974 CATTTATTCC
*
365984 ACCCTT-ATTCCAATAATGT
1 ACCCTTCATACCAA-AATGT
366003 ACCCTTCATACCAAAATGT
1 ACCCTTCATACCAAAATGT
366022 TGTAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.34, C:0.29, G:0.05, T:0.32
Consensus pattern (19 bp):
ACCCTTCATACCAAAATGT
Found at i:368947 original size:32 final size:32
Alignment explanation
Indices: 368911--369008 Score: 178
Period size: 32 Copynumber: 3.1 Consensus size: 32
368901 TATTTTTGAG
368911 TCAGTTAAGTGCATCGCTACTACATTAGTCTT
1 TCAGTTAAGTGCATCGCTACTACATTAGTCTT
*
368943 TCAGTTAAGTGCATCGCTACTACATTAATCTT
1 TCAGTTAAGTGCATCGCTACTACATTAGTCTT
*
368975 TCAGTTAAGTGCATCGCTACTACATTAGCCTT
1 TCAGTTAAGTGCATCGCTACTACATTAGTCTT
369007 TC
1 TC
369009 CAATTCATGT
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 63 1.00
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (32 bp):
TCAGTTAAGTGCATCGCTACTACATTAGTCTT
Found at i:372953 original size:12 final size:13
Alignment explanation
Indices: 372929--372957 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
372919 AATTGAAGTC
372929 ATCTTCTAGCTCA
1 ATCTTCTAGCTCA
372942 ATCTTC-AGCTCA
1 ATCTTCTAGCTCA
372954 ATCT
1 ATCT
372958 AGCTATGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.24, C:0.31, G:0.07, T:0.38
Consensus pattern (13 bp):
ATCTTCTAGCTCA
Found at i:374177 original size:44 final size:44
Alignment explanation
Indices: 374129--374393 Score: 331
Period size: 44 Copynumber: 6.0 Consensus size: 44
374119 ATACCATGAG
* * *
374129 TGGCACATTTCGGTCAATAATGCACCGTTATGCATTTTTATTTA
1 TGGCACATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
374173 TGGCACCA-TTCAT-CCAATAATGCACCGCTT-TGCATTTTCATTTA
1 TGGCA-CATTTC-TGCCAATAATGCACCG-TTATGCATTTTCATTTA
* * * * **
374217 TGGAACCTTTCTGTCAATAATACACAATTATGCATTTTCATTTA
1 TGGCACATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
*
374261 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
1 TGGCACATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * *
374305 TGGCACATTTCTGCCAATAATACATCATTATGCATTTTCATTTA
1 TGGCACATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* *
374349 TGGTATC-TTTCTGCCAATCATGCACCGTTATGCATTTTCATTTA
1 TGGCA-CATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
374393 T
1 T
374394 TTCGGTAACA
Statistics
Matches: 191, Mismatches: 23, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
43 4 0.02
44 182 0.95
45 5 0.03
ACGTcount: A:0.26, C:0.22, G:0.12, T:0.40
Consensus pattern (44 bp):
TGGCACATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
Found at i:377545 original size:21 final size:21
Alignment explanation
Indices: 377501--377549 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
377491 GTTCCCAAAG
* *
377501 TTTCAATTTTTTCAAATTCCT
1 TTTCATTTTTTTCAAATTACT
* *
377522 TTTCATTTTTTTCAATTTAGT
1 TTTCATTTTTTTCAAATTACT
377543 TTTCATT
1 TTTCATT
377550 CCTTCTTGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.20, C:0.14, G:0.02, T:0.63
Consensus pattern (21 bp):
TTTCATTTTTTTCAAATTACT
Found at i:377778 original size:15 final size:13
Alignment explanation
Indices: 377739--377773 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
377729 ATATATTGTT
377739 CAAATTTGTTCCG
1 CAAATTTGTTCCG
377752 CAAATTTGTTCCG
1 CAAATTTGTTCCG
377765 CAAATTTGT
1 CAAATTTGT
377774 GTTCCTGGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (13 bp):
CAAATTTGTTCCG
Found at i:382562 original size:15 final size:15
Alignment explanation
Indices: 382539--382569 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
382529 TTTTCAAATA
*
382539 GTTATACTTATGGTT
1 GTTAAACTTATGGTT
382554 GTTAAACTTATGGTT
1 GTTAAACTTATGGTT
382569 G
1 G
382570 CTAATTGAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.06, G:0.23, T:0.48
Consensus pattern (15 bp):
GTTAAACTTATGGTT
Found at i:384282 original size:40 final size:41
Alignment explanation
Indices: 384244--384382 Score: 192
Period size: 40 Copynumber: 3.4 Consensus size: 41
384234 TCAAGAAAAT
* * *
384244 GATCGATCCCTTTTGAAAAAGGATCAATAAATTGGAAAAGG
1 GATCTATCCCTTTTGAAAAAAGATCAATCAATTGGAAAAGG
384285 GATCTATCCCTTTT-AAAAAAGATCAATCAATTGGAAAAGG
1 GATCTATCCCTTTTGAAAAAAGATCAATCAATTGGAAAAGG
* *
384325 GAT-TATCCCTTTTGAAAAAAGATTAATCCATTGGAAAAGG
1 GATCTATCCCTTTTGAAAAAAGATCAATCAATTGGAAAAGG
* * *
384365 GATCCATCGCTTCTGAAA
1 GATCTATCCCTTTTGAAA
384383 GGTTAGCTAC
Statistics
Matches: 88, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
39 10 0.11
40 54 0.61
41 24 0.27
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (41 bp):
GATCTATCCCTTTTGAAAAAAGATCAATCAATTGGAAAAGG
Found at i:384361 original size:20 final size:20
Alignment explanation
Indices: 384299--384362 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
384289 TATCCCTTTT
* *
384299 AAAAAAGATCAATCAATTGG
1 AAAAAAGATTAATCCATTGG
** * *
384319 AAAAGGGATT-ATCCCTTTTG
1 AAAAAAGATTAAT-CCATTGG
384339 AAAAAAGATTAATCCATTGG
1 AAAAAAGATTAATCCATTGG
384359 AAAA
1 AAAA
384363 GGGATCCATC
Statistics
Matches: 32, Mismatches: 10, Indels: 4
0.70 0.22 0.09
Matches are distributed among these distances:
19 2 0.06
20 28 0.88
21 2 0.06
ACGTcount: A:0.48, C:0.11, G:0.16, T:0.25
Consensus pattern (20 bp):
AAAAAAGATTAATCCATTGG
Found at i:389500 original size:36 final size:36
Alignment explanation
Indices: 389460--389533 Score: 130
Period size: 36 Copynumber: 2.1 Consensus size: 36
389450 GCTCATAATG
*
389460 ATGACTATATGTATGATCCTCATACTTGAGATCATT
1 ATGACTATATGCATGATCCTCATACTTGAGATCATT
*
389496 ATGACTATATGCATGATTCTCATACTTGAGATCATT
1 ATGACTATATGCATGATCCTCATACTTGAGATCATT
389532 AT
1 AT
389534 TATCTCAACA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (36 bp):
ATGACTATATGCATGATCCTCATACTTGAGATCATT
Found at i:390122 original size:2 final size:2
Alignment explanation
Indices: 390115--390149 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
390105 GTTAATATTA
390115 AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT
390150 TTGCACGTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:397572 original size:25 final size:26
Alignment explanation
Indices: 397525--397574 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
397515 CCAGAAGGTG
*
397525 CGCTGACTAGATCTTCTATAAACTGT
1 CGCTGACTAGATCTTCTAGAAACTGT
397551 CGCTGACTAGA-CTTCTAGAAACTG
1 CGCTGACTAGATCTTCTAGAAACTG
397575 CCACATCAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 12 0.52
26 11 0.48
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (26 bp):
CGCTGACTAGATCTTCTAGAAACTGT
Found at i:407700 original size:8 final size:8
Alignment explanation
Indices: 407687--407742 Score: 51
Period size: 8 Copynumber: 6.5 Consensus size: 8
407677 AAAAACCAAT
407687 AAAAAAAC
1 AAAAAAAC
*
407695 AAAAAAGGC
1 AAAAAA-AC
407704 AAAACAAAAGGC
1 -AAA-AAAA--C
407716 AAAAAAAC
1 AAAAAAAC
407724 -AAAAAAC
1 AAAAAAAC
407731 AAAAAAAC
1 AAAAAAAC
407739 AAAA
1 AAAA
407743 TTTCAAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
7 7 0.17
8 18 0.45
9 1 0.03
10 7 0.17
11 6 0.15
12 1 0.03
ACGTcount: A:0.80, C:0.12, G:0.07, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:407722 original size:15 final size:15
Alignment explanation
Indices: 407704--407742 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
407694 CAAAAAAGGC
**
407704 AAAACAAAAGGCAAA
1 AAAACAAAAAACAAA
407719 AAAACAAAAAACAAA
1 AAAACAAAAAACAAA
407734 AAAACAAAA
1 AAAACAAAA
407743 TTTCAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.82, C:0.13, G:0.05, T:0.00
Consensus pattern (15 bp):
AAAACAAAAAACAAA
Found at i:413431 original size:58 final size:57
Alignment explanation
Indices: 413339--413744 Score: 451
Period size: 58 Copynumber: 7.0 Consensus size: 57
413329 CACATTTCCC
* * * * *
413339 ATATGGAAATTCATGCACTTAGAATGAATCTCTTAATGATTTGTACACAAAGTACCAA
1 ATATGGAAATTCATACACTTAGTATGAATTTCTTAAT-ATTTGTACACAAAGTGCCCA
413397 ATATGGAAATTCATACACTTAGTATGAATTTCTTAACT-TTTGTACA-AGAAGTGCCCA
1 ATATGGAAATTCATACACTTAGTATGAATTTCTTAA-TATTTGTACACA-AAGTGCCCA
* * * * *
413454 ATATGGTAATTCATACACTTACTATGAATTTCTTAACATTTTTGCACACTAAGTGCCCA
1 ATATGGAAATTCATACACTTAGTATGAATTTCTT-A-ATATTTGTACACAAAGTGCCCA
* * * * *
413513 ATACGAAAATTCATACACTTAGTATGAATTTCTTAACATTTTTCACACTAAGTGCCCA
1 ATATGGAAATTCATACACTTAGTATGAATTTCTTAATATTTGT-ACACAAAGTGCCCA
* * *
413571 ATACGGAAATTCATACACATT-GTATGAATTTCTTAATATTTG-GCGCCTAAAGTGCCCA
1 ATATGGAAATTCATACAC-TTAGTATGAATTTCTTAATATTTGTAC-AC-AAAGTGCCCA
* * * *
413629 ATACGGAAATTCATACACTTAGTATGTATTTCTTAACATTTTTACACATGAAGTGCCCA
1 ATATGGAAATTCATACACTTAGTATGAATTTCTTAATATTTGTACACA--AAGTGCCCA
* *
413688 ATATGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACAAAGTGCC
1 ATATGGAAATTCATACACTTAGTATGAATTTCTT-A-ATATTTGTACACAAAGTGCC
413745 ATTTGGTAAT
Statistics
Matches: 298, Mismatches: 34, Indels: 31
0.82 0.09 0.09
Matches are distributed among these distances:
56 2 0.01
57 55 0.18
58 132 0.44
59 99 0.33
60 1 0.00
61 9 0.03
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.34
Consensus pattern (57 bp):
ATATGGAAATTCATACACTTAGTATGAATTTCTTAATATTTGTACACAAAGTGCCCA
Found at i:413685 original size:175 final size:174
Alignment explanation
Indices: 413345--413745 Score: 533
Period size: 175 Copynumber: 2.3 Consensus size: 174
413335 TCCCATATGG
* * * * * * *
413345 AAATTCATGCACTTAGAATGAATCTCTTAATGATTTGT-ACACAAAGTACCAAATATGGAAATTC
1 AAATTCATACACTTAGTATGAATTTCTTAA-CATTTTTCACACAAAGTGCCAAATACGGAAATTC
* * *
