Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000846.1 Hibiscus syriacus cultivar Beakdansim tig00001630_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: 988667
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 5
Found at i:548147 original size:25 final size:25
Alignment explanation
Indices: 548119--548178 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
548109 TTTACTCTAG
548119 TGAAAGTAATACACAATTCCATCAA
1 TGAAAGTAATACACAATTCCATCAA
* * * *
548144 TGAAAGTAACACATAATTTCATCGA
1 TGAAAGTAATACACAATTCCATCAA
*
548169 TGAATGTAAT
1 TGAAAGTAAT
548179 GATTGTAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (25 bp):
TGAAAGTAATACACAATTCCATCAA
Found at i:548226 original size:28 final size:28
Alignment explanation
Indices: 548182--548244 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
548172 ATGTAATGAT
*
548182 TGTAAAAGTATGAGTTGTTATTGCAATG
1 TGTAAAACTATGAGTTGTTATTGCAATG
* * *
548210 TGTAAAACTATGGGTTGTTATTGTAATT
1 TGTAAAACTATGAGTTGTTATTGCAATG
548238 TGTAAAA
1 TGTAAAA
548245 AAGTATATGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.33, C:0.03, G:0.22, T:0.41
Consensus pattern (28 bp):
TGTAAAACTATGAGTTGTTATTGCAATG
Found at i:548290 original size:29 final size:28
Alignment explanation
Indices: 548258--548376 Score: 111
Period size: 29 Copynumber: 4.2 Consensus size: 28
548248 TATATGTAAT
548258 TATTATAATTTATAAAAATATTTGCTCTC
1 TATTATAATTTATAAAAATATTT-CTCTC
* *
548287 TATTCTAATTTATAAAAATAATTT-TATTC
1 TATTATAATTTATAAAAAT-ATTTCT-CTC
*
548316 TATTATAATTTATAAAAGA-ATCATC-CTC
1 TATTATAATTTATAAAA-ATAT-TTCTCTC
* * *
548344 TATTTTAATTTATAAAAACATTT-TATC
1 TATTATAATTTATAAAAATATTTCTCTC
548371 TATTAT
1 TATTAT
548377 TGTAATTTAT
Statistics
Matches: 74, Mismatches: 9, Indels: 16
0.75 0.09 0.16
Matches are distributed among these distances:
27 9 0.12
28 23 0.31
29 37 0.50
30 5 0.07
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (28 bp):
TATTATAATTTATAAAAATATTTCTCTC
Found at i:548304 original size:58 final size:57
Alignment explanation
Indices: 548252--548361 Score: 136
Period size: 57 Copynumber: 1.9 Consensus size: 57
548242 AAAAAGTATA
*
548252 TGTAAT-TATTATAATTTATAAAA-ATAT-TTGCTCTCTATTCTAATTTATAAAAATAAT
1 TGTAATCTATTATAATTTATAAAAGA-ATCAT-C-CTCTATTCTAATTTATAAAAATAAT
* * *
548309 TTTATTCTATTATAATTTATAAAAGAATCATCCTCTATTTTAATTTATAAAAA
1 TGTAATCTATTATAATTTATAAAAGAATCATCCTCTATTCTAATTTATAAAAA
548362 CATTTTATCT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
57 24 0.52
58 20 0.43
59 2 0.04
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.47
Consensus pattern (57 bp):
TGTAATCTATTATAATTTATAAAAGAATCATCCTCTATTCTAATTTATAAAAATAAT
Found at i:548931 original size:25 final size:26
Alignment explanation
Indices: 548896--548983 Score: 76
Period size: 25 Copynumber: 3.5 Consensus size: 26
548886 ATTTCAACAA
548896 TGAAACTTAACATAAACTTACGCTAG
1 TGAAACTTAACATAAACTTACGCTAG
* * *
548922 TGAAA-TTAACACTTAATTCTA-G-TGG
1 TGAAACTTAACA-TAAACT-TACGCTAG
* * *
548947 TGAAACTTAACATAGACTTACACCAG
1 TGAAACTTAACATAAACTTACGCTAG
548973 TGAAA-TTAACA
1 TGAAACTTAACA
548984 CTTAATTCCA
Statistics
Matches: 48, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
24 2 0.04
25 22 0.46
26 22 0.46
27 2 0.04
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.28
