Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 74 of 208
Found at i:21518385 original size:10 final size:10
Alignment explanation
Indices: 21518370--21518394 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
21518360 TTTTGGCTTA
21518370 ATAATTTTAC
1 ATAATTTTAC
21518380 ATAATTTTAC
1 ATAATTTTAC
21518390 ATAAT
1 ATAAT
21518395 GTTAGATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (10 bp):
ATAATTTTAC
Found at i:21518510 original size:121 final size:122
Alignment explanation
Indices: 21518313--21518538 Score: 418
Period size: 121 Copynumber: 1.9 Consensus size: 122
21518303 TTTTGGACTT
* *
21518313 AATAATTTTACATATTTTGATAATATTACTAACCATTAACAAAAAAATTTTGGCTTAATAATTTT
1 AATAATTTTACATATTTTGATAATATTACTAACCATTAACAAAAAAAATTTGGCTTAATAATTTC
21518378 ACATAATTTTACATAATGTTAGATTTGGTAAAATGTTTTGTCTGGAACTAACAATTA
66 ACATAATTTTACATAATGTTAGATTTGGTAAAATGTTTTGTCTGGAACTAACAATTA
21518435 AATAATTTTACATATTTTGATAATATTACTAACCATTAA-AAAAAAAATTTGGCTTAATAATTTC
1 AATAATTTTACATATTTTGATAATATTACTAACCATTAACAAAAAAAATTTGGCTTAATAATTTC
*
21518499 ACATACTTTTACATAATGTTAGATTTGGTAAAATGTTTTG
66 ACATAATTTTACATAATGTTAGATTTGGTAAAATGTTTTG
21518539 GCTTAATTAT
Statistics
Matches: 101, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
121 62 0.61
122 39 0.39
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.42
Consensus pattern (122 bp):
AATAATTTTACATATTTTGATAATATTACTAACCATTAACAAAAAAAATTTGGCTTAATAATTTC
ACATAATTTTACATAATGTTAGATTTGGTAAAATGTTTTGTCTGGAACTAACAATTA
Found at i:21518556 original size:53 final size:53
Alignment explanation
Indices: 21518482--21518591 Score: 193
Period size: 53 Copynumber: 2.1 Consensus size: 53
21518472 AAAAAAAAAA
*
21518482 TTTGGCTTAATAATTTCACATACTTTTACATAATGTTAGATTTGGTAAAATGT
1 TTTGGCTTAATAATTTCACATACTTGTACATAATGTTAGATTTGGTAAAATGT
* *
21518535 TTTGGCTTAATTATTTTACATACTTGTACATAATGTTAGATTTGGTAAAATGT
1 TTTGGCTTAATAATTTCACATACTTGTACATAATGTTAGATTTGGTAAAATGT
21518588 TTTG
1 TTTG
21518592 TCTGGAACTA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.30, C:0.08, G:0.15, T:0.47
Consensus pattern (53 bp):
TTTGGCTTAATAATTTCACATACTTGTACATAATGTTAGATTTGGTAAAATGT
Found at i:21521897 original size:125 final size:125
Alignment explanation
Indices: 21521675--21522024 Score: 557
Period size: 123 Copynumber: 2.8 Consensus size: 125
21521665 CCCAAACTTG
*
21521675 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
1 CTACTGTAGCAAAATCGAGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
* *
21521740 TAGCAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTACATGAC
66 TAGAAGCAATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTACATGAC
* *
21521800 CTACTGTAGCAAAATCGAGTCCACGAGGGCGCGATTTCACAATTTCTACTCAAATAGCATCCTCG
1 CTACTGTAGCAAAATCGAGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
21521865 TAGAAGCAATTTTATACTATTTGCTCAGAAACGTC--AAAAAAATTATTTCTTACATGAC
66 TAGAAGCAATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTACATGAC
* * *
21521923 CTACTATAGCAAAATC-ACGTCCACGAGGGTGTGATTTCACAATTTCTTCTCAAATAGCATCCTG
1 CTACTGTAGCAAAATCGA-GTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTG
*
21521987 GTAGAAG-AGATTTTATACAATTTGAC-CAGAAACGTCAA
65 GTAGAAGCA-ATTTTATACTATTTG-CTCAGAAACGTCAA
21522025 CTCGAAATAA
Statistics
Matches: 209, Mismatches: 11, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
122 2 0.01
123 111 0.53
124 1 0.00
125 95 0.45
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (125 bp):
CTACTGTAGCAAAATCGAGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
TAGAAGCAATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTACATGAC
Found at i:21528261 original size:20 final size:19
Alignment explanation
Indices: 21528224--21528291 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 19
21528214 ACAATTTGGC
*
21528224 ATCGATACCATTTAAAAACT
1 ATCGATA-CATTTAAAAAAT
*
21528244 ATCGATACTTTTATAAAAAT
1 ATCGATACATTTA-AAAAAT
* **
21528264 ATTGATACATAAAATAAAAT
1 ATCGATACATTTAA-AAAAT
21528284 ATCGATAC
1 ATCGATAC
21528292 CTGTGGGTGT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
19 6 0.15
20 33 0.85
ACGTcount: A:0.49, C:0.13, G:0.06, T:0.32
Consensus pattern (19 bp):
ATCGATACATTTAAAAAAT
Found at i:21532389 original size:18 final size:18
Alignment explanation
Indices: 21532366--21532402 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
21532356 AAGCTTCCTT
*
21532366 TAAAATTAATAAGTGAAG
1 TAAAATTAAGAAGTGAAG
21532384 TAAAATTAAGAAGTGAAG
1 TAAAATTAAGAAGTGAAG
21532402 T
1 T
21532403 GATGATCTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.19, T:0.27
Consensus pattern (18 bp):
TAAAATTAAGAAGTGAAG
Found at i:21541381 original size:131 final size:131
Alignment explanation
Indices: 21541140--21541382 Score: 319
Period size: 131 Copynumber: 1.9 Consensus size: 131
21541130 ATTTTTAAAA
* * *
21541140 TAAATATTAATATTATAAGTATATTTAAATTTTCTATCTTCATCTTCTACTTCAACCCATTATTC
1 TAAATATTAATATTACAAGTATATTTAAATTTTCTATCTTCATCTTCTACTTCAACCCATCAATC
* *** *
21541205 TTGTTGTCATCTTCCATATTGGATCTTCTTCTTCAATCTATATCATCATCTGAAATCTATATTTT
66 TCGACATCATCTTCCATATTGGATCTTCTTCTACAATCTATATCATCATCTGAAATCTATATTTT
21541270 T
131 T
* * * * *
21541271 TAAATATTAATATTACAAGTATATTT-AATTTCTCTATTTTGATCTTTTGCTTTAACCCATCAAT
1 TAAATATTAATATTACAAGTATATTTAAATTT-TCTATCTTCATCTTCTACTTCAACCCATCAAT
* *
21541335 CTCGACATCATCTTTCATCTT-GATCTTCTTCTACAATCTATCATCATC
65 CTCGACATCATCTTCCATATTGGATCTTCTTCTACAATCTAT-ATCATC
21541383 TAGACCTACT
Statistics
Matches: 95, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
130 24 0.25
131 71 0.75
ACGTcount: A:0.28, C:0.20, G:0.05, T:0.47
Consensus pattern (131 bp):
TAAATATTAATATTACAAGTATATTTAAATTTTCTATCTTCATCTTCTACTTCAACCCATCAATC
TCGACATCATCTTCCATATTGGATCTTCTTCTACAATCTATATCATCATCTGAAATCTATATTTT
T
Found at i:21550498 original size:23 final size:23
Alignment explanation
Indices: 21550468--21550513 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
21550458 TCAAGTAAGA
21550468 ACACTTACTTCTAGGAATTAGAT
1 ACACTTACTTCTAGGAATTAGAT
*
21550491 ACACTTACTTTTAGGAATTAGAT
1 ACACTTACTTCTAGGAATTAGAT
21550514 TAGATGATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (23 bp):
ACACTTACTTCTAGGAATTAGAT
Found at i:21552440 original size:17 final size:17
Alignment explanation
Indices: 21552399--21552442 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
21552389 TTAGTGAATC
*
21552399 GGAAGCTCGTTCGGGTT
1 GGAAGCTTGTTCGGGTT
21552416 GGAAGCTTGTTCGGGTT
1 GGAAGCTTGTTCGGGTT
21552433 GGAAGCTTGT
1 GGAAGCTTGT
21552443 CAAAGTTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.14, C:0.14, G:0.41, T:0.32
Consensus pattern (17 bp):
GGAAGCTTGTTCGGGTT
Found at i:21560212 original size:27 final size:27
Alignment explanation
Indices: 21560174--21560229 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
21560164 TTATCACACT
21560174 ATCCATCAACTATATC-GATACTTTTGG
1 ATCCATCAACTATATCAG-TACTTTTGG
*
21560201 ATCCATCGACTATATCAGTACTTTTGG
1 ATCCATCAACTATATCAGTACTTTTGG
21560228 AT
1 AT
21560230 GTTTTTAAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 26 0.96
28 1 0.04
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (27 bp):
ATCCATCAACTATATCAGTACTTTTGG
Found at i:21568383 original size:165 final size:164
Alignment explanation
Indices: 21567954--21568456 Score: 794
Period size: 165 Copynumber: 3.1 Consensus size: 164
21567944 TAATTTCATA
* * * * *
21567954 AAAAATCCCTTTACAAAATTTGTTTATTTTACAACAAGAACTCATAATATTTCATTAAATTTAAA
1 AAAAAT-CATTTACAAAACTTGTTTA-TTTACAACAAGGACTCATAATCTTTCATTAAATTTCAA
* * ** * * *
21568019 GAATCATGCAAACATGCTCATGGAAAAACCCTAAAACTTCACCAATTTTGCAAATTAGTCCCTAG
64 GAATCATGCAAACATTCTCATGGAAAAACCCTAAAACTTTAATAGTTTTGCAAAATAGTCCCTGG
21568084 GCTAGCTAGATTAAGCTACAACGACTTCAAAAACAT
129 GCTAGCTAGATTAAGCTACAACGACTTCAAAAACAT
* *
21568120 GAAAATCATTTAAAAAACTTGTTTATTT--AACAAGGACTCATAATCTTTCATTAAATTTCAAGA
1 AAAAATCATTTACAAAACTTGTTTATTTACAACAAGGACTCATAATCTTTCATTAAATTTCAAGA
* *
21568183 ATCATCCAAACATTCTCATGGAAAAACCCTAAAACTTTAATAGTTTTGCAAAATAGTCTCTGGGC
66 ATCATGCAAACATTCTCATGGAAAAACCCTAAAACTTTAATAGTTTTGCAAAATAGTCCCTGGGC
* *
21568248 TAACTAGATTAAGCTACAACGACTTTAAAAACAT
131 TAGCTAGATTAAGCTACAACGACTTCAAAAACAT
21568282 AAAAATCATTTACAAAACTTGTTTATTTAACAACAAGGACTCATAATCTTTCATTAAATTTCAAG
1 AAAAATCATTTACAAAACTTGTTTATTT-ACAACAAGGACTCATAATCTTTCATTAAATTTCAAG
*
21568347 AATCATGCAAACATTCTCATGGAAAAACCCTAAAACTTTAATAGTTTTACAAAATAGTCCCTGGG
65 AATCATGCAAACATTCTCATGGAAAAACCCTAAAACTTTAATAGTTTTGCAAAATAGTCCCTGGG
21568412 CTAGCTAGATTAAGCTACAACGACTTCAAAAACAT
130 CTAGCTAGATTAAGCTACAACGACTTCAAAAACAT
21568447 AAAAATCATT
1 AAAAATCATT
21568457 AAAAACGGGA
Statistics
Matches: 309, Mismatches: 25, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
162 146 0.47
164 3 0.01
165 155 0.50
166 5 0.02
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.30
Consensus pattern (164 bp):
AAAAATCATTTACAAAACTTGTTTATTTACAACAAGGACTCATAATCTTTCATTAAATTTCAAGA
ATCATGCAAACATTCTCATGGAAAAACCCTAAAACTTTAATAGTTTTGCAAAATAGTCCCTGGGC
TAGCTAGATTAAGCTACAACGACTTCAAAAACAT
Found at i:21573255 original size:16 final size:16
Alignment explanation
Indices: 21573225--21573254 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
21573215 ACAATTGTTG
21573225 TTCTATTACTATTTTA
1 TTCTATTACTATTTTA
21573241 TTCTATTACT-TTTT
1 TTCTATTACTATTTT
21573255 TTTATCCCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.20, C:0.13, G:0.00, T:0.67
Consensus pattern (16 bp):
TTCTATTACTATTTTA
Found at i:21579562 original size:5 final size:5
Alignment explanation
Indices: 21579538--21579571 Score: 50
Period size: 5 Copynumber: 6.4 Consensus size: 5
21579528 CCGATTCGTC
21579538 AGGAGA AGGAA AGAGAA AGGAA AGGAA AGGAA AG
1 AGGA-A AGGAA AG-GAA AGGAA AGGAA AGGAA AG
21579572 AGAAGTAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 18 0.67
6 9 0.33