413409 ATACACTTAGTATGAATTTCTTAACTTTTGTACAAGAAGTGCCCAATATGGTAATTCATACACTT
65 ATACACTTAGTATGAATTTCTTAACTTTTGGACAAGAAGTGCCCAATACGGAAATTCATACACTT
*
413474 ACTATGAATTTCTTAACATTTTTGCACACTAAGTGCCCAATACGA
130 ACTATGAATTTCTTAACATTTTTACACACTAAGTGCCCAATACGA
* *
413519 AAATTCATACACTTAGTATGAATTTCTTAACATTTTTCACACTAAGTGCCCAATACGGAAATTCA
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTTCACACAAAGTGCCAAATACGGAAATTCA
* *
413584 TACACATT-GTATGAATTTCTTAA-TATTTGGCGCCTA-AAGTGCCCAATACGGAAATTCATACA
66 TACAC-TTAGTATGAATTTCTTAACT-TTT-G-GACAAGAAGTGCCCAATACGGAAATTCATACA
* * * *
413646 CTTAGTATGTATTTCTTAACATTTTTACACA-TGAAGTGCCCAATATGG
127 CTTACTATGAATTTCTTAACATTTTTACACACT-AAGTGCCCAATACGA
413694 AAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACAAAGTGCCA
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTT-CACACAAAGTGCCA
413746 TTTGGTAATC
Statistics
Matches: 199, Mismatches: 21, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
173 6 0.03
174 74 0.37
175 105 0.53
176 14 0.07
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.34
Consensus pattern (174 bp):
AAATTCATACACTTAGTATGAATTTCTTAACATTTTTCACACAAAGTGCCAAATACGGAAATTCA
TACACTTAGTATGAATTTCTTAACTTTTGGACAAGAAGTGCCCAATACGGAAATTCATACACTTA
CTATGAATTTCTTAACATTTTTACACACTAAGTGCCCAATACGA
Found at i:413763 original size:59 final size:59
Alignment explanation
Indices: 413339--413744 Score: 506
Period size: 59 Copynumber: 7.0 Consensus size: 59
413329 CACATTTCCC
* * * * * * *
413339 ATATGGAAATTCATGCACTTAGAATGAATCTCTT-A-ATGATTTGTACACAAAGTACCAA
1 ATATGGAAATTCATACACTTAGTATGAATTTCTTAACAT-TTTTGCACACAAAGTGCCCA
*
413397 ATATGGAAATTCATACACTTAGTATGAATTTCTTAAC--TTTTGTACA-AGAAGTGCCCA
1 ATATGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACA-AAGTGCCCA
* * *
413454 ATATGGTAATTCATACACTTACTATGAATTTCTTAACATTTTTGCACACTAAGTGCCCA
1 ATATGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACAAAGTGCCCA
* * *
413513 ATACGAAAATTCATACACTTAGTATGAATTTCTTAACATTTTT-CACACTAAGTGCCCA
1 ATATGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACAAAGTGCCCA
* * * *
413571 ATACGGAAATTCATACACATT-GTATGAATTTCTTAATA-TTTGGCGC-CTAAAGTGCCCA
1 ATATGGAAATTCATACAC-TTAGTATGAATTTCTTAACATTTTTGCACAC-AAAGTGCCCA
* * * **
413629 ATACGGAAATTCATACACTTAGTATGTATTTCTTAACATTTTTACACATGAAGTGCCCA
1 ATATGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACAAAGTGCCCA
413688 ATATGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACAAAGTGCC
1 ATATGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACAAAGTGCC
413745 ATTTGGTAAT
Statistics
Matches: 305, Mismatches: 31, Indels: 23
0.85 0.09 0.06
Matches are distributed among these distances:
56 1 0.00
57 56 0.18
58 123 0.40
59 125 0.41
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.34
Consensus pattern (59 bp):
ATATGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACAAAGTGCCCA
Found at i:420469 original size:59 final size:59
Alignment explanation
Indices: 420287--420796 Score: 640
Period size: 58 Copynumber: 8.7 Consensus size: 59
420277 TTCCCATATG
* * * * *
420287 GAAATTCATACAATTAGTATTAATCTCTT-A-ATGATTTGCACACAAAGTGCCCAATACA
1 GAAATTCATACACTTAGTATGAATTTCTTAACAT-TTTTGCACACGAAGTGCCCAATACA
* * * *
420345 GAAATTCATACACTTTGTATAAATTTCTTAAC--TTTTGCACACGAAGTGTCTAATACA
1 GAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATACA
* * *
420402 GAAATTCATACACTTGGTATGAATTTCTTAACATTTTTGCACACAAAGTGCCTAATACA
1 GAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATACA
*
420461 GAAATTCATACACTTAGTATGAATTTCTTAACA-TTTTGCACACAAAGTGCCCAATACA
1 GAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATACA
* * * * *
420519 GAAAGTCATACACTTAGTATGAATTTATTAACA-TTTTACACACGAAGTGGCCAATACG
1 GAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATACA
* * *
420577 GAAAGTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGTCTAATAC-
1 GAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATACA
* * * * *
420635 GAAAATCCATACACTTATTTTGAATTTCTTAACATTTTT-CACATGAAGTGCCCAATACG
1 G-AAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATACA
** * * *
420694 GAAAGCCATACACTTAGTATAAATTTCTTAACATTTTTGCACATGAAGTGCCCAATACC
1 GAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATACA
* * *
420753 GAAATTCATACACGTAGTATGAATTTATTAACATTTTTTCACAC
1 GAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACAC
420797 AAAAGGCCAT
Statistics
Matches: 401, Mismatches: 43, Indels: 15
0.87 0.09 0.03
Matches are distributed among these distances:
57 51 0.13
58 183 0.46
59 167 0.42
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (59 bp):
GAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATACA
Found at i:420550 original size:117 final size:118
Alignment explanation
Indices: 420287--420799 Score: 637
Period size: 117 Copynumber: 4.4 Consensus size: 118
420277 TTCCCATATG
* * * * * *
420287 GAAATTCATACAATTAGTATTAATCTCTT-A-ATGATTTGCACACAAAGTGCCCAATACAGAAAT
1 GAAATTCATACACTTAGTATGAATTTATTAACAT-TTTTGCACACAAAGTGCCCAATACAGAAAG
* * *
420350 TCATACACTTTGTATAAATTTCTTAAC--TTTTGCACACGAAGTGTCTAATACA
65 TCATACACTTAGTATAAATTTCTTAACATTTTTGCACACGAAGTGCCCAATACA
* * * *
420402 GAAATTCATACACTTGGTATGAATTTCTTAACATTTTTGCACACAAAGTGCCTAATACAGAAATT
1 GAAATTCATACACTTAGTATGAATTTATTAACATTTTTGCACACAAAGTGCCCAATACAGAAAGT
* *
420467 CATACACTTAGTATGAATTTCTTAACA-TTTTGCACACAAAGTGCCCAATACA
66 CATACACTTAGTATAAATTTCTTAACATTTTTGCACACGAAGTGCCCAATACA
* * * * *
420519 GAAAGTCATACACTTAGTATGAATTTATTAACA-TTTTACACACGAAGTGGCCAATACGGAAAGT
1 GAAATTCATACACTTAGTATGAATTTATTAACATTTTTGCACACAAAGTGCCCAATACAGAAAGT
* * *
420583 CATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGTCTAATAC-
66 CATACACTTAGTATAAATTTCTTAACATTTTTGCACACGAAGTGCCCAATACA
* * * * ** *
420635 GAAAATCCATACACTTATTTTGAATTTCTTAACATTTTT-CACATGAAGTGCCCAATACGGAAAG
1 G-AAATTCATACACTTAGTATGAATTTATTAACATTTTTGCACACAAAGTGCCCAATACAGAAAG
* * *
420699 CCATACACTTAGTATAAATTTCTTAACATTTTTGCACATGAAGTGCCCAATACC
65 TCATACACTTAGTATAAATTTCTTAACATTTTTGCACACGAAGTGCCCAATACA
* *
420753 GAAATTCATACACGTAGTATGAATTTATTAACATTTTTTCACACAAA
1 GAAATTCATACACTTAGTATGAATTTATTAACATTTTTGCACACAAA
420800 AGGCCATTTG
Statistics
Matches: 348, Mismatches: 42, Indels: 13
0.86 0.10 0.03
Matches are distributed among these distances:
115 25 0.07
116 107 0.31
117 205 0.59
118 11 0.03
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.33
Consensus pattern (118 bp):
GAAATTCATACACTTAGTATGAATTTATTAACATTTTTGCACACAAAGTGCCCAATACAGAAAGT
CATACACTTAGTATAAATTTCTTAACATTTTTGCACACGAAGTGCCCAATACA
Found at i:421172 original size:22 final size:20
Alignment explanation
Indices: 421125--421181 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 20
421115 TTTGGCTCTT
421125 TAGTATCAATACCCCTACCA
1 TAGTATCAATACCCCTACCA
*
421145 TAGTATCAATACTACCCTACTA
1 TAGTATCAATAC--CCCTACCA
* *
421167 TGGTATCGATACCCC
1 TAGTATCAATACCCC
421182 GTTCTGATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 15 0.47
22 17 0.53
ACGTcount: A:0.32, C:0.32, G:0.09, T:0.28
Consensus pattern (20 bp):
TAGTATCAATACCCCTACCA
Found at i:426275 original size:40 final size:40
Alignment explanation
Indices: 426220--426341 Score: 226
Period size: 40 Copynumber: 3.0 Consensus size: 40
426210 TGCAGGTTTA
426220 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
* *
426260 TAATACACTTCGGTGTATATGGTGGGCACGACTTTATGTA
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
426300 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
426340 TA
1 TA
426342 GCACTACGGT
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 78 1.00
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:428199 original size:23 final size:23
Alignment explanation
Indices: 428173--428233 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
428163 AACTATGTGG
* *
428173 TCCTTCGAGATATTTCTAAGTGC
1 TCCTTCGAGACAATTCTAAGTGC
* *
428196 TCCTTC-ATGACAATTCTACGTGG
1 TCCTTCGA-GACAATTCTAAGTGC
*
428219 TCCTTCGAGAAAATT
1 TCCTTCGAGACAATT
428234 TTCTACTCGG
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
22 1 0.03
23 29 0.94
24 1 0.03
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (23 bp):
TCCTTCGAGACAATTCTAAGTGC
Found at i:434256 original size:23 final size:23
Alignment explanation
Indices: 434230--434293 Score: 65
Period size: 25 Copynumber: 2.7 Consensus size: 23
434220 GGACAACTAT
* * *
434230 AAGTGGTTCTTCTGGATAATTCA
1 AAGTGGTCCTTCGGGAAAATTCA
*
434253 AAGTGGTCCTTCGGGAAAATTTTCT
1 AAGTGGTCCTTCGGGAAAA--TTCA
*
434278 ATGTGGTCCTTCGGGA
1 AAGTGGTCCTTCGGGA
434294 CGAATCTACA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 16 0.47
25 18 0.53
ACGTcount: A:0.22, C:0.16, G:0.27, T:0.36
Consensus pattern (23 bp):
AAGTGGTCCTTCGGGAAAATTCA
Found at i:435723 original size:20 final size:20
Alignment explanation
Indices: 435695--435736 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
435685 TGTATGGATA
*
435695 CACAGCATGGTGCATCGATG
1 CACAGCATGATGCATCGATG
*
435715 CACATCATGATGCATCGATG
1 CACAGCATGATGCATCGATG
435735 CA
1 CA
435737 TCGATGCACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.29, C:0.26, G:0.24, T:0.21
Consensus pattern (20 bp):
CACAGCATGATGCATCGATG
Found at i:435734 original size:8 final size:8
Alignment explanation
Indices: 435705--435744 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
435695 CACAGCATGG
435705 TGCATCGA
1 TGCATCGA
435713 TGCA-C-A
1 TGCATCGA
435719 T-CAT-GA
1 TGCATCGA
435725 TGCATCGA
1 TGCATCGA