Consensus pattern (26 bp):
TGAAACTTAACATAAACTTACGCTAG
Found at i:548966 original size:51 final size:49
Alignment explanation
Indices: 548896--549135 Score: 261
Period size: 51 Copynumber: 4.8 Consensus size: 49
548886 ATTTCAACAA
* *
548896 TGAAACTTAACATAAACTTACGCTAGTGAAATTAACACTTAATTCTAGTGG
1 TGAAACTTAACATAGACTTACAC-AGTGAAATTAACACTTAATTC-AGTGG
**
548947 TGAAACTTAACATAGACTTACACCAGTGAAATTAACACTTAATTCCAACGG
1 TGAAACTTAACATAGACTTACA-CAGTGAAATTAACACTTAATT-CAGTGG
* *
548998 TGGAACTTAACATAGACTTATACATGTGAAATTAACACTTAATTCATGTGG
1 TGAAACTTAACATAGACTTACACA-GTGAAATTAACACTTAATTCA-GTGG
* * **
549049 TGGAACTTAACATAGAC-TACACCGGTGAAATTAACACCTT--TTCAGTAA
1 TGAAACTTAACATAGACTTACA-CAGTGAAATTAACA-CTTAATTCAGTGG
* * *
549097 TAAAATTTAACATAGACTTACACCGATGAAATTAACACT
1 TGAAACTTAACATAGACTTACACAG-TGAAATTAACACT
549136 CAATATGTTC
Statistics
Matches: 165, Mismatches: 16, Indels: 19
0.82 0.08 0.09
Matches are distributed among these distances:
48 20 0.12
49 19 0.12
50 19 0.12
51 105 0.64
52 2 0.01
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.29
Consensus pattern (49 bp):
TGAAACTTAACATAGACTTACACAGTGAAATTAACACTTAATTCAGTGG
Found at i:548975 original size:26 final size:24
Alignment explanation
Indices: 548946--549034 Score: 65
Period size: 25 Copynumber: 3.5 Consensus size: 24
548936 AATTCTAGTG
548946 GTGAAACTTAACATAGACTTACACCA
1 GTGAAA-TTAACATAGACTTACA-CA
* *
548972 GTGAAATTAACACTTA-A-TTCCAACG
1 GTGAAATTAACA--TAGACTTAC-ACA
* *
548997 GTGGAACTTAACATAGACTTATACA
1 GT-GAAATTAACATAGACTTACACA
549022 TGTGAAATTAACA
1 -GTGAAATTAACA
549035 CTTAATTCAT
Statistics
Matches: 49, Mismatches: 7, Indels: 15
0.69 0.10 0.21
Matches are distributed among these distances:
24 2 0.04
25 24 0.49
26 21 0.43
27 2 0.04
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.27
Consensus pattern (24 bp):
GTGAAATTAACATAGACTTACACA
Found at i:549033 original size:102 final size:101
Alignment explanation
Indices: 548899--549085 Score: 288
Period size: 102 Copynumber: 1.8 Consensus size: 101
548889 TCAACAATGA
*
548899 AACTTAACATAAACTTACGCTAGTGAAATTAACACTTAATTC-TAGTGGTGAAACTTAACATAGA
1 AACTTAACATAAACTTACACTAGTGAAATTAACACTTAATTCAT-GTGGTGAAACTTAACATAGA
548963 CTTACACCAGTGAAATTAACACTTAATTCCAACGGTGG
65 C-TACACCAGTGAAATTAACACTTAATTCCAACGGTGG
* * *
549001 AACTTAACATAGACTTATAC-ATGTGAAATTAACACTTAATTCATGTGGTGGAACTTAACATAGA
1 AACTTAACATAAACTTACACTA-GTGAAATTAACACTTAATTCATGTGGTGAAACTTAACATAGA
*
549065 CTACACCGGTGAAATTAACAC
65 CTACACCAGTGAAATTAACAC
549086 CTTTTCAGTA
Statistics
Matches: 78, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
101 20 0.26
102 57 0.73
103 1 0.01
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (101 bp):
AACTTAACATAAACTTACACTAGTGAAATTAACACTTAATTCATGTGGTGAAACTTAACATAGAC
TACACCAGTGAAATTAACACTTAATTCCAACGGTGG
Found at i:552059 original size:28 final size:30
Alignment explanation
Indices: 552004--552061 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
551994 TAACGTTATT
*
552004 AGTGTACTAGGAATAATTGATTTAGATTAAC
1 AGTGTACTAGGAATAATTGA-TAAGATTAAC
*
552035 AGTGTATTAGGAATAATT-A-AAGATTAA
1 AGTGTACTAGGAATAATTGATAAGATTAA
552062 AGGATTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 7 0.28
30 1 0.04
31 17 0.68
ACGTcount: A:0.43, C:0.03, G:0.19, T:0.34