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (5 bp):
AGGAA
Found at i:21581923 original size:25 final size:25
Alignment explanation
Indices: 21581895--21581963 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 25
21581885 TTATCCCAGT
**
21581895 TAAATTTTGAAAAATTTACCCCTGG
1 TAAATTTTGAAAAATTTACCCCTAA
** *
21581920 TAAATTTTTGACGATTTTACCCCTAA
1 TAAA-TTTTGAAAAATTTACCCCTAA
21581946 TAAAATTTTGAGAAAATT
1 T-AAATTTTGA-AAAATT
21581964 CGTTCAATAT
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
25 4 0.12
26 23 0.70
27 6 0.18
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39
Consensus pattern (25 bp):
TAAATTTTGAAAAATTTACCCCTAA
Found at i:21584095 original size:21 final size:21
Alignment explanation
Indices: 21584069--21584108 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
21584059 CAAAACGACG
*
21584069 TGGTTTTGCCTTTTAACTTAA
1 TGGTTTTGACTTTTAACTTAA
21584090 TGGTTTTGACTTTTAACTT
1 TGGTTTTGACTTTTAACTT
21584109 TAGAAAAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.12, G:0.15, T:0.55
Consensus pattern (21 bp):
TGGTTTTGACTTTTAACTTAA
Found at i:21599702 original size:21 final size:21
Alignment explanation
Indices: 21599676--21599725 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
21599666 ATTACGTTTG
*
21599676 TTTTTTTAACTTAA-GAGTTA
1 TTTTTTTAACTTAATGAATTA
*
21599696 TTTTTTTAATTTAATGAATTA
1 TTTTTTTAACTTAATGAATTA
*
21599717 TTTATTTAA
1 TTTTTTTAA
21599726 ATTATTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.32, C:0.02, G:0.06, T:0.60
Consensus pattern (21 bp):
TTTTTTTAACTTAATGAATTA
Found at i:21600198 original size:22 final size:22
Alignment explanation
Indices: 21600170--21600211 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
21600160 TTTATTGTTC
21600170 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
21600192 AAACATGAGAGCTTAGTACG
1 AAACATGAGAGCTTAGTACG
21600212 AGATGTACAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.38, C:0.14, G:0.26, T:0.21
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:21606102 original size:2 final size:2
Alignment explanation
Indices: 21606095--21606148 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
21606085 ATAACTATGT
21606095 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
21606137 CA CA CA CA CA CA
1 CA CA CA CA CA CA
21606149 TTTTCTAGTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:21607628 original size:14 final size:14
Alignment explanation
Indices: 21607611--21607640 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
21607601 TAACCCCCAA
*
21607611 TTACTAACTTGATT
1 TTACTAACTCGATT
21607625 TTACTAACTCGATT
1 TTACTAACTCGATT
21607639 TT
1 TT
21607641 TGGGATGTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.17, G:0.07, T:0.50
Consensus pattern (14 bp):
TTACTAACTCGATT
Found at i:21620703 original size:23 final size:23
Alignment explanation
Indices: 21620675--21620736 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
21620665 TTCTATGTGC
*
21620675 GCAAGTGATAGTGGCACTACGGT
1 GCAAGTGATAATGGCACTACGGT
* * *
21620698 GCAAGTGAAAACGACACTACGGT
1 GCAAGTGATAATGGCACTACGGT
*
21620721 GCAAGTGTTAATGGCA
1 GCAAGTGATAATGGCA
21620737 TTTCGGTGTA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.32, C:0.18, G:0.31, T:0.19
Consensus pattern (23 bp):
GCAAGTGATAATGGCACTACGGT
Found at i:21639018 original size:31 final size:31
Alignment explanation
Indices: 21638960--21639028 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 31
21638950 TTCGATCGTT
* *
21638960 AATTTTGGTTCTTATACTTTTCGAATTA-GA
1 AATTTTAGTTCTTATACTTTTCAAATTATGA
*
21638990 CAATTTTAGTCTCTT-TACTTTTTAAATTATGA
1 -AATTTTAGT-TCTTATACTTTTCAAATTATGA
21639022 AATTTTA
1 AATTTTA
21639029 ATCCTAACCC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 27 0.82
32 6 0.18
ACGTcount: A:0.29, C:0.10, G:0.09, T:0.52
Consensus pattern (31 bp):
AATTTTAGTTCTTATACTTTTCAAATTATGA
Found at i:21642758 original size:7 final size:7
Alignment explanation
Indices: 21642743--21642774 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
21642733 AAATAAAAGA
*
21642743 TTAGAGT
1 TTAGGGT
21642750 TTAGGGT
1 TTAGGGT
21642757 TTAGGGT
1 TTAGGGT
21642764 TTAGGGT
1 TTAGGGT
21642771 TTAG
1 TTAG
21642775 AATTTTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.19, C:0.00, G:0.38, T:0.44
Consensus pattern (7 bp):
TTAGGGT
Found at i:21643182 original size:125 final size:124
Alignment explanation
Indices: 21642905--21643191 Score: 425
Period size: 124 Copynumber: 2.3 Consensus size: 124
21642895 ATTTATTAAG
*
21642905 GAAATCGCTCCCACGTGGACGCGCTTTTGGTACAGTAGGTCCTGAAAAAATAATTTCGAGTTGAC
1 GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCGAGTTGAC
*
21642970 GTTTCTAAGCAAATAGTATAAAAACGCTTCAAACAGGATGCTTTATCAGAAGAATTTCT
66 GTTTCTAAGCAAATAGTATAAAAACGCTTCAAACAGGATGCTTTATCAGAAGAATATCT
* *
21643029 GAAATCGCTCCCATC-TAGACGCGCTTTTGCTACAGTAGGTCTTGAAAAAATAATTTCGAGTTGA
1 GAAATCGCTCCCA-CGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCGAGTTGA
* * * * * *
21643093 CGTTTCTAAGCAAATAGTGTGTAAAACGCTTTAAGCGGGATGCTTTATGAGAAGAAATAT-T
65 CGTTTCTAAGCAAATAGTAT-AAAAACGCTTCAAACAGGATGCTTTATCAGAAG-AATATCT
* *
21643154 GAAATCGCTCCCACGTGGACGTGTTTTTGCTACAGTAG
1 GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAG
21643192 CATGTTTGGG
Statistics
Matches: 146, Mismatches: 13, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
124 79 0.54
125 63 0.43
126 4 0.03
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (124 bp):
GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCGAGTTGAC
GTTTCTAAGCAAATAGTATAAAAACGCTTCAAACAGGATGCTTTATCAGAAGAATATCT
Found at i:21644105 original size:14 final size:14
Alignment explanation
Indices: 21644086--21644114 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
21644076 GCATACTCAC
21644086 CTCCAGCCCACATG
1 CTCCAGCCCACATG
21644100 CTCCAGCCCACATG
1 CTCCAGCCCACATG
21644114 C
1 C
21644115 ATAATGTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.52, G:0.14, T:0.14
Consensus pattern (14 bp):
CTCCAGCCCACATG
Found at i:21646428 original size:49 final size:49
Alignment explanation
Indices: 21646375--21646544 Score: 304
Period size: 49 Copynumber: 3.5 Consensus size: 49
21646365 TAAGAATATT
* *
21646375 AACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATA
1 AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATA
*
21646424 AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTTAAAATA
1 AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATA
*
21646473 AATTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATA
1 AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATA
21646522 AACTATTTTGTATTTTATTACAT
1 AACTATTTTGTATTTTATTACAT
21646545 TAATATAAAC
Statistics
Matches: 115, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
49 115 1.00
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (49 bp):
AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATA
Found at i:21646990 original size:18 final size:18
Alignment explanation
Indices: 21646964--21647006 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
21646954 GACTAGAAAA
* * *
21646964 AGGAAACATATAAGGGTT
1 AGGATACATAAAAAGGTT
21646982 AGGATACATAAAAAGGTT
1 AGGATACATAAAAAGGTT
21647000 AGGATAC
1 AGGATAC
21647007 GCACCTGGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.47, C:0.07, G:0.26, T:0.21
Consensus pattern (18 bp):
AGGATACATAAAAAGGTT
Found at i:21649288 original size:31 final size:29
Alignment explanation
Indices: 21649250--21649316 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 29
21649240 AATTTCAAAA
*
21649250 TTATATATAAATTATAATTTAATGTGTAATT
1 TTATATATAAATTATAATTT--TGTATAATT
* *
21649281 TTATATATAAATTTTTATTTTGTATAATT
1 TTATATATAAATTATAATTTTGTATAATT
21649310 TTATATA
1 TTATATA
21649317 AGAAATTTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 15 0.45
31 18 0.55
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (29 bp):
TTATATATAAATTATAATTTTGTATAATT
Found at i:21649297 original size:27 final size:29
Alignment explanation
Indices: 21649267--21649325 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
21649257 TAAATTATAA
* *
21649267 TTTA-ATGTGTAATTTTATAT-ATAAATT
1 TTTATATGTATAATTTTATATAAGAAATT
*
21649294 TTTATTTTGTATAATTTTATATAAGAAATT
1 TTTA-TATGTATAATTTTATATAAGAAATT
21649324 TT
1 TT
21649326 GATTTTATCT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 4 0.15
29 14 0.54
30 8 0.31
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.58
Consensus pattern (29 bp):
TTTATATGTATAATTTTATATAAGAAATT
Found at i:21649341 original size:30 final size:29
Alignment explanation
Indices: 21649276--21649333 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
21649266 ATTTAATGTG
* * *
21649276 TAATTTTATATATAAATTTTTATTTTGTA
1 TAATTTTATATAGAAATTTTGATTTTATA
21649305 TAATTTTATATAAGAAATTTTGATTTTAT
1 TAATTTTATAT-AGAAATTTTGATTTTAT
21649334 CTTATTTTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (29 bp):
TAATTTTATATAGAAATTTTGATTTTATA
Found at i:21650509 original size:5 final size:5
Alignment explanation
Indices: 21650499--21650524 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
21650489 GAGATGGAAT
21650499 TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA T
21650525 ATATTTGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:21653444 original size:16 final size:16
Alignment explanation
Indices: 21653393--21653455 Score: 72
Period size: 16 Copynumber: 3.9 Consensus size: 16
21653383 GTAATAAGTT
*
21653393 ATGCGAACCCTTATGC
1 ATGCGAACCCTTATGA
* * *
21653409 ATGAGAACCATTATGT
1 ATGCGAACCCTTATGA
21653425 ATGCGAACCCTTATGA
1 ATGCGAACCCTTATGA
* *
21653441 ATGCAAACACTTATG
1 ATGCGAACCCTTATG
21653456 GATTTATTAT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.27
Consensus pattern (16 bp):
ATGCGAACCCTTATGA
Found at i:21653566 original size:24 final size:24