435733 TGCATCGA
1 TGCATCGA
435741 TGCA
1 TGCA
435745 CAGGAAGGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
5 2 0.07
6 4 0.14
7 4 0.14
8 18 0.64
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.25
Consensus pattern (8 bp):
TGCATCGA
Found at i:435738 original size:28 final size:28
Alignment explanation
Indices: 435705--435764 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
435695 CACAGCATGG
* *
435705 TGCATCGATGCACATCATGATGCATCGA
1 TGCATCGATGCACAGCAAGATGCATCGA
* *
435733 TGCATCGATGCACAGGAAGGTGCATCGA
1 TGCATCGATGCACAGCAAGATGCATCGA
435761 TGCA
1 TGCA
435765 CAGGAGGGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.28, C:0.23, G:0.27, T:0.22
Consensus pattern (28 bp):
TGCATCGATGCACAGCAAGATGCATCGA
Found at i:435758 original size:20 final size:20
Alignment explanation
Indices: 435733--435785 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
435723 GATGCATCGA
435733 TGCATCGATGCACAGGAAGG
1 TGCATCGATGCACAGGAAGG
*
435753 TGCATCGATGCACAGGAGGG
1 TGCATCGATGCACAGGAAGG
435773 TGCATCGATGCAC
1 TGCATCGATGCAC
435786 TAATTGCATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.26, C:0.23, G:0.34, T:0.17
Consensus pattern (20 bp):
TGCATCGATGCACAGGAAGG
Found at i:435873 original size:21 final size:20
Alignment explanation
Indices: 435806--435904 Score: 99
Period size: 21 Copynumber: 4.8 Consensus size: 20
435796 CGGTGTTTGA
*
435806 GTGCATGGATGCACTGCATG
1 GTGCATGGATGCACTGCCTG
* * *
435826 GTGCATCGATGCACTAGTACAG
1 GTGCATGGATGCACT-G-CCTG
*
435848 GTGCATGGATGCACTGCCGGG
1 GTGCATGGATGCACTGCC-TG
*
435869 GTGCATGGATGCACTGCATTG
1 GTGCATGGATGCACTGC-CTG
*
435890 GTGCATGGATTCACT
1 GTGCATGGATGCACT
435905 TTGACACCCT
Statistics
Matches: 65, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
20 15 0.23
21 35 0.54
22 15 0.23
ACGTcount: A:0.20, C:0.21, G:0.33, T:0.25
Consensus pattern (20 bp):
GTGCATGGATGCACTGCCTG
Found at i:435893 original size:42 final size:42
Alignment explanation
Indices: 435806--435904 Score: 119
Period size: 42 Copynumber: 2.4 Consensus size: 42
435796 CGGTGTTTGA
* *
435806 GTGCATGGATGCACTGCATGGTGCATCGATGCACTAGTACAG
1 GTGCATGGATGCACTGCAGGGTGCATCGATGCACTAGCACAG
* * **
435848 GTGCATGGATGCACTGCCGGGGTGCATGGATGCACT-GCATTG
1 GTGCATGGATGCACTG-CAGGGTGCATCGATGCACTAGCACAG
*
435890 GTGCATGGATTCACT
1 GTGCATGGATGCACT
435905 TTGACACCCT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
42 33 0.67
43 16 0.33
ACGTcount: A:0.20, C:0.21, G:0.33, T:0.25
Consensus pattern (42 bp):
GTGCATGGATGCACTGCAGGGTGCATCGATGCACTAGCACAG
Found at i:437299 original size:20 final size:19
Alignment explanation
Indices: 437262--437310 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
437252 TCTAAATTAT
*
437262 TTTTCAAAATTTCATTTTG
1 TTTTCAAAATTACATTTTG
437281 ATTTTCAAAATTA-ACTTTTG
1 -TTTTCAAAATTACA-TTTTG
*
437301 CTTTCAAAAT
1 TTTTCAAAAT
437311 CAAATTATCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.33, C:0.12, G:0.04, T:0.51
Consensus pattern (19 bp):
TTTTCAAAATTACATTTTG
Found at i:437563 original size:12 final size:12
Alignment explanation
Indices: 437546--437570 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
437536 ATCAAATGTC
437546 TTCTTTCCCTTT
1 TTCTTTCCCTTT
437558 TTCTTTCCCTTT
1 TTCTTTCCCTTT
437570 T
1 T
437571 GAAAGCACAT
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:0.32, G:0.00, T:0.68
Consensus pattern (12 bp):
TTCTTTCCCTTT
Found at i:438242 original size:34 final size:32
Alignment explanation
Indices: 438173--438242 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
438163 ACCTTACAAC
* *
438173 TCCCTAGTTTTTACGGGCTAAACTATAACCTT
1 TCCCTAGTTTTTACGGGATAAACTAGAACCTT
* *
438205 TCCCTAGCTTTTATAGGGGATAAGCTAGAACCTT
1 TCCCTAG-TTTT-TACGGGATAAACTAGAACCTT
438239 TCCC
1 TCCC
438243 CTTTATAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 7 0.22
33 4 0.12
34 21 0.66
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (32 bp):
TCCCTAGTTTTTACGGGATAAACTAGAACCTT
Found at i:438633 original size:20 final size:20
Alignment explanation
Indices: 438608--438718 Score: 141
Period size: 20 Copynumber: 5.5 Consensus size: 20
438598 TGTAGCCTTC
* * *
438608 GTGCATGGATACACAACAGG
1 GTGCATCGATGCACAGCAGG
*
438628 GTGCATCGATGCATAGCAGG
1 GTGCATCGATGCACAGCAGG
*
438648 GTGCATCGATGCACAGGAGG
1 GTGCATCGATGCACAGCAGG
*
438668 GTGCATCGATGCATAGCAGG
1 GTGCATCGATGCACAGCAGG
* *
438688 GTGCATCGATACACAGGAGG
1 GTGCATCGATGCACAGCAGG
*
438708 ATGCATCGATG
1 GTGCATCGATG
438719 TACTAATTGT
Statistics
Matches: 78, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 78 1.00
ACGTcount: A:0.28, C:0.20, G:0.34, T:0.18
Consensus pattern (20 bp):
GTGCATCGATGCACAGCAGG
Found at i:438669 original size:40 final size:40
Alignment explanation
Indices: 438608--438718 Score: 177
Period size: 40 Copynumber: 2.8 Consensus size: 40
438598 TGTAGCCTTC
* **
438608 GTGCATGGATACACAACAGGGTGCATCGATGCATAGCAGG
1 GTGCATCGATACACAGGAGGGTGCATCGATGCATAGCAGG
*
438648 GTGCATCGATGCACAGGAGGGTGCATCGATGCATAGCAGG
1 GTGCATCGATACACAGGAGGGTGCATCGATGCATAGCAGG
*
438688 GTGCATCGATACACAGGAGGATGCATCGATG
1 GTGCATCGATACACAGGAGGGTGCATCGATG
438719 TACTAATTGT
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 65 1.00
ACGTcount: A:0.28, C:0.20, G:0.34, T:0.18
Consensus pattern (40 bp):
GTGCATCGATACACAGGAGGGTGCATCGATGCATAGCAGG
Found at i:438809 original size:21 final size:21
Alignment explanation
Indices: 438742--438882 Score: 155
Period size: 21 Copynumber: 6.7 Consensus size: 21
438732 CGGTGTTTGA
* **
438742 GTGCATGGATGCATTGT-ATG
1 GTGCATGGATGCACTGTCGGG
* *
438762 GTGCATCGATGCACTAGT-GCAG
1 GTGCATGGATGCACT-GTCG-GG
438784 GTGCATGGATGCACTGTCGGG
1 GTGCATGGATGCACTGTCGGG
438805 GTGCATGGATGCACTG-CTGGG
1 GTGCATGGATGCACTGTC-GGG
*
438826 GTGCATGGATGCACTGCCGGG
1 GTGCATGGATGCACTGTCGGG
438847 GTGCATGGATGCACTG-CAGGG
1 GTGCATGGATGCACTGTC-GGG
*
438868 GTGTATGGATGCACT
1 GTGCATGGATGCACT
438883 TTGACACACT
Statistics
Matches: 108, Mismatches: 7, Indels: 11
0.86 0.06 0.09
Matches are distributed among these distances:
20 15 0.14
21 76 0.70
22 17 0.16
ACGTcount: A:0.18, C:0.18, G:0.39, T:0.25
Consensus pattern (21 bp):
GTGCATGGATGCACTGTCGGG
Found at i:438815 original size:63 final size:63
Alignment explanation
Indices: 438742--438882 Score: 171
Period size: 63 Copynumber: 2.2 Consensus size: 63
438732 CGGTGTTTGA
* * *
438742 GTGCATGGATGCATTG-TATGGTGCATCGATGCACTAG-TGCAGGTGCATGGATGCACTGTC-GG
1 GTGCATGGATGCACTGCTAGGGTGCATCGATGCACT-GCCG-AGGTGCATGGATGCACTG-CAGG
438804 G
63 G
* * *
438805 GTGCATGGATGCACTGCTGGGGTGCATGGATGCACTGCCGGGGTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTGCTAGGGTGCATCGATGCACTGCCGAGGTGCATGGATGCACTGCAGGG
*
438868 GTGTATGGATGCACT
1 GTGCATGGATGCACT
438883 TTGACACACT
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
62 1 0.01
63 50 0.74
64 17 0.25
ACGTcount: A:0.18, C:0.18, G:0.39, T:0.25
Consensus pattern (63 bp):
GTGCATGGATGCACTGCTAGGGTGCATCGATGCACTGCCGAGGTGCATGGATGCACTGCAGGG
Found at i:439833 original size:44 final size:44
Alignment explanation
Indices: 439783--439957 Score: 244
Period size: 44 Copynumber: 4.0 Consensus size: 44
439773 ATACCATGAG
* * *
439783 TGGCACCTTTCTACCAATAATGCATCATTATGCATTTTCATTTA
1 TGGCACATTTCTGCCAATAATGCATCGTTATGCATTTTCATTTA
* * *
439827 TGGCACCTTTCTGCCAATAATTCATTGTTATGCATTTTCATTTA
1 TGGCACATTTCTGCCAATAATGCATCGTTATGCATTTTCATTTA
* * *
439871 TGGCACATTTCTGCCAGTAATGCACCGTTATGCATTTTCATTAA
1 TGGCACATTTCTGCCAATAATGCATCGTTATGCATTTTCATTTA
*
439915 TGGCACATTTCTGCCAATAATGCA-CTGTTATGTATTTTCATTT
1 TGGCACATTTCTGCCAATAATGCATC-GTTATGCATTTTCATTT
439958 TTTTCGGTAA
Statistics
Matches: 117, Mismatches: 13, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
43 1 0.01
44 116 0.99
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.42
Consensus pattern (44 bp):
TGGCACATTTCTGCCAATAATGCATCGTTATGCATTTTCATTTA
Found at i:446724 original size:54 final size:54
Alignment explanation
Indices: 446599--446916 Score: 318
Period size: 54 Copynumber: 5.9 Consensus size: 54
446589 CCCATAATGA
* * * * * ** **
446599 CAATATAGTAATTCATGAACTCATTATGAATTGCATGGGGTTGCACACTTAGTGC
1 CAATACAGAAATTCATAAACTTATTATGAATTTC-TTAGGTTGCACACACAGTGC
** * *
446654 CAATATGGAAATTCATAAACTTATTATGAATTTATTAGGTTGCAAACACA-TGAC
1 CAATACAGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACACAGTG-C
* * * *
446708 CAAAACATAAATTCATAAACATATTATGAATTTCTTAGGCTGCACACACAGTGC
1 CAATACAGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACACAGTGC
** * * * *
446762 CAATATGGAAATTCATAAATTTATTATGGATTTCATAGGTTGCACACACAGTGT
1 CAATACAGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACACAGTGC
* * *
446816 CGATACAAAAATTCAT-AACTTATTATGAATTTCTTAGGTTGCATACACAGTGC
1 CAATACAGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACACAGTGC
* * * *
446869 CAATACGGAAACTCATAAA-TATATTATAAATTTCTTAAGTTGCACACA
1 CAATACAGAAATTCATAAACT-TATTATGAATTTCTTAGGTTGCACACA
446917 AACTGATCAT
Statistics
Matches: 214, Mismatches: 45, Indels: 9
0.80 0.17 0.03
Matches are distributed among these distances:
53 47 0.22
54 137 0.64
55 30 0.14
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (54 bp):
CAATACAGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACACAGTGC
Found at i:446888 original size:107 final size:108
Alignment explanation
Indices: 446608--446916 Score: 363
Period size: 107 Copynumber: 2.9 Consensus size: 108