Consensus pattern (30 bp):
AGTGTACTAGGAATAATTGATAAGATTAAC
Found at i:556380 original size:16 final size:16
Alignment explanation
Indices: 556359--556390 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
556349 TAAAAGATCC
556359 ATAGTCAAGTATTATT
1 ATAGTCAAGTATTATT
556375 ATAGTCAAGTATTATT
1 ATAGTCAAGTATTATT
556391 TAGATTTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (16 bp):
ATAGTCAAGTATTATT
Found at i:559902 original size:47 final size:46
Alignment explanation
Indices: 559824--559939 Score: 117
Period size: 47 Copynumber: 2.5 Consensus size: 46
559814 ATCAATCTTG
* * * *
559824 ATTAGTGCATTCGTGCACACCTGTATCAGTGT-TTTGTGCACTCATGT
1 ATTAGTGCATACGTGCACTCCTGTATCAGTGTATTTGT--ACCCATGA
* * * *
559871 ATTAGTGCATACGGGCACTCTTGTTTGAGTGTAATTTGTACCCATGA
1 ATTAGTGCATACGTGCACTCCTGTATCAGTGT-ATTTGTACCCATGA
*
559918 ATTAGTGCATGCGTGCACTCCT
1 ATTAGTGCATACGTGCACTCCT
559940 CATTCTAGTG
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
47 51 0.91
49 5 0.09
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (46 bp):
ATTAGTGCATACGTGCACTCCTGTATCAGTGTATTTGTACCCATGA
Found at i:561114 original size:18 final size:18
Alignment explanation
Indices: 561087--561128 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
561077 TGGAACAAAG
*
561087 AGGAGCACCGACACCTCA
1 AGGAGTACCGACACCTCA
561105 AGGAGTACCGACACCTCA
1 AGGAGTACCGACACCTCA
561123 AGGAGT
1 AGGAGT
561129 GCTTGTGGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.33, C:0.31, G:0.26, T:0.10
Consensus pattern (18 bp):
AGGAGTACCGACACCTCA
Found at i:562016 original size:54 final size:54
Alignment explanation
Indices: 561934--562038 Score: 192
Period size: 54 Copynumber: 1.9 Consensus size: 54
561924 TTAGAATCAA
561934 TCTTAGAAATGTCAGGTGTGCGACAAATTCCATGGAGGCTTATGTAGAGCTGAT
1 TCTTAGAAATGTCAGGTGTGCGACAAATTCCATGGAGGCTTATGTAGAGCTGAT
* *
561988 TCTTAGAAATGTCAGGTGTGCGGCAAATTCCATGGAGGGTTATGTAGAGCT
1 TCTTAGAAATGTCAGGTGTGCGACAAATTCCATGGAGGCTTATGTAGAGCT
562039 TTAAGAGGAG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.27, C:0.14, G:0.30, T:0.30
Consensus pattern (54 bp):
TCTTAGAAATGTCAGGTGTGCGACAAATTCCATGGAGGCTTATGTAGAGCTGAT
Found at i:565165 original size:23 final size:23
Alignment explanation
Indices: 565113--565167 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
565103 CGTGTACTTC
*
565113 TGTATTAGTTCTTCTAGCACTCT
1 TGTATTAGTGCTTCTAGCACTCT
**
565136 TACATTAGTGCTTTCT-GCACTCT
1 TGTATTAGTGC-TTCTAGCACTCT
565159 TGTATTAGT
1 TGTATTAGT
565168 ACCATTGGGT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 22 0.85
24 4 0.15
ACGTcount: A:0.18, C:0.20, G:0.15, T:0.47
Consensus pattern (23 bp):
TGTATTAGTGCTTCTAGCACTCT
Found at i:566077 original size:86 final size:86
Alignment explanation
Indices: 565932--566108 Score: 354
Period size: 86 Copynumber: 2.1 Consensus size: 86
565922 CTTTAACTTG
565932 TATTTGGGCATGTGTAGGGGTTAAGGGTGTTACATTTATTTATATCAGAGCTGCAAGTTTAGCCA
1 TATTTGGGCATGTGTAGGGGTTAAGGGTGTTACATTTATTTATATCAGAGCTGCAAGTTTAGCCA
565997 ATTCTCAATCGAAAATGAAGT
66 ATTCTCAATCGAAAATGAAGT
566018 TATTTGGGCATGTGTAGGGGTTAAGGGTGTTACATTTATTTATATCAGAGCTGCAAGTTTAGCCA
1 TATTTGGGCATGTGTAGGGGTTAAGGGTGTTACATTTATTTATATCAGAGCTGCAAGTTTAGCCA
566083 ATTCTCAATCGAAAATGAAGT
66 ATTCTCAATCGAAAATGAAGT
566104 TATTT
1 TATTT
566109 TCAGTCAAAA