Alignment explanation
Indices: 21653538--21653588 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
21653528 ATATTGTGCG
*
21653538 AACCCTCATACGATTTAATATGCA
1 AACCCTCATACGAATTAATATGCA
** *
21653562 AACCCTCATGTGAATTAGTATGCA
1 AACCCTCATACGAATTAATATGCA
21653586 AAC
1 AAC
21653589 TATCATGTCG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.27
Consensus pattern (24 bp):
AACCCTCATACGAATTAATATGCA
Found at i:21657899 original size:3 final size:3
Alignment explanation
Indices: 21657893--21657950 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
21657883 TATGTTGTTG
21657893 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
21657941 TTA TTA TTA T
1 TTA TTA TTA T
21657951 ATTGTGAAAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:21658298 original size:16 final size:16
Alignment explanation
Indices: 21658277--21658312 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
21658267 TTTGGTTCGC
21658277 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
21658293 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
21658309 TGTA
1 TGTA
21658313 ATAGCAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.36, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:21658569 original size:18 final size:17
Alignment explanation
Indices: 21658548--21658582 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
21658538 TTATTATTAA
*
21658548 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
21658566 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
21658583 TCTTATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:21658719 original size:156 final size:157
Alignment explanation
Indices: 21658435--21658750 Score: 571
Period size: 156 Copynumber: 2.0 Consensus size: 157
21658425 TAGAATACCC
*
21658435 TTAGCATAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
* * * *
21658500 TTATCAGTAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTGTAATTAAAA
21658565 TATATAATTTAATAAAATTCTT-ATAA
131 TATATAATTTAATAAAATTCTTAATAA
*
21658591 TTAGCAGAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
21658656 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTGTAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTGTAATTAAAA
21658721 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
21658748 TTA
1 TTA
21658751 ATATTCTTAT
Statistics
Matches: 153, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
156 146 0.95
157 7 0.05
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (157 bp):
TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTGTAATTAAAA
TATATAATTTAATAAAATTCTTAATAA
Found at i:21658852 original size:14 final size:15
Alignment explanation
Indices: 21658803--21658974 Score: 62
Period size: 15 Copynumber: 11.6 Consensus size: 15
21658793 GTAAAATATA
21658803 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
21658818 TATTAAATATATTAT
1 AATTAAATATATTAT
*
21658833 AATTAAAATATATAATTT
1 AATT-AAATATAT--TAT
* *
21658851 AATAAAAT-TCTTAAT
1 AATTAAATATATT-AT
*
21658866 AATT-AATATTCTTAT
1 AATTAAATA-TATTAT
* *
21658881 -A-TGAATTTACTTA-
1 AATTAAATATA-TTAT
* *
21658894 AATCATAATATATGAT
1 AATTA-AATATATTAT
*
21658910 ACTGTAAA-ATA-TA-
1 AAT-TAAATATATTAT
21658923 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
21658938 TATTAAATATATTAT
1 AATTAAATATATTAT
21658953 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
21658966 AATTTAATA
1 AATTAAATA
21658975 AAATTCTTAA
Statistics
Matches: 117, Mismatches: 20, Indels: 41
0.66 0.11 0.23
Matches are distributed among these distances:
12 3 0.03
13 15 0.13
14 26 0.22
15 40 0.34
16 23 0.20
17 5 0.04
18 5 0.04
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:21659110 original size:120 final size:120
Alignment explanation
Indices: 21658687--21659092 Score: 710
Period size: 120 Copynumber: 3.4 Consensus size: 120
21658677 ATCATATTTA
*
21658687 AACATAATTATTATTAAATATATTGTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
21658752 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
21658807 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
21658872 TATTCTTATATGAATTTACTTAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
21658927 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
21658992 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTAT-AAATGA-AAATTT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAAT-ATAAA-TT
* * *
21659047 GAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAA
1 -AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAA
21659093 AATAATTTAA
Statistics
Matches: 276, Mismatches: 7, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
119 7 0.03
120 267 0.97
121 2 0.01
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:21659186 original size:24 final size:25
Alignment explanation
Indices: 21659140--21659187 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
21659130 TATGAATTTG
21659140 TATAATTTAAAATAATAATTATTACA
1 TATAATTTAAAAT-ATAATTATTACA
21659166 TATAATTTAATAAT-TAA-TATTA
1 TATAATTTAA-AATATAATTATTA
21659188 AATTTCATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 5 0.24
25 3 0.14
26 10 0.48
27 3 0.14
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TATAATTTAAAATATAATTATTACA
Found at i:21662166 original size:11 final size:11
Alignment explanation
Indices: 21662150--21662176 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
21662140 GATTTTATCA
21662150 ATTGTTGAGAT
1 ATTGTTGAGAT
21662161 ATTGTTGAGAT
1 ATTGTTGAGAT
21662172 ATTGT
1 ATTGT
21662177 CATTTTATAA
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:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (11 bp):
ATTGTTGAGAT
Found at i:21665644 original size:3 final size:3
Alignment explanation
Indices: 21665636--21665712 Score: 145
Period size: 3 Copynumber: 25.7 Consensus size: 3
21665626 ATGAGGTAAG
*
21665636 TAT TAT TAT TAT TAT TAT TAT TGT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
21665684 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
21665713 AGATAAGTGG
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:21667751 original size:24 final size:24
Alignment explanation
Indices: 21667718--21667776 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
21667708 GAACCTTCAA
* *
21667718 GCAAAACCTTATGTGATTTAGTAT
1 GCAAACCCTTATGTGATCTAGTAT
*
21667742 GCGAACCCTTATGTGATCTAGTAT
1 GCAAACCCTTATGTGATCTAGTAT
21667766 GCAAACCCTTA
1 GCAAACCCTTA
21667777 CATAAATAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (24 bp):
GCAAACCCTTATGTGATCTAGTAT
Found at i:21667882 original size:130 final size:129
Alignment explanation
Indices: 21667640--21667902 Score: 357
Period size: 130 Copynumber: 2.0 Consensus size: 129
21667630 ATTTCATCAG
* **
21667640 AACCCTTACATAAACATGTATACACACAAAATCTGTATAAATTGATAGGTAAACTGTAGCTGATA
1 AACCCTTACATAAACAGGTATACACACAAAATCTGTATAAATTGATAGACAAACTGTAGCTGATA
* ** *
21667705 TATGAACCTTCAAGCAAAACCTTATGTGATTTAGTATGCGAACCCTTATGTGATCTAGTATGCA
66 TATGAACCTTCAAGCAAAACCTTATGTAATTTAGTACACGAACCCTTATGTGATCCAGTATGCA
* * * * *
21667769 AACCCTTACATAAATAGGTATACATACTAACTCTGTTATAAATTGATAGACGAACTGTAGCTGAT
1 AACCCTTACATAAACAGGTATACACACAAAATCTG-TATAAATTGATAGACAAACTGTAGCTGAT
* * *
21667834 ATGA-GAACCTTCATGTAAAACCTTATGTAATTTAGTACACGAAGCCTTATGTGATCCAGTATGC
65 AT-ATGAACCTTCAAGCAAAACCTTATGTAATTTAGTACACGAACCCTTATGTGATCCAGTATGC
*
21667898 G
129 A
21667899 AACC
1 AACC
21667903 TTGTATGTGC
Statistics
Matches: 116, Mismatches: 16, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
129 30 0.26
130 85 0.73
131 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (129 bp):
AACCCTTACATAAACAGGTATACACACAAAATCTGTATAAATTGATAGACAAACTGTAGCTGATA
TATGAACCTTCAAGCAAAACCTTATGTAATTTAGTACACGAACCCTTATGTGATCCAGTATGCA
Found at i:21674754 original size:18 final size:17
Alignment explanation
Indices: 21674718--21674765 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
21674708 CATATATGTA
**
21674718 TATATAAAGCAAAAAAG
1 TATATAAAAAAAAAAAG
21674735 TATATAAAAAAAAGAAAG
1 TATATAAAAAAAA-AAAG
*
21674753 TAAAATAAAAAAA
1 T-ATATAAAAAAA
21674766 TGTAGGTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 11 0.42
18 5 0.19
19 10 0.38
ACGTcount: A:0.73, C:0.02, G:0.08, T:0.17
Consensus pattern (17 bp):
TATATAAAAAAAAAAAG
Found at i:21674778 original size:19 final size:19
Alignment explanation
Indices: 21674731--21674779 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
21674721 ATAAAGCAAA
21674731 AAAGTAT-ATAAAAAAAAG
1 AAAGTATAATAAAAAAAAG
* *
21674749 AAAGTAAAATAAAAAAATG
1 AAAGTATAATAAAAAAAAG
* *
21674768 TAGGTATAATAA
1 AAAGTATAATAA
21674780 TAATAATATA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.67, C:0.00, G:0.12, T:0.20
Consensus pattern (19 bp):
AAAGTATAATAAAAAAAAG
Found at i:21682554 original size:26 final size:25
Alignment explanation
Indices: 21682525--21682605 Score: 62
Period size: 26 Copynumber: 3.2 Consensus size: 25
21682515 TTCGATCACG
21682525 TGTGTAGTACTATGTGCAGGATACTA
1 TGTGTAGTACTATGTGCAGG-TACTA
* *
21682551 TGTGTA-T-CGGATAGT-AATGGTCAC-A
1 TGTGTAGTAC-TAT-GTGCA-GGT-ACTA
21682576 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGG-TACTA
21682602 TGTG
1 TGTG
21682606 AACTGATATC
Statistics
Matches: 42, Mismatches: 4, Indels: 18
0.66 0.06 0.28
Matches are distributed among these distances:
24 1 0.02
25 18 0.43
26 22 0.52
27 1 0.02
ACGTcount: A:0.25, C:0.12, G:0.28, T:0.35
Consensus pattern (25 bp):
TGTGTAGTACTATGTGCAGGTACTA
Found at i:21682604 original size:51 final size:49
Alignment explanation
Indices: 21682417--21682605 Score: 157
Period size: 51 Copynumber: 3.8 Consensus size: 49
21682407 TGAAAGTCAT
* * * * * *
21682417 GGTCACGTGTGTAGTACTATATGCAGGCTACTACGTGTACCAAAATGATA
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACGATAGT-ATA