446598 ACAATATAGT
* * * ** **
446608 AATTCATGAACTCATTATGAATTGCATGGGGTTGCACACTTAGTGCCAATATGGAAATTCATAAA
1 AATTCATAAACTTATTATGAATTTC-TTAGGTTGCACACACAGTGCCAATATGGAAATTCATAAA
* * *
446673 CTTATTATGAATTT-ATTAGGTTGCAAACACATGACCAAAACATA
65 TTTATTATGAATTTCA-TAGGTTGCACACACATGACCAAAACAAA
* *
446717 AATTCATAAACATATTATGAATTTCTTAGGCTGCACACACAGTGCCAATATGGAAATTCATAAAT
1 AATTCATAAACTTATTATGAATTTCTTAGGTTGCACACACAGTGCCAATATGGAAATTCATAAAT
* * * *
446782 TTATTATGGATTTCATAGGTTGCACACACAGTG-TCGATACAAA
66 TTATTATGAATTTCATAGGTTGCACACACA-TGACCAAAACAAA
* * *
446825 AATTCAT-AACTTATTATGAATTTCTTAGGTTGCATACACAGTGCCAATACGGAAACTCATAAAT
1 AATTCATAAACTTATTATGAATTTCTTAGGTTGCACACACAGTGCCAATATGGAAATTCATAAAT
* * * *
446889 ATATTATAAATTTCTTAAGTTGCACACA
66 TTATTATGAATTTCATAGGTTGCACACA
446917 AACTGATCAT
Statistics
Matches: 172, Mismatches: 26, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
107 75 0.44
108 73 0.42
109 24 0.14
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (108 bp):
AATTCATAAACTTATTATGAATTTCTTAGGTTGCACACACAGTGCCAATATGGAAATTCATAAAT
TTATTATGAATTTCATAGGTTGCACACACATGACCAAAACAAA
Found at i:447935 original size:11 final size:11
Alignment explanation
Indices: 447919--447945 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
447909 TTCCCCCTTT
447919 TCCCTCTTAAA
1 TCCCTCTTAAA
447930 TCCCTCTTAAA
1 TCCCTCTTAAA
447941 TCCCT
1 TCCCT
447946 AATAAGGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.22, C:0.41, G:0.00, T:0.37
Consensus pattern (11 bp):
TCCCTCTTAAA
Found at i:453183 original size:54 final size:54
Alignment explanation
Indices: 453057--453386 Score: 365
Period size: 54 Copynumber: 6.1 Consensus size: 54
453047 TTGCACCCGT
* * ** * * ** **
453057 AGTGACAATACAGTAATTCACCAACTCATTATGAATTACATGGGGTTGCACACTT
1 AGTGCCAATACAGAAATTCATAAACTTATTATGAATTTC-TTAGGTTGCACACAC
* *
453112 AGTGCCAATAACA-AAATTCATAAACTTGTTATGAATTTCTTCGGTTGCACACAC
1 AGTGCCAAT-ACAGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACAC
* * *
453166 AGGGCCAATACACAAATTCATAAACATATTATGAATTTCTTAGGTTGCACACAC
1 AGTGCCAATACAGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACAC
* * *
453220 AGTACCAATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTGCACACAC
1 AGTGCCAATACAGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACAC
* * * * *
453274 ATTGCCAATACAGAAATTTATAAACTTTTTTTGAATTTCTTAGGTTGCACACGC
1 AGTGCCAATACAGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACAC
* ** * * * *
453328 AGTGTCAATATGGATATTCATAAACATAATATGAATTTCTTAGGTTTCACACAC
1 AGTGCCAATACAGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACAC
453382 AGTGC
1 AGTGC
453387 TCATTCGATA
Statistics
Matches: 231, Mismatches: 42, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
53 3 0.01
54 197 0.85
55 28 0.12
56 3 0.01
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.32
Consensus pattern (54 bp):
AGTGCCAATACAGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACAC
Found at i:454691 original size:44 final size:44
Alignment explanation
Indices: 454642--454854 Score: 270
Period size: 44 Copynumber: 4.8 Consensus size: 44
454632 ATTACAATGA
454642 ATTTTCATTTATGACACATTTCTGCCAATAATGCACCGTTATGC
1 ATTTTCATTTATGACACATTTCTGCCAATAATGCACCGTTATGC
* *
454686 ATTTTCATTTATGGCACATTTCTGGCAATAATGCACCGTTATGC
1 ATTTTCATTTATGACACATTTCTGCCAATAATGCACCGTTATGC
* ** * * *
454730 ATTTTCATTTATGCCACCCTTGTTCCAATAATGCACCCTTATGC
1 ATTTTCATTTATGACACATTTCTGCCAATAATGCACCGTTATGC
* *
454774 ATTTTGC-TTTATGGA-ACATTTCTAG-CAATAATGTACCGTTATAC
1 ATTTT-CATTTAT-GACACATTTCT-GCCAATAATGCACCGTTATGC
* *
454818 ATTTTCATTTATGGCACCTTTCTGCCAATAATGCACC
1 ATTTTCATTTATGACACATTTCTGCCAATAATGCACC
454855 ATAACACAAC
Statistics
Matches: 143, Mismatches: 20, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
43 3 0.02
44 138 0.97
45 2 0.01
ACGTcount: A:0.26, C:0.23, G:0.12, T:0.39
Consensus pattern (44 bp):
ATTTTCATTTATGACACATTTCTGCCAATAATGCACCGTTATGC
Found at i:454762 original size:88 final size:88
Alignment explanation
Indices: 454642--454854 Score: 311
Period size: 88 Copynumber: 2.4 Consensus size: 88
454632 ATTACAATGA
* * *
454642 ATTTTCATTTATGACACATTTCTGCCAATAATGCACCGTTATGCATTTT-CATTTATGGCACATT
1 ATTTTCATTTATGACACCTTTCTGCCAATAATGCACCCTTATGCATTTTGC-TTTATGGAACATT
* *
454706 TCTGGCAATAATGCACCGTTATGC
65 TCTAGCAATAATGCACCGTTATAC
* * * *
454730 ATTTTCATTTATGCCACCCTTGTTCCAATAATGCACCCTTATGCATTTTGCTTTATGGAACATTT
1 ATTTTCATTTATGACACCTTTCTGCCAATAATGCACCCTTATGCATTTTGCTTTATGGAACATTT
*
454795 CTAGCAATAATGTACCGTTATAC
66 CTAGCAATAATGCACCGTTATAC
*
454818 ATTTTCATTTATGGCACCTTTCTGCCAATAATGCACC
1 ATTTTCATTTATGACACCTTTCTGCCAATAATGCACC
454855 ATAACACAAC
Statistics
Matches: 110, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
88 109 0.99
89 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.12, T:0.39
Consensus pattern (88 bp):
ATTTTCATTTATGACACCTTTCTGCCAATAATGCACCCTTATGCATTTTGCTTTATGGAACATTT
CTAGCAATAATGCACCGTTATAC
Found at i:457863 original size:32 final size:32
Alignment explanation
Indices: 457768--457856 Score: 169
Period size: 32 Copynumber: 2.8 Consensus size: 32
457758 TTTTTGAGTT
457768 AGTTAAGTGCATCGCTACTACATTAGTCTTTC
1 AGTTAAGTGCATCGCTACTACATTAGTCTTTC
457800 AGTTAAGTGCATCGCTACTACATTAGTCTTTC
1 AGTTAAGTGCATCGCTACTACATTAGTCTTTC
*
457832 AGTTAAGTGCATCGCCACTACATTA
1 AGTTAAGTGCATCGCTACTACATTA
457857 CACTTTCCAA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 56 1.00
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (32 bp):
AGTTAAGTGCATCGCTACTACATTAGTCTTTC
Found at i:463262 original size:44 final size:44
Alignment explanation
Indices: 463201--463465 Score: 363
Period size: 44 Copynumber: 6.0 Consensus size: 44
463191 ATACCATGAG
* * *
463201 TGGCACATTTCGGCCAATAATGCACCGTTATGCATTTTTATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
463245 TGGCACCTTTCAT-CCAATAATGCACCGCTT-TGCATTTTCATTTA
1 TGGCACCTTTC-TGCCAATAATGCACCG-TTATGCATTTTCATTTA
* * *
463289 TGGCACCTTTCTGTCAATAATACACAGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
*
463333 TGGCACCTTTCTGCCAATAATGCACCGTTATGCACTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * * *
463377 TGGCACATTTCTGCCAATAATACATCGTAATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* ** *
463421 TGGTATATTTCTGCCAATCATGCACCGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
463465 T
1 T
463466 TTCGGTAGCA
Statistics
Matches: 196, Mismatches: 21, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
43 3 0.02
44 191 0.97
45 2 0.01
ACGTcount: A:0.25, C:0.23, G:0.13, T:0.40
Consensus pattern (44 bp):
TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
Found at i:471350 original size:15 final size:15
Alignment explanation
Indices: 471332--471418 Score: 51
Period size: 15 Copynumber: 5.9 Consensus size: 15
471322 TCTCTCATTT
471332 TTTTTTCTATTTTTC
1 TTTTTTCTATTTTTC
**
471347 TTTTCTTCTCGTTTTC
1 TTTT-TTCTATTTTTC
* *
471363 ATTTTT-T-TTCTTC
1 TTTTTTCTATTTTTC
471376 TTCGTTTTC-A-TTTTC
1 TT--TTTTCTATTTTTC
471391 -TTTTTCTATATTTTC
1 TTTTTTCTAT-TTTTC
*
471406 -TTTTCCTATTTTT
1 TTTTTTCTATTTTT
471419 TTTCTTCTTC
Statistics
Matches: 56, Mismatches: 8, Indels: 17
0.69 0.10 0.21
Matches are distributed among these distances:
12 5 0.09
13 6 0.11
14 6 0.11
15 27 0.48
16 12 0.21
ACGTcount: A:0.07, C:0.17, G:0.02, T:0.74
Consensus pattern (15 bp):
TTTTTTCTATTTTTC
Found at i:471367 original size:6 final size:5
Alignment explanation
Indices: 471342--471441 Score: 51
Period size: 5 Copynumber: 18.4 Consensus size: 5
471332 TTTTTTCTAT
*
471342 TTTTC TTTTC TTCTC GTTTTC ATTTT- TTTTC TTCTTC GTTTTC ATTTTC
1 TTTTC TTTTC TTTTC -TTTTC -TTTTC TTTTC TT-TTC -TTTTC -TTTTC
* * * *
471391 TTTT- TCTATA TTTTC TTTTCC TATTTT TTTTC TTCTTC TGTTTT TTTTC
1 TTTTC T-TTTC TTTTC TTTT-C T-TTTC TTTTC TT-TTC T-TTTC TTTTC
471440 TT
1 TT
471442 CTTATAATAT
Statistics
Matches: 74, Mismatches: 11, Indels: 20
0.70 0.10 0.19
Matches are distributed among these distances:
4 5 0.07
5 33 0.45
6 30 0.41
7 6 0.08
ACGTcount: A:0.05, C:0.18, G:0.03, T:0.74
Consensus pattern (5 bp):
TTTTC
Found at i:471373 original size:21 final size:23
Alignment explanation
Indices: 471342--471394 Score: 92
Period size: 22 Copynumber: 2.4 Consensus size: 23
471332 TTTTTTCTAT
471342 TTTTCTTTTCTTC-TCGTTTTCA
1 TTTTCTTTTCTTCTTCGTTTTCA
471364 TTTT-TTTTCTTCTTCGTTTTCA
1 TTTTCTTTTCTTCTTCGTTTTCA
471386 TTTTCTTTT
1 TTTTCTTTT
471395 TCTATATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
21 8 0.28
22 17 0.59
23 4 0.14
ACGTcount: A:0.04, C:0.19, G:0.04, T:0.74
Consensus pattern (23 bp):
TTTTCTTTTCTTCTTCGTTTTCA
Found at i:471404 original size:21 final size:22
Alignment explanation
Indices: 471342--471410 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 22
471332 TTTTTTCTAT
*
471342 TTTTCTTTTCTTC-TCGTTTTCA
1 TTTTC-TTTCTTCTTCATTTTCA
* *
471364 TTTTTTTTCTTCTTCGTTTTCA
1 TTTTCTTTCTTCTTCATTTTCA
471386 TTTTCTTT-TTCTAT-ATTTTC-
1 TTTTCTTTCTTCT-TCATTTTCA
471406 TTTTC
1 TTTTC
471411 CTATTTTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
20 5 0.12
21 16 0.38
22 21 0.50
ACGTcount: A:0.06, C:0.19, G:0.03, T:0.72
Consensus pattern (22 bp):
TTTTCTTTCTTCTTCATTTTCA
Found at i:471426 original size:20 final size:19
Alignment explanation
Indices: 471403--471444 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
471393 TTTCTATATT
471403 TTCTTTTCCTATTTTTTTTC