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 91 1.00
ACGTcount: A:0.29, C:0.11, G:0.24, T:0.36
Consensus pattern (86 bp):
TATTTGGGCATGTGTAGGGGTTAAGGGTGTTACATTTATTTATATCAGAGCTGCAAGTTTAGCCA
ATTCTCAATCGAAAATGAAGT
Found at i:568532 original size:2 final size:2
Alignment explanation
Indices: 568525--568572 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
568515 GATTAATTAG
568525 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
568567 AT AT AT
1 AT AT AT
568573 GTATCCTATC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:569750 original size:24 final size:24
Alignment explanation
Indices: 569718--569767 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
569708 AAGTCTTATA
569718 ACATTGCGTTTGTGTTGAAATTCC
1 ACATTGCGTTTGTGTTGAAATTCC
569742 ACATTGCGTTTGTGTTGAAATTCC
1 ACATTGCGTTTGTGTTGAAATTCC
569766 AC
1 AC
569768 TTGGCACTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.40
Consensus pattern (24 bp):
ACATTGCGTTTGTGTTGAAATTCC
Found at i:570972 original size:21 final size:21
Alignment explanation
Indices: 570943--571009 Score: 89
Period size: 21 Copynumber: 3.2 Consensus size: 21
570933 GATGAAGTGG
*
570943 AAGTAGATGAATTACCTTTGT
1 AAGTAGATGAATTACCTTGGT
* * *
570964 AAGTTGATGAAGTGCCTTGGT
1 AAGTAGATGAATTACCTTGGT
*
570985 AAATAGATGAATTACCTTGGT
1 AAGTAGATGAATTACCTTGGT
571006 AAGT
1 AAGT
571010 GTCTCTGAAA
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.33, C:0.09, G:0.24, T:0.34
Consensus pattern (21 bp):
AAGTAGATGAATTACCTTGGT
Found at i:571852 original size:210 final size:208
Alignment explanation
Indices: 571460--571877 Score: 676
Period size: 210 Copynumber: 2.0 Consensus size: 208
571450 TCCCACAGAT
571460 AGTAGGTGTGTGGGTTTTCCATGCAATAGAATTCTGGAATGCTTGATCGTGGAATCTTTAGTTCA
1 AGTAGGTGTGTGGGTTTTCCATGCAATAGAATTCTGGAATGCTTGATCGTGGAATCTTTAGTTCA
* *
571525 AACATTCTGAAAATCACAACAGTGAAAGAAACATGTGAAGTGAAAAACTGCAAGAGTTTTATCCT
66 AACATTCTGAAAATCACAACAGTGAAAGAAACATGTGAAGTGAAAAACTCCAAGAGTTTGATCCT
* **
571590 GAAACCTTACAAGTTTCTCCAAGGAAGCAACACATCGAGAGCCAAGAAGTTAATTTTGTACTCTT
131 GAAACCTCACAAGTCACTCCAAGGAAGCAACACATCGAGAGCCAAGAAGTTAATTTTGTACTCTT
571655 TAAAATACTTTTC
196 TAAAATACTTTTC
** * * *
571668 AGTAGGTGTGTGGGTTTTTTTGATGCCATAGAATTTTGGAATGCTTGATTGTGGAATCTTTAGTT
1 AGTAGGTGTGTGGG--TTTTCCATGCAATAGAATTCTGGAATGCTTGATCGTGGAATCTTTAGTT
* * *
571733 CGAACATTCTTAAAATCACAACAGTGAAAGCAACAT-TGAAGTGAAAAACTCCAAGAGTTTGATC
64 CAAACATTCTGAAAATCACAACAGTGAAAGAAACATGTGAAGTGAAAAACTCCAAGAGTTTGATC
*
571797 CTGAAACCTCACAAGTCACTCCAATGAAGCAACACATCGAGAGCCAAGAAAGTTAATTTTGTACT
129 CTGAAACCTCACAAGTCACTCCAAGGAAGCAACACATCGAGAGCCAAG-AAGTTAATTTTGTACT
571862 CTTTAAAATACTTTTC
193 CTTTAAAATACTTTTC
571878 GCTAAAAAGT
Statistics
Matches: 193, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
208 14 0.07
209 70 0.36
210 109 0.56
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (208 bp):
AGTAGGTGTGTGGGTTTTCCATGCAATAGAATTCTGGAATGCTTGATCGTGGAATCTTTAGTTCA
AACATTCTGAAAATCACAACAGTGAAAGAAACATGTGAAGTGAAAAACTCCAAGAGTTTGATCCT
GAAACCTCACAAGTCACTCCAAGGAAGCAACACATCGAGAGCCAAGAAGTTAATTTTGTACTCTT
TAAAATACTTTTC
Found at i:572515 original size:11 final size:11
Alignment explanation
Indices: 572480--572506 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
572470 TTTTTTTGCC