** * ** * *
21682467 GGTCGTATTTGTAGTACTATGTGCAGGCTTTTATGCGTACCAGATAGCT-TC
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTA-C-GATAG-TATA
* * *
21682518 GATCACGTGTGTAGTACTATGTGCAGGATACTATGTGTATCGGATAGTA-A
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTA-C-GATAGTATA
21682568 TGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTG
1 -GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTG
21682606 AACTGATATC
Statistics
Matches: 106, Mismatches: 28, Indels: 9
0.74 0.20 0.06
Matches are distributed among these distances:
50 31 0.29
51 72 0.68
52 2 0.02
53 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (49 bp):
GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACGATAGTATA
Found at i:21685700 original size:83 final size:81
Alignment explanation
Indices: 21685611--21685809 Score: 204
Period size: 83 Copynumber: 2.4 Consensus size: 81
21685601 TTAAACGAAA
* * * * * *
21685611 GGAATAAATCCCGAAATAGAATTGTTTGA-TTACGTCTTTG-TTTGGAAACAAAACAATATCGAA
1 GGAATAAATCCCGAAACAGAATTATTTAATTTA-G--TTCGATTTGGAAACAAAACAAAATCAAA
*
21685674 TAAAATCTTGTTAAACGGC
63 CAAAATCTTGTTAAACGGC
* * * *
21685693 GATAATAAATCCTGAAACAGATTTATTTAATTTAGTTCGAATTTGGAAACAAAATAAAATCAAAC
1 G-GAATAAATCCCGAAACAGAATTATTTAATTTAGTTCG-ATTTGGAAACAAAACAAAATCAAAC
*
21685758 AAAATCTTTTTAAACGGC
64 AAAATCTTGTTAAACGGC
* *
21685776 GGAATAAATCCCAAAACAGATTTTATTTAATTTA
1 GGAATAAATCCCGAAACAGA-ATTATTTAATTTA
21685810 ATATCTCCTT
Statistics
Matches: 97, Mismatches: 15, Indels: 9
0.80 0.12 0.07
Matches are distributed among these distances:
81 3 0.03
82 17 0.18
83 74 0.76
84 3 0.03
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.32
Consensus pattern (81 bp):
GGAATAAATCCCGAAACAGAATTATTTAATTTAGTTCGATTTGGAAACAAAACAAAATCAAACAA
AATCTTGTTAAACGGC
Found at i:21686061 original size:77 final size:78
Alignment explanation
Indices: 21685818--21686126 Score: 467
Period size: 78 Copynumber: 4.0 Consensus size: 78
21685808 TAATATCTCC
* * * * * *
21685818 TTTTTGGAAATAAACCAAATTTGGAATGAAATTGTTGAACGGCGGGAATTAATCCTGAAAAGATT
1 TTTTTGGAAATAAAACAAATTTGGAATAAAATCGTTGAACGGCGGGAATCAATCCCGAAACGATT
21685883 TTTATTTTACTCA
66 TTTATTTTACTCA
* * *
21685896 TTTTTGGAAATAAAACAAAATTGGAATAAAATCGTTGAAAGGCGGGAATCAATCCCGAAATGATT
1 TTTTTGGAAATAAAACAAATTTGGAATAAAATCGTTGAACGGCGGGAATCAATCCCGAAACGATT
*
21685961 TTTATATTACTCA
66 TTTATTTTACTCA
* *
21685974 TTTTTGGAAATAAAACAAATTTGGAATAAAATCGTTGAACGGCGGGAATCGATCTCGAAACGA-T
1 TTTTTGGAAATAAAACAAATTTGGAATAAAATCGTTGAACGGCGGGAATCAATCCCGAAACGATT
*
21686038 TTTATTTTACTCG
66 TTTATTTTACTCA
* * *
21686051 TTTTTTGAAATAAAACAATTTTGGAATAAAATCGTTGAACGACGGGAATCAATCCCGAAACGATT
1 TTTTTGGAAATAAAACAAATTTGGAATAAAATCGTTGAACGGCGGGAATCAATCCCGAAACGATT
21686116 TTTATTTTACT
66 TTTATTTTACT
21686127 TTTAATTTCC
Statistics
Matches: 209, Mismatches: 21, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
77 70 0.33
78 139 0.67
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (78 bp):
TTTTTGGAAATAAAACAAATTTGGAATAAAATCGTTGAACGGCGGGAATCAATCCCGAAACGATT
TTTATTTTACTCA
Found at i:21686101 original size:155 final size:156
Alignment explanation
Indices: 21685818--21686126 Score: 469
Period size: 155 Copynumber: 2.0 Consensus size: 156
21685808 TAATATCTCC
* * * *
21685818 TTTTTGGAAATAAACCAAATTTGGAATGAAATTGTTGAACGGCGGGAATTAATCCTGAAAAGATT
1 TTTTTGGAAATAAAACAAATTTGGAATAAAATCGTTGAACGGCGGGAATCAATCCTGAAAAGATT
*
21685883 TTTATTTTACTCATTTTTGGAAATAAAACAAAATTGGAATAAAATCGTTGAAAGGCGGGAATCAA
66 TTTATTTTACTCATTTTTGGAAATAAAACAAAATTGGAATAAAATCGTTGAAAGACGGGAATCAA
*
21685948 TCCCGAAATGATTTTTATATTACTCA
131 TCCCGAAACGATTTTTATATTACTCA
* *
21685974 TTTTTGGAAATAAAACAAATTTGGAATAAAATCGTTGAACGGCGGGAATCGAT-CTCGAAACGA-
1 TTTTTGGAAATAAAACAAATTTGGAATAAAATCGTTGAACGGCGGGAATCAATCCT-GAAAAGAT
* * ** *
21686037 TTTTATTTTACTCGTTTTTTGAAATAAAACAATTTTGGAATAAAATCGTTGAACGACGGGAATCA
65 TTTTATTTTACTCATTTTTGGAAATAAAACAAAATTGGAATAAAATCGTTGAAAGACGGGAATCA
*
21686102 ATCCCGAAACGATTTTTATTTTACT
130 ATCCCGAAACGATTTTTATATTACT
21686127 TTTAATTTCC
Statistics
Matches: 138, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
155 84 0.61
156 54 0.39
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (156 bp):
TTTTTGGAAATAAAACAAATTTGGAATAAAATCGTTGAACGGCGGGAATCAATCCTGAAAAGATT
TTTATTTTACTCATTTTTGGAAATAAAACAAAATTGGAATAAAATCGTTGAAAGACGGGAATCAA
TCCCGAAACGATTTTTATATTACTCA
Found at i:21688816 original size:23 final size:21
Alignment explanation
Indices: 21688781--21688822 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
21688771 AGCTTTATTT
*
21688781 AATAAATTATTTTGATATAATA
1 AATAAAATATTTTGA-ATAATA
21688803 AATAAAATATTTTTGAATAA
1 AATAAAATA-TTTTGAATAA
21688823 ATATGGTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (21 bp):
AATAAAATATTTTGAATAATA
Found at i:21696296 original size:17 final size:16
Alignment explanation
Indices: 21696268--21696305 Score: 67
Period size: 17 Copynumber: 2.3 Consensus size: 16
21696258 TAAATATTAG
21696268 ATTAAATTAATCTAAT
1 ATTAAATTAATCTAAT
21696284 ATTAAATTTAATCTAAT
1 ATTAAA-TTAATCTAAT
21696301 ATTAA
1 ATTAA
21696306 GATAATCACT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTAAATTAATCTAAT
Found at i:21699628 original size:13 final size:14
Alignment explanation
Indices: 21699609--21699706 Score: 75
Period size: 13 Copynumber: 7.2 Consensus size: 14
21699599 TCATCAGGTG
21699609 GAAAATGATTATAT
1 GAAAATGATTATAT
21699623 -AAAATGATTATAT
1 GAAAATGATTATAT
*
21699636 GAACCA-G-TTATAT
1 GAA-AATGATTATAT
21699649 GGAAAATGCA-TATAT
1 -GAAAATG-ATTATAT
21699664 -AAAATGATTATAT
1 GAAAATGATTATAT
**
21699677 GAATTTG-TTATAT
1 GAAAATGATTATAT
*
21699690 GCAAAT-AGTTATAT
1 GAAAATGA-TTATAT
21699704 GAA
1 GAA
21699707 TTGTGTATAC
Statistics
Matches: 66, Mismatches: 8, Indels: 20
0.70 0.09 0.21
Matches are distributed among these distances:
12 1 0.02
13 40 0.61
14 19 0.29
15 6 0.09
ACGTcount: A:0.46, C:0.04, G:0.14, T:0.36
Consensus pattern (14 bp):
GAAAATGATTATAT
Found at i:21699721 original size:26 final size:25
Alignment explanation
Indices: 21699665--21699730 Score: 64
Period size: 27 Copynumber: 2.5 Consensus size: 25
21699655 TGCATATATA
21699665 AAATGATTATATGAATTTGTTATATGC
1 AAATG-TTATATGAATTTGTTATA-GC
21699692 AAATAGTTATATGAA-TTGTGTATA-C
1 AAAT-GTTATATGAATTTGT-TATAGC
21699717 AAAATGTCTATATG
1 -AAATGT-TATATG
21699731 GATAGATATG
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
25 3 0.09
26 14 0.40
27 17 0.49
28 1 0.03
ACGTcount: A:0.39, C:0.05, G:0.15, T:0.41
Consensus pattern (25 bp):
AAATGTTATATGAATTTGTTATAGC
Found at i:21700693 original size:15 final size:15
Alignment explanation
Indices: 21700673--21700716 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
21700663 CTATGTATGC
* *
21700673 AAAACATAATAGACG
1 AAAACACAAAAGACG
21700688 AAAACACAAAAGACG
1 AAAACACAAAAGACG
*
21700703 GAAACACAAAAGAC
1 AAAACACAAAAGAC
21700717 ATAATAGTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.64, C:0.18, G:0.14, T:0.05
Consensus pattern (15 bp):
AAAACACAAAAGACG
Found at i:21708802 original size:44 final size:44
Alignment explanation
Indices: 21708739--21708826 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
21708729 AATGATAAAA
21708739 AAGTAAAAATTCTAATGCACGATTTCAAAAAGATGAGTTTTAAT
1 AAGTAAAAATTCTAATGCACGATTTCAAAAAGATGAGTTTTAAT
21708783 AAGTAAAAATTCTAATGCACGATTTCAAAAAGATGAGTTTTAAT
1 AAGTAAAAATTCTAATGCACGATTTCAAAAAGATGAGTTTTAAT
21708827 CAATATGACA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.45, C:0.09, G:0.14, T:0.32
Consensus pattern (44 bp):
AAGTAAAAATTCTAATGCACGATTTCAAAAAGATGAGTTTTAAT
Found at i:21731253 original size:16 final size:18
Alignment explanation
Indices: 21731227--21731259 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
21731217 TTAAATTAAC
21731227 TAAACTAA-TTTCTCAAT
1 TAAACTAATTTTCTCAAT
21731244 TAAA-TAATTTTCTCAA
1 TAAACTAATTTTCTCAA
21731260 CCCAATTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.42
Consensus pattern (18 bp):
TAAACTAATTTTCTCAAT
Found at i:21746316 original size:31 final size:31
Alignment explanation
Indices: 21746281--21746341 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 31
21746271 GTGTTCACTT
*
21746281 AACTATT-CAAAAATTTTAGTTTAAGTCATTG
1 AACTATTAAAAAAATTTTA-TTTAAGTCATTG
21746312 AACTATTGAAAAAAATTTTATTTAAGTCAT
1 AACTATT-AAAAAAATTTTATTTAAGTCAT
21746342 GAGGCTGTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 7 0.26
32 10 0.37
33 10 0.37
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.41
Consensus pattern (31 bp):
AACTATTAAAAAAATTTTATTTAAGTCATTG
Found at i:21747960 original size:32 final size:31
Alignment explanation
Indices: 21747905--21747975 Score: 88
Period size: 32 Copynumber: 2.3 Consensus size: 31
21747895 ACTGGTTTTT
* * *
21747905 TTAATTGATATGAGTTATCAAATTAAATTAA
1 TTAATTTATATGAGCTATCAAATTAAAGTAA
* *
21747936 TTAATTTATCATGAGCTATTAAATTCAAGTAA
1 TTAATTTAT-ATGAGCTATCAAATTAAAGTAA
21747968 TTAATTTA
1 TTAATTTA
21747976 CAAGTTTATG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 8 0.24
32 26 0.76
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (31 bp):
TTAATTTATATGAGCTATCAAATTAAAGTAA
Found at i:21748135 original size:17 final size:17
Alignment explanation
Indices: 21748104--21748146 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
21748094 AAATTTAAAC
21748104 ATTTT-ATTAAAATAAT
1 ATTTTAATTAAAATAAT
*
21748120 ATTTTAATTAAGATAAT
1 ATTTTAATTAAAATAAT
*
21748137 -TTTTATTTAA
1 ATTTTAATTAA
21748147 TAAATTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
ATTTTAATTAAAATAAT
Found at i:21748146 original size:16 final size:16
Alignment explanation
Indices: 21748104--21748143 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
21748094 AAATTTAAAC
21748104 ATTTTATTAAAATAAT
1 ATTTTATTAAAATAAT
*
21748120 ATTTTAATTAAGATAAT
1 ATTTT-ATTAAAATAAT
21748137 -TTTTATT
1 ATTTTATT