1 TTCTTTT-CTATTTTTTTTC
*
471423 TTC--TTCTGTTTTTTTTC
1 TTCTTTTCTATTTTTTTTC
471440 TTCTT
1 TTCTT
471445 ATAATATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 5
0.76 0.04 0.20
Matches are distributed among these distances:
17 14 0.74
18 2 0.11
20 3 0.16
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.76
Consensus pattern (19 bp):
TTCTTTTCTATTTTTTTTC
Found at i:471435 original size:26 final size:26
Alignment explanation
Indices: 471332--471435 Score: 73
Period size: 26 Copynumber: 4.2 Consensus size: 26
471322 TCTCTCATTT
* *
471332 TTTTTTCTATTTTTCTT-TTCTTCTCG
1 TTTTTCCTATTTTTTTTCTTCTTCT-G
471358 -TTTT-C-ATTTTTTTTCTTCTTC-G
1 TTTTTCCTATTTTTTTTCTTCTTCTG
* *
471380 -TTTTCAT-TTTCTTTTTCTATATT-T-
1 TTTTTCCTATTT-TTTTTCT-TCTTCTG
471404 TCTTTTCCTATTTTTTTTCTTCTTCTG
1 T-TTTTCCTATTTTTTTTCTTCTTCTG
471431 TTTTT
1 TTTTT
471436 TTTCTTCTTA
Statistics
Matches: 62, Mismatches: 5, Indels: 22
0.70 0.06 0.25
Matches are distributed among these distances:
22 5 0.08
23 11 0.18
24 14 0.23
25 10 0.16
26 18 0.29
27 4 0.06
ACGTcount: A:0.06, C:0.17, G:0.03, T:0.74
Consensus pattern (26 bp):
TTTTTCCTATTTTTTTTCTTCTTCTG
Found at i:472550 original size:6 final size:6
Alignment explanation
Indices: 472533--472563 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
472523 ACCCTTGTAT
*
472533 CATGAC CGTGAC CATGAC CATGAC CATGAC C
1 CATGAC CATGAC CATGAC CATGAC CATGAC C
472564 CATAGGTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.29, C:0.35, G:0.19, T:0.16
Consensus pattern (6 bp):
CATGAC
Found at i:476886 original size:20 final size:19
Alignment explanation
Indices: 476861--476910 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 19
476851 TGTTTTCATT
476861 GAAAAATACAAA-AAAATAAA
1 GAAAAATA-AAAGAAAA-AAA
476881 GAAAAAATAAAAGAAAAAAA
1 G-AAAAATAAAAGAAAAAAA
476901 GAAAAA-AAAA
1 GAAAAATAAAA
476911 TTATCAAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 4 0.14
19 5 0.18
20 8 0.29
21 11 0.39
ACGTcount: A:0.84, C:0.02, G:0.08, T:0.06
Consensus pattern (19 bp):
GAAAAATAAAAGAAAAAAA
Found at i:476887 original size:12 final size:12
Alignment explanation
Indices: 476870--476910 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
476860 TGAAAAATAC
476870 AAAAAAATAAAG
1 AAAAAAATAAAG
476882 -AAAAAATAAAAG
1 AAAAAAAT-AAAG
*
476894 AAAAAAAGAAA-
1 AAAAAAATAAAG
476905 AAAAAA
1 AAAAAA
476911 TTATCAAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
11 13 0.50
12 7 0.27
13 6 0.23
ACGTcount: A:0.88, C:0.00, G:0.07, T:0.05
Consensus pattern (12 bp):
AAAAAAATAAAG
Found at i:476908 original size:11 final size:12
Alignment explanation
Indices: 476870--476910 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
476860 TGAAAAATAC
*
476870 AAAAAAATAAAG
1 AAAAAAAGAAAG
476882 AAAAAATA-AAAG
1 AAAAAA-AGAAAG
476894 AAAAAAAGAAA-
1 AAAAAAAGAAAG
476905 AAAAAA
1 AAAAAA
476911 TTATCAAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 7 0.26
12 19 0.70
13 1 0.04
ACGTcount: A:0.88, C:0.00, G:0.07, T:0.05
Consensus pattern (12 bp):
AAAAAAAGAAAG
Found at i:483668 original size:20 final size:20
Alignment explanation
Indices: 483640--483710 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
483630 GATCCCTTTT
*
483640 GAAAA-GGATCAATCAATTG
1 GAAAAGGGATCAATCCATTG
* * *
483659 GAAAAGGGATCTATCCCTTTT
1 GAAAAGGGATCAAT-CCATTG
**
483680 GAAAAAAGATCAATCCATTG
1 GAAAAGGGATCAATCCATTG
483700 GAAAAGGGATC
1 GAAAAGGGATC
483711 CATCGCTTAT
Statistics
Matches: 39, Mismatches: 11, Indels: 3
0.74 0.21 0.06
Matches are distributed among these distances:
19 5 0.13
20 20 0.51
21 14 0.36
ACGTcount: A:0.42, C:0.14, G:0.21, T:0.23
Consensus pattern (20 bp):
GAAAAGGGATCAATCCATTG
Found at i:483701 original size:41 final size:41
Alignment explanation
Indices: 483626--483724 Score: 137
Period size: 41 Copynumber: 2.4 Consensus size: 41
483616 TCAAGAAAAT
* *
483626 GATCGATCCCTTTTG-AAAAGGATCAATCAATTGGAAAAGG
1 GATCCATCCCTTTTGAAAAAAGATCAATCAATTGGAAAAGG
* *
483666 GATCTATCCCTTTTGAAAAAAGATCAATCCATTGGAAAAGG
1 GATCCATCCCTTTTGAAAAAAGATCAATCAATTGGAAAAGG
* *
483707 GATCCATCGCTTATGAAA
1 GATCCATCCCTTTTGAAA
483725 GTTTAGCTAC
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 14 0.27
41 38 0.73
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.26
Consensus pattern (41 bp):
GATCCATCCCTTTTGAAAAAAGATCAATCAATTGGAAAAGG
Found at i:490750 original size:76 final size:72
Alignment explanation
Indices: 490643--490789 Score: 165
Period size: 76 Copynumber: 2.0 Consensus size: 72
490633 CCCGAATATA
* *
490643 TTAAGTAAACATTAAAAGAATCAATTTAGATTACAACTCTTTTAATCGGTATA-TAATTCGAAAT
1 TTAAATAAACATTAAAAGAATCAATTCAGATTACAACTC-TTTAAT--GTATATTAATT-G-AAT
490707 AATTAAATAAGT
61 AATTAAATAAGT
* *
490719 TTAAATAAACATT-AAAGATTAT-AATTCAGATTATAAGTCTTTAATGTATATTTAATTGAATAA
1 TTAAATAAACATTAAAAGA--ATCAATTCAGATTACAACTCTTTAATGTATA-TTAATTGAATAA
490782 TTAAATAA
63 TTAAATAA
490790 TATTTATTGT
Statistics
Matches: 63, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
73 18 0.29
74 1 0.02
75 16 0.25
76 26 0.41
77 2 0.03
ACGTcount: A:0.47, C:0.07, G:0.08, T:0.38
Consensus pattern (72 bp):
TTAAATAAACATTAAAAGAATCAATTCAGATTACAACTCTTTAATGTATATTAATTGAATAATTA
AATAAGT
Found at i:497268 original size:317 final size:319
Alignment explanation
Indices: 496827--497468 Score: 1204
Period size: 317 Copynumber: 2.0 Consensus size: 319
496817 TATCAAGAAA
496827 TAATAAATGGGCTATACAAGTGTGATTATTCTAAGACTTGTGCCTATCTAGATATAAAGACAAAA
1 TAATAAATGGGCTATACAAGTGTGATTATTCTAAGACTTGTGCCTATCTAGATATAAAGACAAAA
496892 GGATGTAAACATAAAAGAGTTAATCACGAAGATGATATGTTGAATCATAATTTCTTGTAACTTAG
66 GGATGTAAACATAAAAGAGTTAATCACGAAGATGATATGTTGAATCATAATTTCTTGTAACTTAG
496957 GTGACAATGATATATTGCTAGTTGTCACTCGTTGTATGTAATATTAGAA-TGTTCTAATAATTAC
131 GTGACAATGATATATTGCTAGTTGTCACTCGTTGTATGTAATATTAGAATTGTTCTAATAATTAC
497021 TACTAACGTTACAAGAACCTTCAGGGTCACACCCTAGGATTGAAATGAGGAAAAATGTATAATTT
196 TACTAACGTTACAAGAACCTTCAGGGTCACACCCTAGGATTGAAATGAGGAAAAATGTATAATTT
497086 G-TG-TGTTACTAAAA-ATATCTAGATTTATG-ATGTATACCTGATATACATATGATTT
261 GTTGATGTTACTAAAATATATCTAGATTTATGAATGTATACCTGATATACATATGATTT
497141 TAATAAATGGGCTATACAAGTGTGATTATTCTAAGACTTGTGCCTATTCTAGATATAAAGGACAA
1 TAATAAATGGGCTATACAAGTGTGATTATTCTAAGACTTGTGCCTA-TCTAGATATAAA-GACAA
497206 AAGGATGTAAAACATAAAAGAGTTAATCACGAAGATGATATGTTGAATCATAATTTCTTGTAACT
64 AAGGATGT-AAACATAAAAGAGTTAATCACGAAGATGATATGTTGAATCATAATTTCTTGTAACT
497271 TAGGTGACAATGATATATTGCTAGTTGTCACTCGTTGTATGTAATATTAGAATTGTTCTAATAAT
128 TAGGTGACAATGATATATTGCTAGTTGTCACTCGTTGTATGTAATATTAGAATTGTTCTAATAAT
497336 TACTACTAACGTTACAAGAACCTTCAGGGTCACACCCTAGGATTGAAATGAGGAAAAATGTATAA
193 TACTACTAACGTTACAAGAACCTTCAGGGTCACACCCTAGGATTGAAATGAGGAAAAATGTATAA
497401 TTTGTTGTATGTTACTAAAATATATCTAGATTTATGATATGTATACCTGATATACATATGATTT
258 TTTGTTG-ATGTTACTAAAATATATCTAGATTTATGA-ATGTATACCTGATATACATATGATTT
497465 TAAT
1 TAAT
497469 TATCCCGAAT
Statistics
Matches: 318, Mismatches: 0, Indels: 10
0.97 0.00 0.03
Matches are distributed among these distances:
314 46 0.14
315 12 0.04
316 13 0.04
317 108 0.34
318 81 0.25
319 2 0.01
321 11 0.03
322 15 0.05
324 30 0.09
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.35
Consensus pattern (319 bp):
TAATAAATGGGCTATACAAGTGTGATTATTCTAAGACTTGTGCCTATCTAGATATAAAGACAAAA
GGATGTAAACATAAAAGAGTTAATCACGAAGATGATATGTTGAATCATAATTTCTTGTAACTTAG
GTGACAATGATATATTGCTAGTTGTCACTCGTTGTATGTAATATTAGAATTGTTCTAATAATTAC
TACTAACGTTACAAGAACCTTCAGGGTCACACCCTAGGATTGAAATGAGGAAAAATGTATAATTT
GTTGATGTTACTAAAATATATCTAGATTTATGAATGTATACCTGATATACATATGATTT
Found at i:500845 original size:22 final size:21
Alignment explanation
Indices: 500804--501010 Score: 198
Period size: 22 Copynumber: 9.6 Consensus size: 21
500794 AATAATAATA
* * *
500804 TATATAATATTTTTTCAAAAC
1 TATATTATATATTTTAAAAAC
*
500825 TATATTATATATTTTAAAAAAT
1 TATATTATATATTTT-AAAAAC
* * *
500847 TATATAATATGTTTTCAAAAC
1 TATATTATATATTTTAAAAAC
*
500868 TATATTATATATTTTCAAAAAT
1 TATATTATATATTTT-AAAAAC
* * *
500890 TATATAATATGTTTTCAAAAC
1 TATATTATATATTTTAAAAAC
*
500911 TATATTATATATTTTCAAAAAT
1 TATATTATATATTTT-AAAAAC
* * *
500933 TATATAATATGTTTTCAAAAC
1 TATATTATATATTTTAAAAAC
*
500954 TATATTATATATTTTCAAAAAT
1 TATATTATATATTTT-AAAAAC
* *
500976 TATATAATATGTTTTCAAAAAAC
1 TATATTATATATTTT--AAAAAC
500999 TATATTATATAT
1 TATATTATATAT
501011 ATTATATGCA
Statistics
Matches: 147, Mismatches: 34, Indels: 8
0.78 0.18 0.04
Matches are distributed among these distances:
21 64 0.44
22 68 0.46
23 15 0.10
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (21 bp):
TATATTATATATTTTAAAAAC
Found at i:500851 original size:43 final size:43
Alignment explanation
Indices: 500804--501010 Score: 378
Period size: 43 Copynumber: 4.8 Consensus size: 43
500794 AATAATAATA
* *
500804 TATATAATATTTTTTCAAAACTATATTATATATTTTAAAAAAT
1 TATATAATATGTTTTCAAAACTATATTATATATTTTCAAAAAT
500847 TATATAATATGTTTTCAAAACTATATTATATATTTTCAAAAAT
1 TATATAATATGTTTTCAAAACTATATTATATATTTTCAAAAAT
500890 TATATAATATGTTTTCAAAACTATATTATATATTTTCAAAAAT
1 TATATAATATGTTTTCAAAACTATATTATATATTTTCAAAAAT
500933 TATATAATATGTTTTCAAAACTATATTATATATTTTCAAAAAT
1 TATATAATATGTTTTCAAAACTATATTATATATTTTCAAAAAT
500976 TATATAATATGTTTTCAAAAAACTATATTATATAT
1 TATATAATATGTTTTC--AAAACTATATTATATAT
501011 ATTATATGCA
Statistics
Matches: 160, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
43 143 0.89
45 17 0.11