572480 TTTTTCTCTTT
1 TTTTTCTCTTT
572491 TTTTTCTCTTT
1 TTTTTCTCTTT
572502 TTTTT
1 TTTTT
572507 TTGTTTTTTA
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:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTCTCTTT
Found at i:573310 original size:18 final size:18
Alignment explanation
Indices: 573287--573324 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
573277 ACCAGCCCTC
573287 CAAATCATAA-TGAGAAGA
1 CAAATCA-AAGTGAGAAGA
*
573305 CAAATCAAAGTGTGAAGA
1 CAAATCAAAGTGAGAAGA
573323 CA
1 CA
573325 TTCCTCTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.53, C:0.13, G:0.18, T:0.16
Consensus pattern (18 bp):
CAAATCAAAGTGAGAAGA
Found at i:575595 original size:21 final size:21
Alignment explanation
Indices: 575561--575600 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
575551 GTGGAACTAT
*
575561 ATGAATTACCTTGGTAAGTCG
1 ATGAAGTACCTTGGTAAGTCG
*
575582 ATGAAGTACGTTGGTAAGT
1 ATGAAGTACCTTGGTAAGT
575601 GTCTCTGATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.10, G:0.28, T:0.33
Consensus pattern (21 bp):
ATGAAGTACCTTGGTAAGTCG
Found at i:575946 original size:2 final size:2
Alignment explanation
Indices: 575901--575937 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
575891 TGCACATCTT
*
575901 TA TA T- TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
575938 GTTTATATAC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:582291 original size:22 final size:21
Alignment explanation
Indices: 582259--582304 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 21
582249 CCACCTCCAT
582259 TTCATCATCAACACCATCAAC
1 TTCATCATCAACACCATCAAC
*
582280 TTCATCCATCAAGACCATCAAC
1 TTCAT-CATCAACACCATCAAC
582302 TTC
1 TTC
582305 GCAGCCATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.35, C:0.37, G:0.02, T:0.26
Consensus pattern (21 bp):
TTCATCATCAACACCATCAAC
Found at i:584028 original size:24 final size:23
Alignment explanation
Indices: 583991--584051 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 23
583981 AAACATGTCT
* *
583991 CTTGATGTTTCAAAGATAATGCCA
1 CTTGAAGTTCCAAAGA-AATGCCA
* *
584015 TTTGAAGTTCCAAAAGAAATGTCA
1 CTTGAAGTTCC-AAAGAAATGCCA
584039 CTTGAAGTTCCAA
1 CTTGAAGTTCCAA
584052 GAGTTGTGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
23 2 0.06
24 24 0.77
25 5 0.16
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.31
Consensus pattern (23 bp):
CTTGAAGTTCCAAAGAAATGCCA
Found at i:585866 original size:22 final size:21
Alignment explanation
Indices: 585829--585870 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
585819 CCACCTTTTT
585829 TTCATCATCAACACCATCAAC
1 TTCATCATCAACACCATCAAC
*
585850 TTCATCCATCAAGACCATCAA
1 TTCAT-CATCAACACCATCAA
585871 TTCCGCAGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.38, C:0.36, G:0.02, T:0.24
Consensus pattern (21 bp):
TTCATCATCAACACCATCAAC
Found at i:587272 original size:15 final size:16
Alignment explanation
Indices: 587254--587284 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
587244 TATTTTTTTA
587254 TTTTTTTA-CTTTTCT
1 TTTTTTTACCTTTTCT
587269 TTTTTTTACCTTTTCT
1 TTTTTTTACCTTTTCT
587285 ATTTATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTTTTACCTTTTCT
Found at i:587273 original size:16 final size:17
Alignment explanation