21748144 TAATAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 3 0.14
16 9 0.41
17 10 0.45
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
ATTTTATTAAAATAAT
Found at i:21748661 original size:43 final size:43
Alignment explanation
Indices: 21748614--21748707 Score: 109
Period size: 43 Copynumber: 2.2 Consensus size: 43
21748604 TTAAATTTAC
* *
21748614 ATAAA-AAAAAGAGTAAAATTTTAATGGGTATTTAATGAAAATA
1 ATAAATAAAAA-ACTAAAATATTAATGGGTATTTAATGAAAATA
** * *
21748657 ATAAATAAAAAACTAAAATATTAATTTGTGTTTAATGAGAATA
1 ATAAATAAAAAACTAAAATATTAATGGGTATTTAATGAAAATA
21748700 ATTAAATA
1 A-TAAATA
21748708 TTATGATTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
43 32 0.74
44 11 0.26
ACGTcount: A:0.55, C:0.01, G:0.11, T:0.33
Consensus pattern (43 bp):
ATAAATAAAAAACTAAAATATTAATGGGTATTTAATGAAAATA
Found at i:21749698 original size:22 final size:22
Alignment explanation
Indices: 21749651--21749703 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
21749641 AACTAGACTT
* *
21749651 GTATCAGTAAAAGGGTTCCCAT
1 GTATCGGTAAAAGGGTTCCCAA
* *
21749673 GTATTGGTAAAAGGGTTCTCAA
1 GTATCGGTAAAAGGGTTCCCAA
21749695 GTATCGGTA
1 GTATCGGTA
21749704 GAAGTTTGGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.30, C:0.13, G:0.26, T:0.30
Consensus pattern (22 bp):
GTATCGGTAAAAGGGTTCCCAA
Found at i:21751675 original size:25 final size:24
Alignment explanation
Indices: 21751647--21751705 Score: 66
Period size: 23 Copynumber: 2.4 Consensus size: 24
21751637 AGCTCCAGAT
*
21751647 AGCCATAAATCGGGAAGTTTAAGCG
1 AGCCAT-AATCGGGAAGCTTAAGCG
* *
21751672 AGCCAT-ATCGGGAAGCTTCAGGG
1 AGCCATAATCGGGAAGCTTAAGCG
21751695 AGCCATTAATC
1 AGCCA-TAATC
21751706 AAGAAGCTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 19 0.66
24 1 0.03
25 9 0.31
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.20
Consensus pattern (24 bp):
AGCCATAATCGGGAAGCTTAAGCG
Found at i:21751729 original size:26 final size:25
Alignment explanation
Indices: 21751694--21751751 Score: 71
Period size: 26 Copynumber: 2.3 Consensus size: 25
21751684 AAGCTTCAGG
21751694 GAGCCATTAATCAAGAAGCTCAAAAA
1 GAGCCATTAATCAAGAAGCTC-AAAA
* ** *
21751720 GAGCCTTTAATCGGGAAGCTCCAAA
1 GAGCCATTAATCAAGAAGCTCAAAA
21751745 GAGCCAT
1 GAGCCAT
21751752 ATAACGGGAC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 9 0.33
26 18 0.67
ACGTcount: A:0.40, C:0.22, G:0.21, T:0.17
Consensus pattern (25 bp):
GAGCCATTAATCAAGAAGCTCAAAA
Found at i:21751759 original size:25 final size:25
Alignment explanation
Indices: 21751499--21751760 Score: 66
Period size: 25 Copynumber: 10.6 Consensus size: 25
21751489 GCCCTCTCTT
* *
21751499 GAGCCATATAACAGGAAGCTCCAGA
1 GAGCCATATAACGGGAAGCTCCAAA
* *
21751524 GAGCCAT-TAACGGGAAGCT-TATTCA
1 GAGCCATATAACGGGAAGCTCCA--AA
*** *
21751549 G-GTTGTATATCGGGAAGCT-CATAA
1 GAGCCATATAACGGGAAGCTCCA-AA
** **
21751573 GAGCCATA-ATTGGGAAGCT-CATGT
1 GAGCCATATAACGGGAAGCTCCA-AA
* * * * *
21751597 GAGCTA-ATAACAGGTAGCTTCGAA
1 GAGCCATATAACGGGAAGCTCCAAA
* *
21751621 GAGCCAT-TAAACGAGAAGCTCCAGA
1 GAGCCATAT-AACGGGAAGCTCCAAA
* ** *
21751646 TAGCCATA-AATCGGGAAG-TTTAAGC
1 GAGCCATATAA-CGGGAAGCTCCAA-A
* **
21751671 GAGCCATAT--CGGGAAGCTTCAGG
1 GAGCCATATAACGGGAAGCTCCAAA
** *
21751694 GAGCCAT-TAATCAAGAAGCTCAAAAA
1 GAGCCATATAA-CGGGAAGCTC-CAAA
*
21751720 GAGCC-TTTAATCGGGAAGCTCCAAA
1 GAGCCATATAA-CGGGAAGCTCCAAA
21751745 GAGCCATATAACGGGA
1 GAGCCATATAACGGGA
21751761 CACTCATAAG
Statistics
Matches: 168, Mismatches: 50, Indels: 38
0.66 0.20 0.15
Matches are distributed among these distances:
22 1 0.01
23 16 0.10
24 54 0.32
25 75 0.45
26 22 0.13
ACGTcount: A:0.35, C:0.19, G:0.26, T:0.19
Consensus pattern (25 bp):
GAGCCATATAACGGGAAGCTCCAAA
Found at i:21753919 original size:58 final size:57
Alignment explanation
Indices: 21753787--21753977 Score: 162
Period size: 58 Copynumber: 3.4 Consensus size: 57
21753777 GGCTAAGATA
* *
21753787 GCCACAAAAGG-ATCCATTTAACAGAGGTAGCCACAAAGACATTCTTTTAATAGAGTTC
1 GCCAC-AAAGGCATCCTTTTAACAGAGGTA-CCACAAAGACATTCTTTTAACAGAGTTC
* *
21753845 GCCATAAAGGCATCCTTTTAACAGAGGTCACCACAAAGAC-TTCCTTTTAACAGA-TATT
1 GCCACAAAGGCATCCTTTTAACAGAGGT-ACCACAAAGACATT-CTTTTAACAGAGT-TC
* * * * * * *
21753903 GCTACAAATGCTTCCTTTTAATAGAGATTACCACAAA-AGCA-TCTTTT--CAGAGATA
1 GCCACAAAGGCATCCTTTTAACAGAG-GTACCACAAAGA-CATTCTTTTAACAGAGTTC
*
21753958 GCCACAAAGGCGTCCTTTTA
1 GCCACAAAGGCATCCTTTTA
21753978 TAGAAATTGC
Statistics
Matches: 110, Mismatches: 15, Indels: 19
0.76 0.10 0.13
Matches are distributed among these distances:
55 22 0.20
57 14 0.13
58 72 0.65
59 2 0.02
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (57 bp):
GCCACAAAGGCATCCTTTTAACAGAGGTACCACAAAGACATTCTTTTAACAGAGTTC
Found at i:21753945 original size:87 final size:83
Alignment explanation
Indices: 21753830--21753993 Score: 188
Period size: 84 Copynumber: 1.9 Consensus size: 83
21753820 CAAAGACATT
* * * * *
21753830 CTTTTAATAGAGTTCGCCATAAAGGCATCCTTTTAACAGAGGTCA-CCACAAAGACTTCCTTTTA
1 CTTTTAATAGAGTTCACCACAAAAGCAT-CTTTT--CAGAGAT-AGCCACAAAGACGTCCTTTT-
*
21753894 ACAGATATTGCTACAAATGCTTC
61 ACAGAAATTGCTACAAATGCTTC
* *
21753917 CTTTTAATAGAGATT-ACCACAAAAGCATCTTTTCAGAGATAGCCACAAAGGCGTCCTTTTATAG
1 CTTTTAATAGAG-TTCACCACAAAAGCATCTTTTCAGAGATAGCCACAAAGACGTCCTTTTACAG
21753981 AAATTGCTACAAA
65 AAATTGCTACAAA
21753994 GGAACTTTTT
Statistics
Matches: 67, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
83 16 0.24
84 22 0.33
86 5 0.07
87 22 0.33
88 2 0.03
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (83 bp):
CTTTTAATAGAGTTCACCACAAAAGCATCTTTTCAGAGATAGCCACAAAGACGTCCTTTTACAGA
AATTGCTACAAATGCTTC
Found at i:21753993 original size:28 final size:29
Alignment explanation
Indices: 21753803--21753995 Score: 128
Period size: 29 Copynumber: 6.8 Consensus size: 29
21753793 AAAGGATCCA
* * *
21753803 TTTAACAGAGGTAGCCACAAAGACATT-CT
1 TTTAACAGAGATTGCCACAAAGGC-TTCCT
* * *
21753832 TTTAATAGAG-TTCGCCATAAAGGCATCCT
1 TTTAACAGAGATT-GCCACAAAGGCTTCCT
* ** *
21753861 TTTAACAGAGGTCACCACAAAGACTTCCT
1 TTTAACAGAGATTGCCACAAAGGCTTCCT
* * *
21753890 TTTAACAGATATTGCTACAAATGCTTCCT
1 TTTAACAGAGATTGCCACAAAGGCTTCCT
* * * *
21753919 TTTAATAGAGATTACCACAAAAGCAT-CT
1 TTTAACAGAGATTGCCACAAAGGCTTCCT
* *
21753947 TTT--CAGAGATAGCCACAAAGGCGTCCT
1 TTTAACAGAGATTGCCACAAAGGCTTCCT
* * *
21753974 TTT-ATAGAAATTGCTACAAAGG
1 TTTAACAGAGATTGCCACAAAGG
21753996 AACTTTTTTA
Statistics
Matches: 126, Mismatches: 33, Indels: 11
0.74 0.19 0.06
Matches are distributed among these distances:
26 16 0.13
27 5 0.04
28 21 0.17
29 83 0.66
30 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (29 bp):
TTTAACAGAGATTGCCACAAAGGCTTCCT
Found at i:21758626 original size:45 final size:44
Alignment explanation
Indices: 21758553--21758709 Score: 197
Period size: 45 Copynumber: 3.5 Consensus size: 44
21758543 CACATAGCAT
* * * * *
21758553 CACCCTTATAGTCAATGATACTCGGTGGAATCAGCACATAACAAC
1 CACCTTTATAATCAATG-TACCCAGTGGAATCAGCACACAACAAC
*
21758598 CACCTTCATAATCAATAGTACCCAGTGGAATCAGCACACAACAAC
1 CACCTTTATAATCAAT-GTACCCAGTGGAATCAGCACACAACAAC
* *
21758643 CACCTTTATAATCAATGATACCCGGTGGAATCAGCACACAGCAAC
1 CACCTTTATAATCAATG-TACCCAGTGGAATCAGCACACAACAAC
*
21758688 CATCTTTATAATCAATGGTACC
1 CACCTTTATAATCAAT-GTACC
21758710 TGGTACACGT
Statistics
Matches: 99, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
44 1 0.01
45 96 0.97
46 2 0.02
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.22
Consensus pattern (44 bp):
CACCTTTATAATCAATGTACCCAGTGGAATCAGCACACAACAAC
Found at i:21769847 original size:33 final size:33
Alignment explanation
Indices: 21769805--21769902 Score: 187
Period size: 33 Copynumber: 3.0 Consensus size: 33
21769795 CGACCATAAC
*
21769805 GCACACTTTGTGTAAGCTTCCCATGTATCCGAG
1 GCACACTTTGTGTAAGCTTCCCATGTATCCGAA
21769838 GCACACTTTGTGTAAGCTTCCCATGTATCCGAA
1 GCACACTTTGTGTAAGCTTCCCATGTATCCGAA
21769871 GCACACTTTGTGTAAGCTTCCCATGTATCCGA
1 GCACACTTTGTGTAAGCTTCCCATGTATCCGA
21769903 TATTATTCTA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 64 1.00
ACGTcount: A:0.22, C:0.28, G:0.19, T:0.31
Consensus pattern (33 bp):
GCACACTTTGTGTAAGCTTCCCATGTATCCGAA
Found at i:21770809 original size:15 final size:14
Alignment explanation
Indices: 21770772--21770810 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
21770762 GTGTATCTCA
21770772 GCCGTGTGTGACAC
1 GCCGTGTGTGACAC
*
21770786 ACCGCTGTGTGACAC
1 GCCG-TGTGTGACAC
21770801 GGCCGTGTGT
1 -GCCGTGTGT
21770811 CCCCTGTAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 3 0.14
15 15 0.71
16 3 0.14
ACGTcount: A:0.13, C:0.28, G:0.36, T:0.23
Consensus pattern (14 bp):
GCCGTGTGTGACAC
Found at i:21773373 original size:20 final size:21
Alignment explanation
Indices: 21773348--21773403 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 21
21773338 AGTCAATTTT
21773348 TATCGATACTTTATATA-AAG
1 TATCGATACTTTATATATAAG
*
21773368 TATCGAT-CTTTAGGA-ATAAG
1 TATCGATACTTTA-TATATAAG
21773388 TATCGATACTTTATAT
1 TATCGATACTTTATAT
21773404 TGGTATTGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
19 6 0.20
20 19 0.63
21 5 0.17
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.41
Consensus pattern (21 bp):
TATCGATACTTTATATATAAG
Found at i:21784516 original size:21 final size:21
Alignment explanation
Indices: 21784490--21784543 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
21784480 ACATTAATCG
21784490 TTCCATACAAACGATACATTC
1 TTCCATACAAACGATACATTC
* * *
21784511 TTCCATACAAATGGTACATTT
1 TTCCATACAAACGATACATTC
*
21784532 TTCCATAGAAAC
1 TTCCATACAAAC
21784544 TTCATCATTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.37, C:0.24, G:0.07, T:0.31
Consensus pattern (21 bp):
TTCCATACAAACGATACATTC
Found at i:21808073 original size:27 final size:27
Alignment explanation
Indices: 21808047--21808524 Score: 525
Period size: 27 Copynumber: 17.7 Consensus size: 27
21808037 ATACGTTCGA
* *