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (43 bp):
TATATAATATGTTTTCAAAACTATATTATATATTTTCAAAAAT
Found at i:502031 original size:34 final size:35
Alignment explanation
Indices: 501988--502058 Score: 135
Period size: 34 Copynumber: 2.1 Consensus size: 35
501978 TTTAGAAACA
501988 AATTAGATGTGCGCACATCATAACATATT-GGTAC
1 AATTAGATGTGCGCACATCATAACATATTGGGTAC
502022 AATTAGATGTGCGCACATCATAACATATTGGGTAC
1 AATTAGATGTGCGCACATCATAACATATTGGGTAC
502057 AA
1 AA
502059 AAATGGAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 29 0.81
35 7 0.19
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.28
Consensus pattern (35 bp):
AATTAGATGTGCGCACATCATAACATATTGGGTAC
Found at i:503821 original size:16 final size:16
Alignment explanation
Indices: 503800--503830 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
503790 ATTCAGGCTC
503800 CATCCAAAACCCTAAT
1 CATCCAAAACCCTAAT
*
503816 CATCCAAAGCCCTAA
1 CATCCAAAACCCTAA
503831 CCGATTGGGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.39, G:0.03, T:0.16
Consensus pattern (16 bp):
CATCCAAAACCCTAAT
Found at i:505845 original size:46 final size:45
Alignment explanation
Indices: 505773--505864 Score: 130
Period size: 46 Copynumber: 2.0 Consensus size: 45
505763 TCTTTTACTA
* * * * *
505773 TTAATCCCATAAGCTCGTAAGTTTATTTTACCAATATACTTTCCAT
1 TTAATACCATAAGCTCATAAGCTTATTTTACC-ATACACTTGCCAT
505819 TTAATACCATAAGCTCATAAGCTTATTTTACCATACACTTGCCAT
1 TTAATACCATAAGCTCATAAGCTTATTTTACCATACACTTGCCAT
505864 T
1 T
505865 ATTCCATAAC
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
45 12 0.29
46 29 0.71
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.39
Consensus pattern (45 bp):
TTAATACCATAAGCTCATAAGCTTATTTTACCATACACTTGCCAT
Found at i:508334 original size:26 final size:26
Alignment explanation
Indices: 508305--508354 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
508295 GATGCTTGCA
508305 AAAAGGATGTTAACAAGAAAATACTC
1 AAAAGGATGTTAACAAGAAAATACTC
508331 AAAAGGATGTTAACAAGAAAATAC
1 AAAAGGATGTTAACAAGAAAATAC
508355 CTCTTTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.56, C:0.10, G:0.16, T:0.18
Consensus pattern (26 bp):
AAAAGGATGTTAACAAGAAAATACTC
Found at i:508530 original size:29 final size:31
Alignment explanation
Indices: 508497--508568 Score: 78
Period size: 29 Copynumber: 2.4 Consensus size: 31
508487 CAAATTTTGG
*
508497 TTAGTGACCAAAATATAAA-TTTTG-AAAGT
1 TTAGTGACCAAAATATAAACTTTGGAAAAGT
* *
508526 TTAGTTG-CTAAAGTATAAACTTTGGAAAAGT
1 TTAG-TGACCAAAATATAAACTTTGGAAAAGT
*
508557 TTAATGACCAAA
1 TTAGTGACCAAA
508569 GTAGTAATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
29 14 0.41
30 8 0.24
31 12 0.35
ACGTcount: A:0.43, C:0.08, G:0.15, T:0.33
Consensus pattern (31 bp):
TTAGTGACCAAAATATAAACTTTGGAAAAGT
Found at i:508570 original size:31 final size:30
Alignment explanation
Indices: 508497--508571 Score: 75
Period size: 31 Copynumber: 2.5 Consensus size: 30
508487 CAAATTTTGG
* *
508497 TTAG-TGACCAAAATATAAATTTTGAAAGT
1 TTAGATGACCAAAGTATAAATTTGGAAAGT
* *
508526 TTAGTTG-CTAAAGTATAAACTTTGGAAAAGT
1 TTAGATGACCAAAGTATAAA-TTTGG-AAAGT
508557 TTA-ATGACCAAAGTA
1 TTAGATGACCAAAGTA
508572 GTAATTTTCC
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
29 14 0.38
30 8 0.22
31 15 0.41
ACGTcount: A:0.43, C:0.08, G:0.16, T:0.33
Consensus pattern (30 bp):
TTAGATGACCAAAGTATAAATTTGGAAAGT
Found at i:513322 original size:35 final size:35
Alignment explanation
Indices: 513259--513358 Score: 119
Period size: 35 Copynumber: 2.7 Consensus size: 35
513249 TTTCGTCCTA
*
513259 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
1 CTAGGATTC-AACTC-CTAAAATAGGATAGAATTCTG
*
513296 CTAGGATTCAACTCCTAAAATAGGATAGAATTTTG
1 CTAGGATTCAACTCCTAAAATAGGATAGAATTCTG
** *
513331 CTATGTTTTAAACTCCTAAAGATAGGAT
1 CTA-GGATTCAACTCCTAAA-ATAGGAT
513359 CCACAAGCAC
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
35 22 0.39
36 18 0.32
37 16 0.29
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (35 bp):
CTAGGATTCAACTCCTAAAATAGGATAGAATTCTG
Found at i:513670 original size:23 final size:22
Alignment explanation
Indices: 513639--513700 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
513629 CTTTTCTTTT
513639 TTTTCATGTAATATTTTTTTTAC
1 TTTT-ATGTAATATTTTTTTTAC
*
513662 ATTTTATGT-ATTTTCTTTTTTAC
1 -TTTTATGTAATATT-TTTTTTAC
513685 -TTTA-GTATATATTTTT
1 TTTTATGTA-ATATTTTT
513701 ATTTTTTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
20 2 0.06
21 7 0.21
22 8 0.24
23 12 0.36
24 4 0.12
ACGTcount: A:0.21, C:0.06, G:0.05, T:0.68
Consensus pattern (22 bp):
TTTTATGTAATATTTTTTTTAC
Found at i:513697 original size:24 final size:23
Alignment explanation
Indices: 513654--513699 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
513644 ATGTAATATT
*
513654 TTTTTTACATTTTATGTATTTTC
1 TTTTTTACATTTTATATATTTTC
513677 TTTTTTAC-TTTAGTATATATTTT
1 TTTTTTACATTT--TATATATTTT
513700 TATTTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 3 0.15
23 8 0.40
24 9 0.45
ACGTcount: A:0.20, C:0.07, G:0.04, T:0.70
Consensus pattern (23 bp):
TTTTTTACATTTTATATATTTTC
Found at i:513798 original size:38 final size:37
Alignment explanation
Indices: 513747--513831 Score: 129
Period size: 37 Copynumber: 2.3 Consensus size: 37
513737 ATTATCAGTT
*
513747 TTATTAATTTATATATATATA-TTTTACTTTTT-TTA
1 TTATTTATTTATATATATATATTTTTACTTTTTATTA
*
513782 TTTTTTATGTTATATATATATATTTTTACTTTTTATTA
1 TTATTTAT-TTATATATATATATTTTTACTTTTTATTA
513820 TTATTTATTTAT
1 TTATTTATTTAT
513832 TTGTTTTATT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
35 6 0.14
36 13 0.30
37 15 0.34
38 10 0.23
ACGTcount: A:0.28, C:0.02, G:0.01, T:0.68
Consensus pattern (37 bp):
TTATTTATTTATATATATATATTTTTACTTTTTATTA
Found at i:513816 original size:44 final size:45
Alignment explanation
Indices: 513768--513883 Score: 116
Period size: 44 Copynumber: 2.6 Consensus size: 45
513758 TATATATATA
*
513768 TTTTACTT-TTTTTATTTTTTATGTTATATATATATA-TTTTTACT
1 TTTTACTTATTTTTATTTATT-TGTTATATATATATATTTTTTACT
* * * *
513812 TTTTA-TTATTATTTATTTATTTGTTTTATTTCTATATTTTTTTCT
1 TTTTACTTATT-TTTATTTATTTGTTATATATATATATTTTTTACT
* *
513857 TTTT-CTTCTTTTTCTTTATTT-TTATAT
1 TTTTACTTATTTTTATTTATTTGTTATAT
513884 TTATTTTACT
Statistics
Matches: 60, Mismatches: 8, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
43 7 0.12
44 29 0.48
45 24 0.40
ACGTcount: A:0.18, C:0.06, G:0.02, T:0.74
Consensus pattern (45 bp):
TTTTACTTATTTTTATTTATTTGTTATATATATATATTTTTTACT
Found at i:513996 original size:15 final size:15
Alignment explanation
Indices: 513978--514007 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
513968 TATTTATTTC
513978 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
513993 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
514008 ACATGGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (15 bp):
TTACCTTTTTATCTA
Found at i:516435 original size:8 final size:8
Alignment explanation
Indices: 516422--516460 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
516412 GAACATTTCA
*
516422 TGCATTCT
1 TGCATTTT
516430 TGCA-TTT
1 TGCATTTT
516437 TGCATTTT
1 TGCATTTT
*
516445 TGCCTTTT
1 TGCATTTT
516453 TGCATTTT
1 TGCATTTT
516461 CATCTACATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.10, C:0.18, G:0.13, T:0.59
Consensus pattern (8 bp):
TGCATTTT
Found at i:517600 original size:24 final size:24
Alignment explanation
Indices: 517573--517641 Score: 70
Period size: 24 Copynumber: 3.0 Consensus size: 24
517563 ATAAAAAAGG
517573 CAAAAAAAAAAAAGAAGCAAAAAA
1 CAAAAAAAAAAAAGAAGCAAAAAA
**
517597 CAAAAGCAAAAAAGAA-C-AAAAA
1 CAAAAAAAAAAAAGAAGCAAAAAA
* * **
517619 GAAAAAAGAAAAAGGGGCAAAAA
1 CAAAAAAAAAAAAGAAGCAAAAA
517642 GCACATGCAA
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
22 15 0.43
23 2 0.06
24 18 0.51
ACGTcount: A:0.77, C:0.09, G:0.14, T:0.00
Consensus pattern (24 bp):
CAAAAAAAAAAAAGAAGCAAAAAA
Found at i:517607 original size:23 final size:24
Alignment explanation
Indices: 517574--517631 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
517564 TAAAAAAGGC
517574 AAAAAA-AAAAAAGAAGCAAAAA-
1 AAAAAAGAAAAAAGAAGCAAAAAG
*
517596 ACAAAAGCAAAAAAGAA-CAAAAAG
1 AAAAAAG-AAAAAAGAAGCAAAAAG
517620 AAAAAAGAAAAA
1 AAAAAAGAAAAA
517632 GGGGCAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 5 0.16
23 11 0.35
24 15 0.48
ACGTcount: A:0.83, C:0.07, G:0.10, T:0.00
Consensus pattern (24 bp):
AAAAAAGAAAAAAGAAGCAAAAAG
Found at i:517614 original size:16 final size:16
Alignment explanation
Indices: 517581--517628 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 16
517571 GGCAAAAAAA
517581 AAAAAGAAGCAAAA-AAC
1 AAAAAGAA--AAAAGAAC
517598 -AAAAGCAAAAAAGAAC
1 AAAAAG-AAAAAAGAAC
517614 AAAAAGAAAAAAGAA
1 AAAAAGAAAAAAGAA
517629 AAAGGGGCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
15 4 0.14
16 17 0.61
17 7 0.25
ACGTcount: A:0.79, C:0.08, G:0.12, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAAAAGAAC
Found at i:518263 original size:22 final size:22
Alignment explanation
Indices: 518235--518285 Score: 86
Period size: 22 Copynumber: 2.3 Consensus size: 22
518225 CCCCATCAAT
518235 CCTTTGAGCATCAAATAG-CAAA
1 CCTTTGAGCATCAAAT-GCCAAA
518257 CCTTTGAGCATCAAATGCCAAA
1 CCTTTGAGCATCAAATGCCAAA
518279 CCTTTGA
1 CCTTTGA
518286 CCAAACACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 1 0.04
22 27 0.96
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.25