Indices: 587254--587294 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 17
587244 TATTTTTTTA
587254 TTTTTTTA-CTTTTC-T
1 TTTTTTTACCTTTTCAT
587269 TTTTTTTACCTTTTCTAT
1 TTTTTTTACCTTTTC-AT
587287 TTATTTTT
1 TT-TTTTT
587295 TATTTTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 8 0.36
16 6 0.27
18 3 0.14
19 5 0.23
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTTTTACCTTTTCAT
Found at i:587374 original size:21 final size:20
Alignment explanation
Indices: 587333--587376 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
587323 ATCTAACAAC
*
587333 AAATAATTGAAACTAAACTA
1 AAATAATTGAAACGAAACTA
* *
587353 AAATAAATTGAAAGGAACCTA
1 AAAT-AATTGAAACGAAACTA
587374 AAA
1 AAA
587377 ATGTTTAACT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.61, C:0.09, G:0.09, T:0.20
Consensus pattern (20 bp):
AAATAATTGAAACGAAACTA
Found at i:590621 original size:15 final size:15
Alignment explanation
Indices: 590601--590635 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
590591 AAATTCATTA
590601 CATTGGAATGATAGT
1 CATTGGAATGATAGT
590616 CATTGGAATGATAGT
1 CATTGGAATGATAGT
*
590631 TATTG
1 CATTG
590636 ATACTTGCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.31, C:0.06, G:0.26, T:0.37
Consensus pattern (15 bp):
CATTGGAATGATAGT
Found at i:592377 original size:23 final size:24
Alignment explanation
Indices: 592350--592419 Score: 106
Period size: 23 Copynumber: 3.0 Consensus size: 24
592340 TATATCAATT
592350 ATTTGTGCACTCATGTATTAGTGC
1 ATTTGTGCACTCATGTATTAGTGC
* *
592374 -TTTGTGTATTCATGTATTAGTGC
1 ATTTGTGCACTCATGTATTAGTGC
*
592397 ATCTGTGCACTCATGTATTAGTG
1 ATTTGTGCACTCATGTATTAGTG
592420 AAATTTTGCA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
23 21 0.52
24 19 0.47
ACGTcount: A:0.20, C:0.14, G:0.21, T:0.44
Consensus pattern (24 bp):
ATTTGTGCACTCATGTATTAGTGC
Found at i:592429 original size:24 final size:23
Alignment explanation
Indices: 592332--592420 Score: 97
Period size: 23 Copynumber: 3.8 Consensus size: 23
592322 AGTGCATTCA
* * * *
592332 TGCACTCATATATCAATTATTTG
1 TGCACTCATGTATTAGTGATTTG
*
592355 TGCACTCATGTATTAGTGCTTTG
1 TGCACTCATGTATTAGTGATTTG
* * *
592378 TGTATTCATGTATTAGTGCATCTG
1 TGCACTCATGTATTAGTG-ATTTG
592402 TGCACTCATGTATTAGTGA
1 TGCACTCATGTATTAGTGA
592421 AATTTTGCAA
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
23 35 0.65
24 19 0.35
ACGTcount: A:0.24, C:0.16, G:0.18, T:0.43
Consensus pattern (23 bp):
TGCACTCATGTATTAGTGATTTG
Found at i:592573 original size:25 final size:25
Alignment explanation
Indices: 592517--592575 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 25
592507 ATATTACTAC
* *
592517 TTTTTGCACTCTTGTATTAGTATCA
1 TTTTTGTACTCCTGTATTAGTATCA
*
592542 -TTGTGTACTCCTGTATTTAGTA-CA
1 TTTTTGTACTCCTGTA-TTAGTATCA
592566 TTTTTGTACT
1 TTTTTGTACT
592576 TTTGGTACTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
24 14 0.50
25 14 0.50
ACGTcount: A:0.19, C:0.15, G:0.14, T:0.53
Consensus pattern (25 bp):
TTTTTGTACTCCTGTATTAGTATCA
Found at i:593819 original size:6 final size:6
Alignment explanation
Indices: 593801--593839 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
593791 TTTTCAGAAA
*
593801 TTTCAT ATTTCAT TTTCAT CTTTCAT TTTCAT ATTCAT T
1 TTTCAT -TTTCAT TTTCAT -TTTCAT TTTCAT TTTCAT T