21808047 AGGGTAAAATGATCGAAATA-CCCTCG-
1 AGGGTAAAATGACCGTAATACCCCT-GT
* * * *
21808073 ATGGGTAAAATGACTGAAATGCCCTTGT
1 A-GGGTAAAATGACCGTAATACCCCTGT
21808101 AGGGTAAAATGACCGTAATACCCC-GAT
1 AGGGTAAAATGACCGTAATACCCCTG-T
* *
21808128 AGGATAAAATGACCGTAATGCCCCTGT
1 AGGGTAAAATGACCGTAATACCCCTGT
*
21808155 AGGGTAAAATGACCGTAATACCCCGGT
1 AGGGTAAAATGACCGTAATACCCCTGT
* * *
21808182 AGGATAAAATGACCATAATACCCCTAT
1 AGGGTAAAATGACCGTAATACCCCTGT
* *
21808209 AGGATAAAATGACTGTAATACCCCTGT
1 AGGGTAAAATGACCGTAATACCCCTGT
* * *
21808236 AGGATAAAATGACCGTAATGCCTCTGT
1 AGGGTAAAATGACCGTAATACCCCTGT
* *
21808263 AGGGTAAAATAACCGTAATACCCCTAT
1 AGGGTAAAATGACCGTAATACCCCTGT
** * *
21808290 AGGGTAAAATGATTGTAATGCCTCC-AT
1 AGGGTAAAATGACCGTAATACC-CCTGT
*
21808317 AGGGTAAAA-GAACCGAAATACCCCTGT
1 AGGGTAAAATG-ACCGTAATACCCCTGT
*
21808344 AGGGTAAAATGACCGTAATACCCCGGT
1 AGGGTAAAATGACCGTAATACCCCTGT
* *
21808371 AGGGTAAAATGATCGTAATGCCCCTGT
1 AGGGTAAAATGACCGTAATACCCCTGT
* * ** *
21808398 AGGGTAAAATGATCGTAGTACCTTTAT
1 AGGGTAAAATGACCGTAATACCCCTGT
* *
21808425 AGGGTAAAATGATCGTAATACCTCTGT
1 AGGGTAAAATGACCGTAATACCCCTGT
* *
21808452 AGGGTAAAATGACCGTAATGCCTCTGT
1 AGGGTAAAATGACCGTAATACCCCTGT
* *
21808479 AGGGTAAAATTACTGTAATACCCCTGT
1 AGGGTAAAATGACCGTAATACCCCTGT
*
21808506 AGGGTAAAATGACCATAAT
1 AGGGTAAAATGACCGTAAT
21808525 GCCCTGGTGG
Statistics
Matches: 384, Mismatches: 59, Indels: 17
0.83 0.13 0.04
Matches are distributed among these distances:
26 5 0.01
27 371 0.97
28 8 0.02
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.24
Consensus pattern (27 bp):
AGGGTAAAATGACCGTAATACCCCTGT
Found at i:21808753 original size:26 final size:26
Alignment explanation
Indices: 21808715--21808768 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
21808705 TTGGCTACAT
21808715 ATACTATTACTGGCAGCTTTGCTGCG
1 ATACTATTACTGGCAGCTTTGCTGCG
* *
21808741 ATACTGTTGCTGGCAGCTTTGCTGCG
1 ATACTATTACTGGCAGCTTTGCTGCG
21808767 AT
1 AT
21808769 GCTACTAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.17, C:0.22, G:0.26, T:0.35
Consensus pattern (26 bp):
ATACTATTACTGGCAGCTTTGCTGCG
Found at i:21808780 original size:26 final size:26
Alignment explanation
Indices: 21808715--21808780 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 26
21808705 TTGGCTACAT
* *
21808715 ATACTATTACTGGCAGCTTTGCTGCG
1 ATACTACTAATGGCAGCTTTGCTGCG
** **
21808741 ATACTGTTGCTGGCAGCTTTGCTGCG
1 ATACTACTAATGGCAGCTTTGCTGCG
*
21808767 ATGCTACTAATGGC
1 ATACTACTAATGGC
21808781 TTTGTGCCGG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.18, C:0.23, G:0.26, T:0.33
Consensus pattern (26 bp):
ATACTACTAATGGCAGCTTTGCTGCG
Found at i:21808817 original size:32 final size:32
Alignment explanation
Indices: 21808771--21808955 Score: 110
Period size: 32 Copynumber: 5.8 Consensus size: 32
21808761 GCTGCGATGC
* * *
21808771 TACTAATGGCTTTGTGCCGGTCATAGTACCAT
1 TACTGATGGCTGTGTGCCGATCATAGTACCAT
* * * * ** *
21808803 TACTGATGGCTTTGTGTCAATCATATTGTCGT
1 TACTGATGGCTGTGTGCCGATCATAGTACCAT
* * **
21808835 TA-TCGATGGCTGTGTGCCGGTCAT-TTCATTAT
1 TACT-GATGGCTGTGTGCCGATCATAGT-ACCAT
* * *
21808867 TACTGATGGCAGTGTGCTGATCATA-T-CAAT
1 TACTGATGGCTGTGTGCCGATCATAGTACCAT
* *
21808897 GCTACTGATGGCTTTGTGCCGATCAT-GTTACCGT
1 --TACTGATGGCTGTGTGCCGATCATAG-TACCAT
*
21808931 TATTGATGGCTGTGTGCCGATCATA
1 TACTGATGGCTGTGTGCCGATCATA
21808956 TCACTGCTAT
Statistics
Matches: 116, Mismatches: 27, Indels: 19
0.72 0.17 0.12
Matches are distributed among these distances:
30 2 0.02
31 3 0.03
32 107 0.92
33 2 0.02
34 2 0.02
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.37
Consensus pattern (32 bp):
TACTGATGGCTGTGTGCCGATCATAGTACCAT
Found at i:21808907 original size:64 final size:64
Alignment explanation
Indices: 21808767--21808979 Score: 191
Period size: 64 Copynumber: 3.3 Consensus size: 64
21808757 CTTTGCTGCG
* * ** * * *
21808767 ATGCTACTAATGGCTTTGTGCCGGTCATAG-TACCATTACTGATGGCTTTGTGTCAATCATAT-T
1 ATGCTACTGATGGCTTTGTGCCGATCAT-GTTACCATTACTGATGGCAGTGTGCCGATCATATCA
* * * * ** *
21808830 GTCGTTA-TCGATGGCTGTGTGCCGGTCAT-TTCATTATTACTGATGGCAGTGTGCTGATCATAT
1 AT-GCTACT-GATGGCTTTGTGCCGATCATGTT-ACCATTACTGATGGCAGTGTGCCGATCATAT
21808893 CA
63 CA
* * *
21808895 ATGCTACTGATGGCTTTGTGCCGATCATGTTACCGTTATTGATGGCTGTGTGCCGATCATATCA
1 ATGCTACTGATGGCTTTGTGCCGATCATGTTACCATTACTGATGGCAGTGTGCCGATCATATCA
* *
21808959 CTGCTATTGATGGCTTTGTGC
1 ATGCTACTGATGGCTTTGTGC
21808980 TTATCACATT
Statistics
Matches: 119, Mismatches: 24, Indels: 13
0.76 0.15 0.08
Matches are distributed among these distances:
63 3 0.03
64 112 0.94
65 4 0.03
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (64 bp):
ATGCTACTGATGGCTTTGTGCCGATCATGTTACCATTACTGATGGCAGTGTGCCGATCATATCA
Found at i:21808967 original size:32 final size:32
Alignment explanation
Indices: 21808839--21808979 Score: 138
Period size: 32 Copynumber: 4.4 Consensus size: 32
21808829 TGTCGTTATC
* * * **
21808839 GATGGCTGTGTGCCGGTCATTTCATTATTACT
1 GATGGCTGTGTGCCGATCATATCACTGCTACT
* * *
21808871 GATGGCAGTGTGCTGATCATATCAATGCTACT
1 GATGGCTGTGTGCCGATCATATCACTGCTACT
* * * * * *
21808903 GATGGCTTTGTGCCGATCATGTTACCGTTATT
1 GATGGCTGTGTGCCGATCATATCACTGCTACT
*
21808935 GATGGCTGTGTGCCGATCATATCACTGCTATT
1 GATGGCTGTGTGCCGATCATATCACTGCTACT
*
21808967 GATGGCTTTGTGC
1 GATGGCTGTGTGC
21808980 TTATCACATT
Statistics
Matches: 87, Mismatches: 22, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 87 1.00
ACGTcount: A:0.18, C:0.19, G:0.26, T:0.37
Consensus pattern (32 bp):
GATGGCTGTGTGCCGATCATATCACTGCTACT
Found at i:21813532 original size:28 final size:26
Alignment explanation
Indices: 21813492--21813543 Score: 68
Period size: 28 Copynumber: 1.9 Consensus size: 26
21813482 GAATTTGAGT
*
21813492 AATTAGGGCTAAATTGTAAAATAATA
1 AATTAGGGCTAAAATGTAAAATAATA
*
21813518 AATTAAGGGACTAAAATGTGAAATAA
1 AATT-AGGG-CTAAAATGTAAAATAA
21813544 ATGAAATGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 4 0.18
27 4 0.18
28 14 0.64
ACGTcount: A:0.52, C:0.04, G:0.17, T:0.27
Consensus pattern (26 bp):
AATTAGGGCTAAAATGTAAAATAATA
Found at i:21817207 original size:14 final size:15
Alignment explanation
Indices: 21817190--21817220 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
21817180 CTACTGTGTG
21817190 TTTTC-TTTACTTTT
1 TTTTCTTTTACTTTT
21817204 TTTTCTTTTACTTTT
1 TTTTCTTTTACTTTT
21817219 TT
1 TT
21817221 CTTGTTTGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.06, C:0.13, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTTCTTTTACTTTT
Found at i:21818796 original size:24 final size:24
Alignment explanation
Indices: 21818764--21818812 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
21818754 AAACATGCAA
* *
21818764 CAGAGTATGTTGCCAATTGTGAGT
1 CAGAGTATGTTGCCAAATGTAAGT
21818788 CAGAGTATGTTGCCAAATGTAAGT
1 CAGAGTATGTTGCCAAATGTAAGT
21818812 C
1 C
21818813 CTGCCAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.31
Consensus pattern (24 bp):
CAGAGTATGTTGCCAAATGTAAGT
Found at i:21820213 original size:21 final size:21
Alignment explanation
Indices: 21820174--21820213 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
21820164 TAAGTTTTCA
*
21820174 TTTTATTAAGTTTTAATTATG
1 TTTTATTAAGTTTCAATTATG
* *
21820195 TTTTCTTAAGTTTCCATTA
1 TTTTATTAAGTTTCAATTA
21820214 AGTTAATAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.07, G:0.07, T:0.60
Consensus pattern (21 bp):
TTTTATTAAGTTTCAATTATG
Found at i:21827610 original size:10 final size:10
Alignment explanation
Indices: 21827554--21827614 Score: 52
Period size: 10 Copynumber: 6.0 Consensus size: 10
21827544 AATAAAATAT
*
21827554 TTTAA-ATAT
1 TTTAATATAA
21827563 TTTAATATAA
1 TTTAATATAA
*
21827573 TTTTATATAAAA
1 -TTTA-ATATAA
* * *
21827585 TTAAAAATAT
1 TTTAATATAA
21827595 TTTAATATAA
1 TTTAATATAA
21827605 TTTAATATAA
1 TTTAATATAA
21827615 AATTAATTAT
Statistics
Matches: 40, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
9 5 0.12
10 23 0.57
11 7 0.17
12 5 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (10 bp):
TTTAATATAA
Found at i:21827627 original size:32 final size:32
Alignment explanation
Indices: 21827557--21827620 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
21827547 AAAATATTTT
*
21827557 AAATATTTTAATATAATTTTATATAAAATTAA
1 AAATATTTTAATATAATTTAATATAAAATTAA
21827589 AAATATTTTAATATAATTTAATATAAAATTAA
1 AAATATTTTAATATAATTTAATATAAAATTAA
21827621 TTATATTAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (32 bp):
AAATATTTTAATATAATTTAATATAAAATTAA
Found at i:21827694 original size:26 final size:26
Alignment explanation
Indices: 21827657--21827749 Score: 69
Period size: 26 Copynumber: 3.3 Consensus size: 26
21827647 ATATTATTTT
*
21827657 TATTAAAGTATATTTAATAATAATTA
1 TATTAAAATATATTTAATAATAATTA
* * *
21827683 TATTAAAATATAATTAAATTATTTATTATTTT
1 TATTAAAATAT-ATTTAA-TA---A-TAATTA
* **
21827715 TATTAAATTATATTTAATAATAATCC
1 TATTAAAATATATTTAATAATAATTA
21827741 TATTAAAAT
1 TATTAAAAT
21827750 CTAATAACAA
Statistics
Matches: 51, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
26 21 0.41
27 6 0.12
28 2 0.04
30 2 0.04
31 6 0.12
32 14 0.27
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.49
Consensus pattern (26 bp):
TATTAAAATATATTTAATAATAATTA
Found at i:21827713 original size:58 final size:58
Alignment explanation
Indices: 21827618--21827754 Score: 202
Period size: 58 Copynumber: 2.3 Consensus size: 58
21827608 AATATAAAAT
* *
21827618 TAATTATATTAAGAATGTTATTAAATTATATATTATTTTTATTAAAGTATATTTAATAA
1 TAATTATATTAA-AATATAATTAAATTATATATTATTTTTATTAAAGTATATTTAATAA
* *
21827677 TAATTATATTAAAATATAATTAAATTATTTATTATTTTTATTAAATTATATTTAATAA
1 TAATTATATTAAAATATAATTAAATTATATATTATTTTTATTAAAGTATATTTAATAA
** *
21827735 TAATCCTATTAAAATCTAAT
1 TAATTATATTAAAATATAAT
21827755 AACAATAATC
Statistics
Matches: 71, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
58 59 0.83
59 12 0.17