Consensus pattern (22 bp):
CCTTTGAGCATCAAATGCCAAA
Found at i:519322 original size:102 final size:102
Alignment explanation
Indices: 519146--519722 Score: 1046
Period size: 102 Copynumber: 5.6 Consensus size: 102
519136 GTGCTCACTA
*
519146 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGA
1 TTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGA
*
519211 AACATAAACATTGAAAACATTTCCCTTGAAATGAGTT
66 AACATAAACATTGAAAACATTTCCCTTGAAATGAATT
* ** *
519248 TTGTCTCTCTTGAGATAATTTCCCTTGAAACAAAATTCCGTCTCCATTGAGACAGTTTCTCTTGA
1 TTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGA
*
519313 AACATAAACATTGGAAACATTTCCCTTGAAATGAATT
66 AACATAAACATTGAAAACATTTCCCTTGAAATGAATT
519350 TTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGA
1 TTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGA
519415 AACATAAACATTGAAAACATTTCCCTTGAAATGAATT
66 AACATAAACATTGAAAACATTTCCCTTGAAATGAATT
519452 TTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGA
1 TTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGA
519517 AACATAAACATTGAAAACATTTCCCTTGAAATGAATT
66 AACATAAACATTGAAAACATTTCCCTTGAAATGAATT
*
519554 TTGTCTCTCTTGAGATAGTTTCCCTCGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGA
1 TTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGA
519619 AACATAAACATTGAAAACATTTCCCTTGAAATGAATT
66 AACATAAACATTGAAAACATTTCCCTTGAAATGAATT
* * *
519656 TCGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTTCTCTTG
1 TTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG-TTTCTCTTG
519721 AA
65 AA
519723 GCATCATCTT
Statistics
Matches: 457, Mismatches: 17, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
102 446 0.98
103 11 0.02
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.37
Consensus pattern (102 bp):
TTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGA
AACATAAACATTGAAAACATTTCCCTTGAAATGAATT
Found at i:519399 original size:37 final size:37
Alignment explanation
Indices: 519332--519418 Score: 122
Period size: 37 Copynumber: 2.4 Consensus size: 37
519322 ATTGGAAACA
** * *
519332 TTTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
519368 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
*
519405 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
519419 TAAACATTGA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 12 0.27
37 33 0.73
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
Found at i:519501 original size:37 final size:37
Alignment explanation
Indices: 519434--519520 Score: 122
Period size: 37 Copynumber: 2.4 Consensus size: 37
519424 ATTGAAAACA
** * *
519434 TTTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
519470 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
*
519507 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
519521 TAAACATTGA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 12 0.27
37 33 0.73
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
Found at i:519593 original size:37 final size:37
Alignment explanation
Indices: 519550--519622 Score: 110
Period size: 37 Copynumber: 2.0 Consensus size: 37
519540 CCTTGAAATG
* *
519550 AATTTTGTCTCTCTTGAGATAGTTTCCCTCGAAACAA
1 AATTTTGTCTCCCTTGAGACAGTTTCCCTCGAAACAA
* *
519587 AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 AATTTTGTCTCCCTTGAGACAGTTTCCCTCGAAACA
519623 TAAACATTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.38
Consensus pattern (37 bp):
AATTTTGTCTCCCTTGAGACAGTTTCCCTCGAAACAA
Found at i:519865 original size:37 final size:37
Alignment explanation
Indices: 519795--519866 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
519785 TGGAACTAAG
* * **
519795 TTTTATCTCTCTTGAGACAGTTTTTCTTAAAACAAAA
1 TTTTATCTCCCTTAAGACAGTTTCCCTTAAAACAAAA
* *
519832 TTTTATCTCCCTTAAGACCGTTTCCCTTGAAACAA
1 TTTTATCTCCCTTAAGACAGTTTCCCTTAAAACAA
519867 CAAATATCTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.29, C:0.22, G:0.08, T:0.40
Consensus pattern (37 bp):
TTTTATCTCCCTTAAGACAGTTTCCCTTAAAACAAAA
Found at i:520444 original size:105 final size:105
Alignment explanation
Indices: 520327--521215 Score: 866
Period size: 105 Copynumber: 8.5 Consensus size: 105
520317 GAAGCCAAAC
* * *
520327 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTC-AGACAACGCAAAT
1 TTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC-TCGAGACAACACAAGT
* * ** *
520391 TCAACTTCACGACGAAGGGACCGCTGCCTGTCAACAACAAC
65 TCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAACAAT
** *
520432 TTCTCAATTTCAGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACACAAGTT
1 TTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTT
*
520497 CAACTTCACAACGAAGGGACGGCTGGTTGTCAACAATAAT
66 CAACTTCACAACGAAGGGACGGCTGGTTGTCAACAACAAT
* * * * * *
520537 TTC-CTAGTTTCAGGGCCAATTTCAACTTCACAGCGAAGGATATTGGACCCAAGACAGCACAAGC
1 TTCTC-AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGT
* * ** *
520601 TCAACTTCACAGCGAAGGGGCGGCTGACTGT---CGACAA-
65 TCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAACAAT
* * * * **
520638 ---GCAATTTCGGAGCTAATCTCAACTTCACAGCGAAAAATATTGGACTCGAGACAACACAAGTT
1 TTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTT
*
520700 CAACTTCACAGCGAAGGGACGGCTGGTTGTCAACAAACAAT
66 CAACTTCACAACGAAGGGACGGCTGGTTGTCAAC-AACAAT
* * * * * *
520741 TTCCCAATTCCAGAGCCGATTTCAACTCCAC-GAC-AGAGGATATCGTGCTACCCGAGACAACAC
1 TTCTCAATTTCAGAGCCAATTTCAACTTCACAG-CGA-AGGATAT--TG-GACTCGAGACAACAC
520804 AAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACT
61 AAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC-AACAA-T
* ** * * * * *
520851 TT-TCAGTTTCA-TCCGCGATTTTAACTCCAC-GACGGAGGATATCGTGCCACTCGAGACAACAC
1 TTCTCAATTTCAGAGC-CAATTTCAACTTCACAG-CGAAGGATAT--TG-GACTCGAGACAACAC
* *
520913 AAATTCAACTTCACAACGAAGGGACGGCTGGTTGTTAACAA-ACAT
61 AAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAACA-AT
* * **
520958 TTTTCAAATTTCAGAGCTAATTTCAACTTCGTAGCGAAGGATATTGGACTCGAGACAACACAAGT
1 TTCTC-AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGT
* *
521023 TCAACTTCACAACGAAGGGACGGCTGATTGTCAACAA-GA-
65 TCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAACAAT
* * * * * *
521062 TT-TC--GTTCAGAGTCAATTTCATCTTCACAGCGAAGGATATTAGACTCGAGACAGCACAAGCT
1 TTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTT
* **
521124 CAACTTCACAGCGAAGAGG-CGGCTGACTGTCAACAAACAAT
66 CAACTTCACAACGAAG-GGACGGCTGGTTGTCAAC-AACAAT
* * * * *
521165 TTCCCAGTTCCAGAACCAATTTCAACTTCACAGCGGAGGATATTGGACTCG
1 TTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCG
521216 GAACAATATT
Statistics
Matches: 656, Mismatches: 97, Indels: 61
0.81 0.12 0.07
Matches are distributed among these distances:
98 76 0.12
99 1 0.00
100 78 0.12
101 5 0.01
102 9 0.01
103 4 0.01
104 6 0.01
105 177 0.27
106 116 0.18
107 6 0.01
108 8 0.01
109 165 0.25
110 5 0.01
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (105 bp):
TTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTT
CAACTTCACAACGAAGGGACGGCTGGTTGTCAACAACAAT
Found at i:520696 original size:98 final size:97
Alignment explanation
Indices: 520551--521214 Score: 402
Period size: 109 Copynumber: 6.4 Consensus size: 97
520541 TAGTTTCAGG
* * *
520551 GCCAATTTCAACTTCACAGCGAAGGATATTGGACCCAAGACAGCACAAGCTCAACTTCACAGCGA
1 GCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAGCGA
* ** *
520616 AGGGGCGGCTGACTGTCGACAAGCAATTTCGGA
66 AGGGACGGCTGGTTGTCAACAA-CAATTTCGGA
* * ** *
520649 GCTAATCTCAACTTCACAGCGAAAAATATTGGACTCGAGACAACACAAGTTCAACTTCACAGCGA
1 GCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAGCGA
*
520714 AGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTCCAGA
66 AGGGACGGCTGGTTGTCAAC-AACAA--T-----TT-CGGA
* * * * *
520755 GCCGATTTCAACTCCAC-GAC-AGAGGATATCGTGCTACCCGAGACAACACAAGTTCAACTTCAC
1 GCCAATTTCAACTTCACAG-CGA-AGGATAT--TG-GACTCAAGACAACACAAGTTCAACTTCAC
* *
520818 AACGAAGGGACGGCTGGTTGTCAACGAACAACTTTTCAGTTTCA
61 AGCGAAGGGACGGCTGGTTGTCAAC-AACAA--TTTC-G---GA
* * * * * * * *
520862 TCCGCGATTTTAACTCCAC-GACGGAGGATATCGTGCCACTCGAGACAACACAAATTCAACTTCA
1 -GC-CAATTTCAACTTCACAG-CGAAGGATAT--TG-GACTCAAGACAACACAAGTTCAACTTCA
* * *
520926 CAACGAAGGGACGGCTGGTTGTTAACAAACATTTTTCAAATTTCAGA
60 CAGCGAAGGGACGGCTGGTTG-T--C-AACA----AC-AATTTCGGA
* ** * *
520973 GCTAATTTCAACTTCGTAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGA
1 GCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAGCGA
* *
521038 AGGGACGGCTGATTGTCAACAA-GATTTCGTTCAGA
66 AGGGACGGCTGGTTGTCAACAACAATTTCG----GA
* * * * * *
521073 GTCAATTTCATCTTCACAGCGAAGGATATTAGACTCGAGACAGCACAAGCTCAACTTCACAGCGA
1 GCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAGCGA
**
521138 AGAGG-CGGCTGACTGTCAACAAACAATTTCCCAGTTCCAGA
66 AG-GGACGGCTGGTTGTCAAC-AACAATTT--C-G-----GA
* *
521179 ACCAATTTCAACTTCACAGCGGAGGATATTGGACTC
1 GCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
521215 GGAACAATAT
Statistics
Matches: 458, Mismatches: 66, Indels: 76
0.76 0.11 0.13
Matches are distributed among these distances:
96 5 0.01
98 76 0.17
99 2 0.00
100 75 0.16
101 4 0.01
102 8 0.02
103 2 0.00
104 3 0.01
105 6 0.01
106 104 0.23
107 3 0.01
108 3 0.01
109 151 0.33
110 3 0.01
111 1 0.00
112 2 0.00
113 3 0.01
115 4 0.01
116 1 0.00
117 2 0.00
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (97 bp):
GCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAGCGA
AGGGACGGCTGGTTGTCAACAACAATTTCGGA