593840 ACACAACAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
6 17 0.59
7 12 0.41
ACGTcount: A:0.21, C:0.18, G:0.00, T:0.62
Consensus pattern (6 bp):
TTTCAT
Found at i:593819 original size:13 final size:13
Alignment explanation
Indices: 593801--593839 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
593791 TTTTCAGAAA
593801 TTTCATATTTCAT
1 TTTCATATTTCAT
*
593814 TTTCATCTTTCAT
1 TTTCATATTTCAT
593827 TTTCATA-TTCAT
1 TTTCATATTTCAT
593839 T
1 T
593840 ACACAACAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 6 0.25
13 18 0.75
ACGTcount: A:0.21, C:0.18, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTCATATTTCAT
Found at i:593940 original size:19 final size:19
Alignment explanation
Indices: 593878--593943 Score: 87
Period size: 19 Copynumber: 3.5 Consensus size: 19
593868 TTCATTTCTG
* *
593878 ATTCAGAACTTACTTTCAA
1 ATTCATAACTTAATTTCAA
593897 ATTCATAACTTAATTTCAA
1 ATTCATAACTTAATTTCAA
* *
593916 ATTCATAGCTTATTTTCAA
1 ATTCATAACTTAATTTCAA
*
593935 AATCATAAC
1 ATTCATAAC
593944 CCAATGCATA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 41 1.00
ACGTcount: A:0.39, C:0.18, G:0.03, T:0.39
Consensus pattern (19 bp):
ATTCATAACTTAATTTCAA
Found at i:600950 original size:5 final size:5
Alignment explanation
Indices: 600917--600972 Score: 51
Period size: 5 Copynumber: 10.8 Consensus size: 5
600907 GTTTTCTTAT
* * *
600917 TTTTA TTTATT TTTTA TTTGA TGTTA TTTTA TTTTA TTTT- TTATTA TTTTTA
1 TTTTA TTT-TA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TT-TTA -TTTTA
600969 TTTT
1 TTTT
600973 TATCTAATAT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
4 2 0.05
5 30 0.73
6 7 0.17
7 2 0.05
ACGTcount: A:0.18, C:0.00, G:0.04, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:600973 original size:27 final size:27
Alignment explanation
Indices: 600913--600975 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
600903 AGTCGTTTTC
600913 TTATTTTTA-TTTATTTTTTATTTGATG
1 TTATTTTTATTTTATTTTTTATTT-ATG
*
600940 TTA-TTTTATTTTATTTTTTA-TTATTT
1 TTATTTTTATTTTATTTTTTATTTA-TG
600966 TTATTTTTAT
1 TTATTTTTAT
600976 CTAATATCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
25 1 0.03
26 11 0.34
27 20 0.62
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (27 bp):
TTATTTTTATTTTATTTTTTATTTATG
Found at i:601138 original size:20 final size:19
Alignment explanation
Indices: 601109--601152 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
601099 TTTTTAATTC
601109 TATTTATTTTCT-TCTTCTT
1 TATTTATTTT-TATCTTCTT
*
601128 TATTCTATTTTTATTTTCTT
1 TATT-TATTTTTATCTTCTT
601148 TATTT
1 TATTT
601153 TGACTTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.75
Consensus pattern (19 bp):
TATTTATTTTTATCTTCTT
Found at i:601159 original size:11 final size:9
Alignment explanation
Indices: 601085--601206 Score: 55
Period size: 9 Copynumber: 13.8 Consensus size: 9
601075 TATATTACTA
601085 TTATTTTCT
1 TTATTTTCT
601094 TTATTTT-T
1 TTATTTTCT
* *
601102 TTAATTCTAT
1 TT-ATTTTCT
601112 TTATTTTC-
1 TTATTTTCT
*
601120 -T-TCTTCT
1 TTATTTTCT
*
601127 TTATTCTATTT
1 TTATT-T-TCT
601138 TTATTTTCT
1 TTATTTTCT
601147 TTATTTTGACT
1 TTATTTT--CT
601158 TTA--TT-T
1 TTATTTTCT
*
601164 TTATTTCCT
1 TTATTTTCT
* *
601173 CTATATTCAT
1 TTATTTTC-T
601183 TT-TATTTCT
1 TTAT-TTTCT
601192 TTA-TTTCT
1 TTATTTTCT