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (58 bp):
TAATTATATTAAAATATAATTAAATTATATATTATTTTTATTAAAGTATATTTAATAA
Found at i:21831130 original size:29 final size:29
Alignment explanation
Indices: 21831088--21831175 Score: 142
Period size: 29 Copynumber: 3.0 Consensus size: 29
21831078 TCGTGGAAGA
* *
21831088 GGTGGAGAAATTGTTCGTTGAGAATTCGT
1 GGTGAAGAACTTGTTCGTTGAGAATTCGT
21831117 GGTGAAGAACTTGTTC-TGTGAGAATTCGT
1 GGTGAAGAACTTGTTCGT-TGAGAATTCGT
21831146 GGTGAAGAACTTGTTCGTTGAGAATTCGT
1 GGTGAAGAACTTGTTCGTTGAGAATTCGT
21831175 G
1 G
21831176 TCAATGTGGT
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
28 1 0.02
29 53 0.96
30 1 0.02
ACGTcount: A:0.24, C:0.09, G:0.33, T:0.34
Consensus pattern (29 bp):
GGTGAAGAACTTGTTCGTTGAGAATTCGT
Found at i:21831289 original size:24 final size:24
Alignment explanation
Indices: 21831261--21831323 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
21831251 TTTTTAGAAG
*
21831261 ATTTAGTATTTATTAATATAATAT
1 ATTTAGTATTTATTAACATAATAT
* *
21831285 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGTATTTATTAACATAATAT
* *
21831309 ATTTGGTATTGATTA
1 ATTTAGTATTTATTA
21831324 GAATTAAGTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.37, C:0.03, G:0.10, T:0.51
Consensus pattern (24 bp):
ATTTAGTATTTATTAACATAATAT
Found at i:21831787 original size:18 final size:18
Alignment explanation
Indices: 21831754--21831793 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
21831744 ATTAAAAATC
*
21831754 ATATTTTTTATATTTAAT
1 ATATTTTTTATATTTAAA
21831772 ATATTTTTTA-ATTTTAAA
1 ATATTTTTTATA-TTTAAA
21831790 ATAT
1 ATAT
21831794 ATAGTAACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 1 0.05
18 19 0.95
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
ATATTTTTTATATTTAAA
Found at i:21835677 original size:15 final size:15
Alignment explanation
Indices: 21835657--21835694 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
21835647 AAATTATATG
**
21835657 AAAAGTAATAATGTT
1 AAAAGTAATAATAAT
21835672 AAAAGTAATAATAAT
1 AAAAGTAATAATAAT
21835687 AAAAGTAA
1 AAAAGTAA
21835695 AAAACATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.63, C:0.00, G:0.11, T:0.26
Consensus pattern (15 bp):
AAAAGTAATAATAAT
Found at i:21838481 original size:2 final size:2
Alignment explanation
Indices: 21838476--21838500 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
21838466 TATATATATA
21838476 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
21838501 TTGGGATCGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:21839315 original size:45 final size:41
Alignment explanation
Indices: 21839162--21839318 Score: 156
Period size: 40 Copynumber: 3.8 Consensus size: 41
21839152 GTCCGATATA
* *
21839162 AGTAAGACCATAGCTAAAAGATGCTATGGCATCATA-AATG
1 AGTAAGACCATAGCTGAAAGATGCTATGACATCATATAATG
* * * *
21839202 AGTAAGACCATAGCTGTAATATGTTATGGCATCATAT-ATG
1 AGTAAGACCATAGCTGAAAGATGCTATGACATCATATAATG
* *** *
21839242 AGTAAGACCTTAGCTGAAAGACATTATGACATCATGATAGAAG
1 AGTAAGACCATAGCTGAAAGATGCTATGACATCAT-ATA-ATG
*
21839285 AGTGTAAGACCATTGCTGAAAGATGCTATGACAT
1 A--GTAAGACCATAGCTGAAAGATGCTATGACAT
21839319 ATTTTGATAG
Statistics
Matches: 95, Mismatches: 16, Indels: 7
0.81 0.14 0.06
Matches are distributed among these distances:
40 64 0.67
41 2 0.02
43 3 0.03
45 26 0.27
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (41 bp):
AGTAAGACCATAGCTGAAAGATGCTATGACATCATATAATG
Found at i:21840949 original size:26 final size:25
Alignment explanation
Indices: 21840900--21840954 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
21840890 CAACAAAACT
* * *
21840900 AAAATCTAACCTAAAAAGAAAAGAG
1 AAAACCTAAACTAAAAAGAAAAGAA
*
21840925 AAAACCTAAACTAAAAATGACAAGAA
1 AAAACCTAAACTAAAAA-GAAAAGAA
21840951 AAAA
1 AAAA
21840955 AAAGGAAAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 15 0.60
26 10 0.40
ACGTcount: A:0.67, C:0.13, G:0.09, T:0.11
Consensus pattern (25 bp):
AAAACCTAAACTAAAAAGAAAAGAA
Found at i:21843971 original size:11 final size:11
Alignment explanation
Indices: 21843955--21843979 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
21843945 AAAAGCGTTG
21843955 GAATATGCTAA
1 GAATATGCTAA
21843966 GAATATGCTAA
1 GAATATGCTAA
21843977 GAA
1 GAA
21843980 GTGTTGGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.08, G:0.20, T:0.24
Consensus pattern (11 bp):
GAATATGCTAA
Found at i:21844966 original size:40 final size:40
Alignment explanation
Indices: 21844922--21845070 Score: 102
Period size: 39 Copynumber: 4.0 Consensus size: 40
21844912 TACGCCAAAT
21844922 ATGAGTAAGACCATAACTGAAAGATGCTATGGCATCATAA
1 ATGAGTAAGACCATAACTGAAAGATGCTATGGCATCATAA
* ** *
21844962 ATGAGT-AG-----GA--GAAAGATTTTGTGGCATCATAA
1 ATGAGTAAGACCATAACTGAAAGATGCTATGGCATCATAA
* * *
21844994 ATGAGTAAAACCATAGCTAAAAGAT-CTTATGGCATCAT-A
1 ATGAGTAAGACCATAACTGAAAGATGC-TATGGCATCATAA
* * ** * *
21845033 ACGAGTAAGAGCATAGTTGAAAGATGTTATGACATCAT
1 ATGAGTAAGACCATAACTGAAAGATGCTATGGCATCAT
21845071 GATAGAAGTG
Statistics
Matches: 82, Mismatches: 17, Indels: 21
0.68 0.14 0.17
Matches are distributed among these distances:
32 25 0.30
33 1 0.01
34 1 0.01
39 33 0.40
40 22 0.27
ACGTcount: A:0.41, C:0.12, G:0.21, T:0.26
Consensus pattern (40 bp):
ATGAGTAAGACCATAACTGAAAGATGCTATGGCATCATAA
Found at i:21844976 original size:32 final size:32
Alignment explanation
Indices: 21844940--21845000 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
21844930 GACCATAACT
21844940 GAAAGATGCTATGGCATCATAAATGAGTAGGA
1 GAAAGATGCTATGGCATCATAAATGAGTAGGA
** *
21844972 GAAAGATTTTGTGGCATCATAAATGAGTA
1 GAAAGATGCTATGGCATCATAAATGAGTA
21845001 AAACCATAGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.39, C:0.08, G:0.26, T:0.26
Consensus pattern (32 bp):
GAAAGATGCTATGGCATCATAAATGAGTAGGA
Found at i:21845056 original size:39 final size:40
Alignment explanation
Indices: 21844972--21845070 Score: 110
Period size: 39 Copynumber: 2.5 Consensus size: 40
21844962 ATGAGTAGGA
* * *
21844972 GAAAGATTTTGTGGCATCATAAATGAGTAAAACCATAGCT
1 GAAAGATCTTATGGCATCATAAACGAGTAAAACCATAGCT
* * * *
21845012 AAAAGATCTTATGGCATCAT-AACGAGTAAGAGCATAGTT
1 GAAAGATCTTATGGCATCATAAACGAGTAAAACCATAGCT
* *
21845051 GAAAGATGTTATGACATCAT
1 GAAAGATCTTATGGCATCAT
21845071 GATAGAAGTG
Statistics
Matches: 49, Mismatches: 10, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
39 32 0.65
40 17 0.35
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.27
Consensus pattern (40 bp):
GAAAGATCTTATGGCATCATAAACGAGTAAAACCATAGCT
Found at i:21845254 original size:26 final size:27
Alignment explanation
Indices: 21845207--21845276 Score: 88
Period size: 26 Copynumber: 2.6 Consensus size: 27
21845197 CTGTTGGGAC
* * * *
21845207 AATAAACACGAGATAGTTTATCGGGAT
1 AATAAAAACGGGATAGTCTATCAGGAT
*
21845234 AAT-AAAATGGGATAGTCTATCAGGAT
1 AATAAAAACGGGATAGTCTATCAGGAT
21845260 AATAAAAACGGGATAGT
1 AATAAAAACGGGATAGT
21845277 TTTTTAGGAT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
26 21 0.58
27 15 0.42
ACGTcount: A:0.44, C:0.09, G:0.23, T:0.24
Consensus pattern (27 bp):
AATAAAAACGGGATAGTCTATCAGGAT
Found at i:21845285 original size:27 final size:27
Alignment explanation
Indices: 21845207--21845292 Score: 93
Period size: 27 Copynumber: 3.2 Consensus size: 27
21845197 CTGTTGGGAC
* * *
21845207 AATAAACACGAGATAGTTTATCGGGAT
1 AATAAAAACGGGATAGTTTATCAGGAT
* *
21845234 AAT-AAAATGGGATAGTCTATCAGGAT
1 AATAAAAACGGGATAGTTTATCAGGAT
* *
21845260 AATAAAAACGGGATAGTTTTTTAGGAT
1 AATAAAAACGGGATAGTTTATCAGGAT
*
21845287 AGTAAA
1 AATAAA
21845293 CAGGGGAAAT
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
26 21 0.44
27 27 0.56
ACGTcount: A:0.43, C:0.07, G:0.22, T:0.28
Consensus pattern (27 bp):
AATAAAAACGGGATAGTTTATCAGGAT
Found at i:21848986 original size:43 final size:44
Alignment explanation
Indices: 21848939--21849061 Score: 142
Period size: 43 Copynumber: 2.8 Consensus size: 44
21848929 TTGGCTTTGC
* * * * *
21848939 GCCATATTTTTTAACAAATACTATGTATTGGTGTTGGA-TTTAT
1 GCCATATTATTTAGCAGATACTATGTACTGGTGTTGGACATTAT
* * *
21848982 GCCATAGTATTTAGCAGGTACTATGTACTGGTGTT-GACATTGT
1 GCCATATTATTTAGCAGATACTATGTACTGGTGTTGGACATTAT
* *
21849025 GCCATATTATTCAGCAGATACTATGTACTAGTGTTGG
1 GCCATATTATTTAGCAGATACTATGTACTGGTGTTGG
21849062 TTATTTTACC
Statistics
Matches: 66, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
42 2 0.03
43 63 0.95
44 1 0.02
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.40
Consensus pattern (44 bp):
GCCATATTATTTAGCAGATACTATGTACTGGTGTTGGACATTAT
Found at i:21851556 original size:5 final size:5
Alignment explanation
Indices: 21851541--21851577 Score: 65
Period size: 5 Copynumber: 7.2 Consensus size: 5
21851531 TTTTAATATT
21851541 TTAATA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA T
1 TTAA-A TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA T
21851578 ATTTATTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 27 0.87
6 4 0.13
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
TTAAA
Found at i:21851607 original size:63 final size:67
Alignment explanation
Indices: 21851523--21851651 Score: 167
Period size: 63 Copynumber: 2.0 Consensus size: 67
21851513 ATTTCAAAAA
*
21851523 TAATAATATTTTAATATTTTAATATTAAA-TTA-A-ATTAA-ATTAAATTAAATTAAATATTTAT
1 TAATAATATTTTAATAATTTAATATTAAAGTTATATATTAATATTAAATTAAATTAAATATTTAT
21851584 TT
66 TT
* * * * *
21851586 TAATATTATTTTATTAATTTAATATTAAAGTTATTATCTTAATATTAAATTAAATTTAATGTTTA
1 TAATAATATTTTAATAATTTAATATTAAAGTTA-TATATTAATATTAAATTAAATTAAATATTTA
21851651 T
65 T
21851652 CTTGTAGATA
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
63 26 0.47
64 3 0.05
66 1 0.02
67 4 0.07
68 21 0.38
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.53
Consensus pattern (67 bp):
TAATAATATTTTAATAATTTAATATTAAAGTTATATATTAATATTAAATTAAATTAAATATTTAT
TT
Found at i:21851619 original size:20 final size:19