Found at i:521206 original size:424 final size:413
Alignment explanation
Indices: 520331--521214 Score: 1062
Period size: 424 Copynumber: 2.1 Consensus size: 413
520321 CCAAACTTCT
* * * * *
520331 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAATTCAAC
1 CAATTCCAGAGCCAATTTCAACTTCACAGCGGAGGATATTGGACTCCAGACAACACAAATTCAAC
* * *
520396 TTCACGACGAAGGGACCGCTGCCTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTC
66 TTCACAACGAAGGGACCGCTGCCTGTCAACAACAACTTCTCAATTTCACAGCCAATTTCAACTCC
* * *
520461 ACAATGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTG
131 ACAACGAAGGATATTGCACTCCAGACAACACAAATTCAACTTCACAACGAAGGGACGGCTGGTTG
* * *
520526 TCAACAATAATTTCCTAGTTTCAGGGCCAATTTCAACTTCACAGCGAAGGATATTGGACCCAAGA
196 TCAACAATAATTTCCAAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACCCAAGA
* * * *
520591 CAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCGACAAGCAATTTCGGAGCTAATC
261 CAACACAAGCTCAACTTCACAACGAAGGGACGGCTGACTGTCAACAAG-AATTTCGGAGCTAATC
* *
520656 TCAACTTCACAGCGAAAAATATTGGACTCGAGACAACACAAGTTCAACTTCACAGCGAAGGGACG
325 TCAACTTCACAGCGAAAAATATTAGACTCGAGACAACACAAGCTCAACTTCACAGCGAAGGGACG
**
520721 GCTGGTTGTCAACAAACAATTTCC
390 GCTGACTGTCAACAAACAATTTCC
* * * * *
520745 CAATTCCAGAGCCGATTTCAACTCCAC-GACAGAGGATATCGTG-CTACCCGAGACAACACAAGT
1 CAATTCCAGAGCCAATTTCAACTTCACAG-CGGAGGATATTG-GACT--CC-AGACAACACAAAT
* ** * * * *
520808 TCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTTTCAGTTTCATCCG-CGATTT
61 TCAACTTCACAACGAAGGGACCGCTGCCTGTCAAC-AACAACTTCTCAATTTCA-CAGCCAATTT
* * * *
520872 TAACTCCACGACGGAGGATATCGTGCCACTCGAGACAACACAAATTCAACTTCACAACGAAGGGA
124 CAACTCCACAACGAAGGATAT--TG-CACTCCAGACAACACAAATTCAACTTCACAACGAAGGGA
* * * **
520937 CGGCTGGTTGTTAACAA-ACATTTTTCAAATTTCAGAGCTAATTTCAACTTCGTAGCGAAGGATA
186 CGGCTGGTTGTCAACAATA-A-TTTCCAAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATA
* * * *
521001 TTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAG-ATTT
249 TTGGACCCAAGACAACACAAGCTCAACTTCACAACGAAGGGACGGCTGACTGTCAACAAGAATTT
* * ** *
521065 CGTTCAGAG-TCAATTTCATCTTCACAGCGAAGGATATTAGACTCGAGACAGCACAAGCTCAACT
314 CG----GAGCT-AATCTCAACTTCACAGCGAAAAATATTAGACTCGAGACAACACAAGCTCAACT
521129 TCACAGCGAAGAGG-CGGCTGACTGTCAACAAACAATTTCC
374 TCACAGCGAAG-GGACGGCTGACTGTCAACAAACAATTTCC
* *
521169 CAGTTCCAGAACCAATTTCAACTTCACAGCGGAGGATATTGGACTC
1 CAATTCCAGAGCCAATTTCAACTTCACAGCGGAGGATATTGGACTC
521215 GGAACAATAT
Statistics
Matches: 392, Mismatches: 58, Indels: 32
0.81 0.12 0.07
Matches are distributed among these distances:
414 35 0.09
415 1 0.00
416 1 0.00
417 42 0.11
418 37 0.09
419 1 0.00
420 9 0.02
421 53 0.14
422 89 0.23
423 2 0.01
424 119 0.30
425 3 0.01
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (413 bp):
CAATTCCAGAGCCAATTTCAACTTCACAGCGGAGGATATTGGACTCCAGACAACACAAATTCAAC
TTCACAACGAAGGGACCGCTGCCTGTCAACAACAACTTCTCAATTTCACAGCCAATTTCAACTCC
ACAACGAAGGATATTGCACTCCAGACAACACAAATTCAACTTCACAACGAAGGGACGGCTGGTTG
TCAACAATAATTTCCAAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACCCAAGA
CAACACAAGCTCAACTTCACAACGAAGGGACGGCTGACTGTCAACAAGAATTTCGGAGCTAATCT
CAACTTCACAGCGAAAAATATTAGACTCGAGACAACACAAGCTCAACTTCACAGCGAAGGGACGG
CTGACTGTCAACAAACAATTTCC
Found at i:521739 original size:35 final size:35
Alignment explanation
Indices: 521676--521775 Score: 119
Period size: 35 Copynumber: 2.7 Consensus size: 35
521666 TTTCGTCCTA
*
521676 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
1 CTAGGATTC-AACTC-CTAAAATAGGATAGAATTCTG
*
521713 CTAGGATTCAACTCCTAAAATAGGATAGAATTTTG
1 CTAGGATTCAACTCCTAAAATAGGATAGAATTCTG
** *
521748 CTATGTTTTAAACTCCTAAAGATAGGAT
1 CTA-GGATTCAACTCCTAAA-ATAGGAT
521776 CCATAAGCAC
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
35 22 0.39
36 18 0.32
37 16 0.29
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (35 bp):
CTAGGATTCAACTCCTAAAATAGGATAGAATTCTG
Found at i:522085 original size:24 final size:23
Alignment explanation
Indices: 522039--522120 Score: 64
Period size: 23 Copynumber: 3.5 Consensus size: 23
522029 ATTTTTTTGT
**
522039 TATTTTTCTTTTTTTTTTCATGTAA
1 TATTTTT-TTTTACTTTT-ATGTAA
522064 TATTTTTTTTTACATTTTATGT-A
1 TATTTTTTTTTAC-TTTTATGTAA
522087 T-TTTCTTTTTTAC-TTTA-GTATA
1 TATTT-TTTTTTACTTTTATGTA-A
522109 TATTTTTATTTT
1 TATTTTT-TTTT
522121 TTTAGATTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
20 2 0.04
21 4 0.08
22 7 0.14
23 17 0.35
24 8 0.16
25 11 0.22
ACGTcount: A:0.18, C:0.06, G:0.04, T:0.72
Consensus pattern (23 bp):
TATTTTTTTTTACTTTTATGTAA
Found at i:522197 original size:6 final size:6
Alignment explanation
Indices: 522188--522297 Score: 50
Period size: 6 Copynumber: 17.7 Consensus size: 6
522178 ATATTTACTT
* * * * *
522188 TTTTTA TTTTTT TATTTTA TATATA -TATTA TTTTTA CTTTTTTA TTATTA
1 TTTTTA TTTTTA T-TTTTA TTTTTA TTTTTA TTTTTA --TTTTTA TTTTTA
522238 -TTTTA TTTATT- TGTTTTA TTTCTATA TTTTT- TTCTTT- TTCTTTA
1 TTTTTA TTT-TTA T-TTTTA TTT-T-TA TTTTTA TT-TTTA TT-TTTA
*
522282 TTTTTA TATTTA TTTT
1 TTTTTA TTTTTA TTTT
522298 ACTTACTATT
Statistics
Matches: 80, Mismatches: 12, Indels: 24
0.69 0.10 0.21
Matches are distributed among these distances:
5 8 0.10
6 47 0.59
7 14 0.17
8 11 0.14
ACGTcount: A:0.19, C:0.04, G:0.01, T:0.76
Consensus pattern (6 bp):
TTTTTA
Found at i:522211 original size:30 final size:29
Alignment explanation
Indices: 522175--522267 Score: 96
Period size: 30 Copynumber: 3.0 Consensus size: 29
522165 TTTATATATA
522175 TATATATTTACTTTTTTTATTTTTTTATTT
1 TATATATTTA-TTTTTTTATTTTTTTATTT
* *
522205 TATATATATATTATTTTTACTTTTTTATTAT
1 TATATATTTATT-TTTTTATTTTTTTATT-T
* * *
522236 TATTTTATTTATTTGTTTTATTTCTATATTT
1 TA-TATATTTATTT-TTTTATTTTTTTATTT
522267 T
1 T
522268 TTTCTTTTTC
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
29 2 0.04
30 24 0.46
31 6 0.12
32 20 0.38
ACGTcount: A:0.23, C:0.03, G:0.01, T:0.73
Consensus pattern (29 bp):
TATATATTTATTTTTTTATTTTTTTATTT
Found at i:522230 original size:25 final size:23
Alignment explanation
Indices: 522192--522276 Score: 79
Period size: 23 Copynumber: 3.7 Consensus size: 23
522182 TTACTTTTTT
*
522192 TATTTTTTTA-TTTTATA-TATA
1 TATTTTTTTACTTTTTTATTATA
522213 TATTATTTTTACTTTTTTATTAT-
1 TATT-TTTTTACTTTTTTATTATA
* *
522236 TATTTTATTTATTTGTTTTATTTCTA
1 TATTTT-TTTACTT-TTTTA-TTATA
522262 TATTTTTTT-CTTTTT
1 TATTTTTTTACTTTTT
522277 CTTTATTTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
21 4 0.08
22 8 0.15
23 19 0.36
24 10 0.19
25 6 0.11
26 6 0.11
ACGTcount: A:0.20, C:0.04, G:0.01, T:0.75
Consensus pattern (23 bp):
TATTTTTTTACTTTTTTATTATA
Found at i:522239 original size:36 final size:37
Alignment explanation
Indices: 522157--522243 Score: 115
Period size: 38 Copynumber: 2.4 Consensus size: 37
522147 TATTATCAGT
*
522157 TTTATTAATTTATATATATATATATTTACTTTTTTTA
1 TTTATTATTTTATATATATATATATTTACTTTTTTTA
* *
522194 TTTTTTTATTTTATATATATATTATTTTTAC-TTTTTTA
1 -TTTATTATTTTATATATATA-TATATTTACTTTTTTTA
522232 -TTATTATTTTAT
1 TTTATTATTTTAT
522244 TTATTTGTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
36 11 0.25
38 25 0.57
39 8 0.18
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (37 bp):
TTTATTATTTTATATATATATATATTTACTTTTTTTA
Found at i:522258 original size:38 final size:39
Alignment explanation
Indices: 522165--522245 Score: 119
Period size: 41 Copynumber: 2.1 Consensus size: 39
522155 GTTTTATTAA
* *
522165 TTTATATATATA-TATATTTACTTTTTTTATTTTTTTAT
1 TTTATATATATATTATTTTTACTTTTTTTATTATTTTAT
522203 TTTATATATATATTATTTTTACTTTTTTATTATTATTTTAT
1 TTTATATATATATTATTTTTAC-TTTTT-TTATTATTTTAT
522244 TT
1 TT
522246 ATTTGTTTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
38 12 0.32
39 8 0.21
40 5 0.13
41 13 0.34
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (39 bp):
TTTATATATATATTATTTTTACTTTTTTTATTATTTTAT
Found at i:522264 original size:83 final size:79
Alignment explanation
Indices: 522142--522295 Score: 175
Period size: 83 Copynumber: 1.9 Consensus size: 79
522132 TATAAATATA
* *
522142 TTTTTTATTATCAGTTTTATTAATTTATATATATATATATTTACTTTTTTTATTTTTTTATTTTA
1 TTTTTTATTATCAGTTTTATTAATTTATATATATATATATTT--TTTTCTT-TTTCTTTATTTT-
522207 TATATATATTATTTTTAC
62 TATATATATTATTTTTAC
* * * * * *
522225 TTTTTTATTATTA-TTTTATTTATTTGTTTTATTTCTATATTTTTTTCTTTTTCTTTATTTTTAT
1 TTTTTTATTATCAGTTTTATTAATTT-ATATATATATATATTTTTTTCTTTTTCTTTATTTTTAT
*
522289 ATTTATT
65 ATATATT
522296 TTACTTACTA
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
79 9 0.15
80 11 0.18
81 6 0.10
82 11 0.18
83 24 0.39
ACGTcount: A:0.23, C:0.04, G:0.01, T:0.72
Consensus pattern (79 bp):
TTTTTTATTATCAGTTTTATTAATTTATATATATATATATTTTTTTCTTTTTCTTTATTTTTATA
TATATTATTTTTAC
Found at i:522265 original size:26 final size:25
Alignment explanation
Indices: 522189--522296 Score: 82
Period size: 26 Copynumber: 4.3 Consensus size: 25
522179 TATTTACTTT
* *
522189 TTTTATTTTTTTATTTTATATATATA
1 TTTTATTTATTT-TTTTATTTATATA
*
522215 TTATT-TTTACTTTTTTA-TTAT-TA
1 TT-TTATTTATTTTTTTATTTATATA
*
522238 TTTTATTTATTTGTTTTATTTCTATA
1 TTTTATTTATTT-TTTTATTTATATA
* *
522264 TTTT-TTTCTTTTTCTTTATTTTTATA
1 TTTTATTT-ATTTT-TTTATTTATATA
522290 -TTTATTT
1 TTTTATTT
522297 TACTTACTAT
Statistics
Matches: 67, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
22 2 0.03
23 10 0.15
24 8 0.12
25 15 0.22
26 30 0.45
27 2 0.03
ACGTcount: A:0.19, C:0.04, G:0.01, T:0.76
Consensus pattern (25 bp):
TTTTATTTATTTTTTTATTTATATA
Done.