Alignment explanation
Indices: 21851541--21851645 Score: 78
Period size: 20 Copynumber: 5.5 Consensus size: 19
21851531 TTTTAATATT
21851541 TTAATATTAA-ATTAAATTAAA
1 TTAAT-TTAATATTAAATT--A
*
21851562 TTAAATTAA-ATTAAA-TA
1 TTAATTTAATATTAAATTA
* **
21851579 TTTATTTTAATATTATTTTA
1 -TTAATTTAATATTAAATTA
21851599 TTAATTTAATATTAAAGTTA
1 TTAATTTAATATTAAA-TTA
21851619 TT-ATCTTAATATTAAATTA
1 TTAAT-TTAATATTAAATTA
21851638 --AATTTAAT
1 TTAATTTAAT
21851646 GTTTATCTTG
Statistics
Matches: 70, Mismatches: 8, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
17 6 0.09
18 9 0.13
19 23 0.33
20 28 0.40
21 4 0.06
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (19 bp):
TTAATTTAATATTAAATTA
Found at i:21851619 original size:25 final size:25
Alignment explanation
Indices: 21851544--21851639 Score: 65
Period size: 25 Copynumber: 3.8 Consensus size: 25
21851534 TAATATTTTA
21851544 ATATTAA-ATTAAATTAAA-TTAAATT
1 ATATTAATATTAAATTAAAGTT--ATT
* **
21851569 AAATTAAATATTTATTTTAATA-TTATT
1 ATATT-AATA-TTAAATTAA-AGTTATT
*
21851596 TTATTAAT-TTAATATTAAAGTTATT
1 ATATTAATATTAA-ATTAAAGTTATT
*
21851621 ATCTTAATATTAAATTAAA
1 ATATTAATATTAAATTAAA
21851640 TTTAATGTTT
Statistics
Matches: 55, Mismatches: 9, Indels: 14
0.71 0.12 0.18
Matches are distributed among these distances:
24 4 0.07
25 25 0.45
26 9 0.16
27 7 0.13
28 7 0.13
29 3 0.05
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (25 bp):
ATATTAATATTAAATTAAAGTTATT
Found at i:21855766 original size:40 final size:40
Alignment explanation
Indices: 21855711--21855792 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
21855701 TTGAAGGACC
*
21855711 AATAGCGTAAATATTTTAAGGGTGGAATAATCTAGAAACT
1 AATAGCGTAAATATTTTAACGGTGGAATAATCTAGAAACT
*
21855751 AATAGTGTAAATATTTTAACGGTGGAATAATCTAGAAACT
1 AATAGCGTAAATATTTTAACGGTGGAATAATCTAGAAACT
21855791 AA
1 AA
21855793 GGAAAATGGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.44, C:0.07, G:0.18, T:0.30
Consensus pattern (40 bp):
AATAGCGTAAATATTTTAACGGTGGAATAATCTAGAAACT
Found at i:21858321 original size:25 final size:22
Alignment explanation
Indices: 21858288--21858338 Score: 59
Period size: 25 Copynumber: 2.2 Consensus size: 22
21858278 TTTGTAATTG
21858288 AAAAAAAATATT-CGAAGTATATAA
1 AAAAAAAAT-TTACGAAGT-TA-AA
21858312 AAAAATAAATTTACGAAGTTAAA
1 AAAAA-AAATTTACGAAGTTAAA
21858335 AAAA
1 AAAA
21858339 GTATTGAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
23 6 0.24
24 9 0.36
25 10 0.40
ACGTcount: A:0.65, C:0.04, G:0.08, T:0.24
Consensus pattern (22 bp):
AAAAAAAATTTACGAAGTTAAA
Found at i:21859321 original size:30 final size:29
Alignment explanation
Indices: 21859277--21859380 Score: 95
Period size: 30 Copynumber: 3.4 Consensus size: 29
21859267 GATTGAGAGC
21859277 GAAAAAGA-ATGTGAGCAAGAAAAGAAAGTT
1 GAAAAAGAGA-GTGAGCAAGAAAAGAAA-TT
* * *
21859307 GAAAACGAGAGTGAGAGAAAGCAAAACGAGATT
1 GAAAAAGAGAGT--GAGCAAG-AAAA-GAAATT
21859340 GAAAAAGA-ATGTGAGCAAGAAAAGCAAATT
1 GAAAAAGAGA-GTGAGCAAGAAAAG-AAATT
21859370 GAAAAAGAGAG
1 GAAAAAGAGAG
21859381 CGAGAATGTG
Statistics
Matches: 60, Mismatches: 6, Indels: 16
0.73 0.07 0.20
Matches are distributed among these distances:
29 1 0.02
30 26 0.43
31 8 0.13
32 7 0.12
33 15 0.25
34 3 0.05
ACGTcount: A:0.56, C:0.06, G:0.28, T:0.11
Consensus pattern (29 bp):
GAAAAAGAGAGTGAGCAAGAAAAGAAATT
Found at i:21861957 original size:21 final size:20
Alignment explanation
Indices: 21861928--21861970 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
21861918 AGCTTGTTTG
21861928 AGCTCATTTTAATTTATTCCT
1 AGCTCA-TTTAATTTATTCCT
* * *
21861949 AGCTTATTTACTTTATTTCT
1 AGCTCATTTAATTTATTCCT
21861969 AG
1 AG
21861971 AATAAACTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.23, C:0.16, G:0.07, T:0.53
Consensus pattern (20 bp):
AGCTCATTTAATTTATTCCT
Found at i:21868022 original size:39 final size:39
Alignment explanation
Indices: 21867963--21868218 Score: 332
Period size: 39 Copynumber: 6.5 Consensus size: 39
21867953 TGTAATTATA
* *
21867963 CCTGACTGCACATACGTGCCCCTTTTGTACTTCGGTACC
1 CCTGAATGCACATACGTGCCCCTGTTGTACTTCGGTACC
* * * *
21868002 CCTGAATACACATACATGCCCCTATTGTACTTCGATACC
1 CCTGAATGCACATACGTGCCCCTGTTGTACTTCGGTACC
* * * *
21868041 CCTAAATGCACATACATGCCCCTGTTGTACTTCAGCACC
1 CCTGAATGCACATACGTGCCCCTGTTGTACTTCGGTACC
***
21868080 CCTGAATGCACATACGTGCATTTGTTGTACTTCGGTACC
1 CCTGAATGCACATACGTGCCCCTGTTGTACTTCGGTACC
* *
21868119 CCTGAATGCACATACGTTCCCCTGTTGTACTTCAGTACC
1 CCTGAATGCACATACGTGCCCCTGTTGTACTTCGGTACC
**
21868158 CCTGAATGCACATACGTGCCCCTGTTGTACTTCTATACC
1 CCTGAATGCACATACGTGCCCCTGTTGTACTTCGGTACC
* *
21868197 CCTGATTCGCACTTACGTGCCC
1 CCTGAAT-GCACATACGTGCCC
21868219 TTGATTATAT
Statistics
Matches: 188, Mismatches: 28, Indels: 1
0.87 0.13 0.00
Matches are distributed among these distances:
39 175 0.93
40 13 0.07
ACGTcount: A:0.21, C:0.34, G:0.16, T:0.30
Consensus pattern (39 bp):
CCTGAATGCACATACGTGCCCCTGTTGTACTTCGGTACC
Found at i:21868142 original size:20 final size:20
Alignment explanation
Indices: 21868114--21868181 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
21868104 TTGTACTTCG
21868114 GTACCCCTGAATGCACATAC
1 GTACCCCTGAATGCACATAC
* * * *
21868134 GTTCCCCTG-TTGTAC-TTC
1 GTACCCCTGAATGCACATAC
21868152 AGTACCCCTGAATGCACATAC
1 -GTACCCCTGAATGCACATAC
*
21868173 GTGCCCCTG
1 GTACCCCTG
21868182 TTGTACTTCT
Statistics
Matches: 36, Mismatches: 9, Indels: 6
0.71 0.18 0.12
Matches are distributed among these distances:
18 2 0.06
19 12 0.33
20 20 0.56
21 2 0.06
ACGTcount: A:0.21, C:0.35, G:0.18, T:0.26
Consensus pattern (20 bp):
GTACCCCTGAATGCACATAC
Found at i:21868161 original size:19 final size:19
Alignment explanation
Indices: 21868137--21868200 Score: 51
Period size: 19 Copynumber: 3.3 Consensus size: 19
21868127 CACATACGTT
21868137 CCCCTGTTGTACTTCAGTA
1 CCCCTGTTGTACTTCAGTA
* * * *
21868156 CCCCTGAATGCACAT-ACGTG
1 CCCCTG-TTGTACTTCA-GTA
21868176 CCCCTGTTGTACTTCTA-TA
1 CCCCTGTTGTACTTC-AGTA
21868195 CCCCTG
1 CCCCTG
21868201 ATTCGCACTT
Statistics
Matches: 33, Mismatches: 8, Indels: 8
0.67 0.16 0.16
Matches are distributed among these distances:
19 19 0.58
20 13 0.39
21 1 0.03
ACGTcount: A:0.17, C:0.36, G:0.16, T:0.31
Consensus pattern (19 bp):
CCCCTGTTGTACTTCAGTA
Found at i:21883354 original size:10 final size:11
Alignment explanation
Indices: 21883329--21883354 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
21883319 ACTAAATAAT
21883329 AAAAAAGTTTC
1 AAAAAAGTTTC
21883340 AAAAAAGTTTC
1 AAAAAAGTTTC
21883351 AAAA
1 AAAA
21883355 CTAAAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.08, G:0.08, T:0.23
Consensus pattern (11 bp):
AAAAAAGTTTC
Found at i:21883863 original size:18 final size:17
Alignment explanation
Indices: 21883830--21883864 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
21883820 AATGAATGGG
*
21883830 AAATAAGAAATAAAATA
1 AAATAAAAAATAAAATA
21883847 AAATAAAAAAGTAAAATA
1 AAATAAAAAA-TAAAATA
21883865 CCTGCCATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (17 bp):
AAATAAAAAATAAAATA
Found at i:21885025 original size:20 final size:19
Alignment explanation
Indices: 21884988--21885050 Score: 56
Period size: 20 Copynumber: 3.3 Consensus size: 19
21884978 TTGATTTTTA
21884988 AAAAAATATAAAAATATTAT
1 AAAAAATATAAAAATATT-T
* * *
21885008 AAAAATTATTAAATTATTT
1 AAAAAATATAAAAATATTT
* * *
21885027 AAAAAGTATGAAAAT-TCT
1 AAAAAATATAAAAATATTT
21885045 AAAAAA
1 AAAAAA
21885051 ATATTTTTTA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
18 7 0.20
19 13 0.37
20 15 0.43
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (19 bp):
AAAAAATATAAAAATATTT
Found at i:21885424 original size:24 final size:24
Alignment explanation
Indices: 21885397--21885454 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
21885387 AGCTTCTTGA
21885397 TGGGCCCTATACTATGCTTCTAAG
1 TGGGCCCTATACTATGCTTCTAAG
*
21885421 TGGGCCCTATGCTATGCTTCTAAG
1 TGGGCCCTATACTATGCTTCTAAG
21885445 TGGGCCCTAT
1 TGGGCCCTAT
21885455 CGTTGGCTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.17, C:0.26, G:0.24, T:0.33
Consensus pattern (24 bp):
TGGGCCCTATACTATGCTTCTAAG
Found at i:21886016 original size:24 final size:25
Alignment explanation
Indices: 21885971--21886033 Score: 58
Period size: 24 Copynumber: 2.5 Consensus size: 25
21885961 GCGTTTAATT
21885971 TTTTAATTAATTTTTAAATAATATCTTA
1 TTTTAATTAA-TTTT--ATAATATCTTA
* *
21885999 TTTTAATTAATTTT-TAATTTGTTA
1 TTTTAATTAATTTTATAATATCTTA
*
21886023 TTCTAA-TAATT
1 TTTTAATTAATT
21886034 AAATATAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
23 5 0.16
24 13 0.41
27 4 0.12
28 10 0.31
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (25 bp):
TTTTAATTAATTTTATAATATCTTA
Found at i:21886490 original size:34 final size:32
Alignment explanation
Indices: 21886438--21886509 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 32
21886428 ATTTCTGTTA
*
21886438 AATTATAATTACTTTTTTAATATATAAATATCAC
1 AATTATAATTAATTTTTTAA-AT-TAAATATCAC
* *
21886472 AATT-TAATTAATATTTTTAAATTAAATATTAT
1 AATTATAATTAAT-TTTTTAAATTAAATATCAC
21886504 AATTAT
1 AATTAT
21886510 TTTAAAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
32 12 0.36
33 10 0.30
34 11 0.33
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (32 bp):
AATTATAATTAATTTTTTAAATTAAATATCAC
Found at i:21886517 original size:24 final size:25
Alignment explanation
Indices: 21886483--21886537 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
21886473 ATTTAATTAA
* *
21886483 TATTTTTAAAT-TAAATATTATAAT
1 TATTTTAAAATATAAATATAATAAT
* *
21886507 TATTTTAAAATATTAATCTAATAAT
1 TATTTTAAAATATAAATATAATAAT
21886532 TATTTT
1 TATTTT
21886538 TACTAAATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 10 0.38
25 16 0.62
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (25 bp):
TATTTTAAAATATAAATATAATAAT
Done.