601200 TTATTTT
1 TTATTTT
601207 TATTTTTATT
Statistics
Matches: 84, Mismatches: 13, Indels: 32
0.65 0.10 0.25
Matches are distributed among these distances:
6 8 0.10
7 1 0.01
8 13 0.15
9 40 0.48
10 10 0.12
11 12 0.14
ACGTcount: A:0.16, C:0.11, G:0.01, T:0.72
Consensus pattern (9 bp):
TTATTTTCT
Found at i:601162 original size:26 final size:26
Alignment explanation
Indices: 601133--601206 Score: 78
Period size: 26 Copynumber: 2.8 Consensus size: 26
601123 TTCTTTATTC
*
601133 TATTTTTATTTTCTTTATTTTGACTT
1 TATTTTTATTTTCTTTATTTTCACTT
* * * *
601159 TATTTTTATTTCCTCTATATTCATTT
1 TATTTTTATTTTCTTTATTTTCACTT
601185 TATTTCTT-TATTTCTTTATTTT
1 TATTT-TTAT-TTTCTTTATTTT
601207 TATTTTTATT
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
26 27 0.71
27 11 0.29
ACGTcount: A:0.16, C:0.11, G:0.01, T:0.72
Consensus pattern (26 bp):
TATTTTTATTTTCTTTATTTTCACTT
Found at i:601185 original size:41 final size:42
Alignment explanation
Indices: 601131--601211 Score: 101
Period size: 41 Copynumber: 2.0 Consensus size: 42
601121 TCTTCTTTAT
* * *
601131 TCTATTTTTATTTTCTTTATTT-TGACTTTATTTTTATTTCC
1 TCTATATTCATTTTATTTATTTATGACTTTATTTTTATTTCC
* **
601172 TCTATATTCATTTTATTTCTTTATTTCTTTATTTTTATTT
1 TCTATATTCATTTTATTTATTTATGACTTTATTTTTATTT
601212 TTATTTTATT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
41 18 0.55
42 15 0.45
ACGTcount: A:0.16, C:0.11, G:0.01, T:0.72
Consensus pattern (42 bp):
TCTATATTCATTTTATTTATTTATGACTTTATTTTTATTTCC
Found at i:601216 original size:12 final size:12
Alignment explanation
Indices: 601199--601304 Score: 60
Period size: 12 Copynumber: 8.7 Consensus size: 12
601189 TCTTTATTTC
601199 TTTATTTTTATT
1 TTTATTTTTATT
601211 TTTA-TTTTATT
1 TTTATTTTTATT
* *
601222 CTTGTTTTTATTT
1 TTTATTTTTA-TT
*
601235 ATTTATTATATATGT
1 -TTTATT-TTTAT-T
*
601250 TGTTATTATTT-TA
1 T-TTATT-TTTATT
*
601263 TTTATTTTTTATC
1 TTTA-TTTTTATT
601276 TTTATTTTTA-T
1 TTTATTTTTATT
*
601287 TCT-TTTTTA-T
1 TTTATTTTTATT
601297 TTTATTTT
1 TTTATTTT
601305 CTTTATCTCA
Statistics
Matches: 74, Mismatches: 11, Indels: 19
0.71 0.11 0.18
Matches are distributed among these distances:
10 9 0.12
11 15 0.20
12 21 0.28
13 10 0.14
14 7 0.09
15 12 0.16
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.76
Consensus pattern (12 bp):
TTTATTTTTATT
Found at i:601233 original size:23 final size:22
Alignment explanation
Indices: 601203--601304 Score: 68
Period size: 23 Copynumber: 4.5 Consensus size: 22
601193 TATTTCTTTA
601203 TTTTTATTTTTATTTTATTCTTG
1 TTTTTATTTTTATTTTATT-TTG
*
601226 TTTTTATTTATTTATTATATATGTTG
1 TTTTTA-TT-TTTATT-T-TATTTTG
* *
601252 TTATTA-TTTTA-TTTATTTTT
1 TTTTTATTTTTATTTTATTTTG
601272 TATCTTTATTTTTATTCTT-TTTT-
1 T-T-TTTATTTTTATT-TTATTTTG
*
601295 ATTTTATTTT
1 TTTTTATTTT
601305 CTTTATCTCA
Statistics
Matches: 64, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
20 6 0.09
21 10 0.16
22 5 0.08
23 15 0.23
24 8 0.12
25 8 0.12
26 9 0.14
27 3 0.05
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.76
Consensus pattern (22 bp):
TTTTTATTTTTATTTTATTTTG
Found at i:601235 original size:27 final size:27
Alignment explanation
Indices: 601205--601302 Score: 80
Period size: 27 Copynumber: 3.6 Consensus size: 27
601195 TTTCTTTATT
601205 TTTATTTTTATTTTATTCTTGTTTTTA
1 TTTATTTTTATTTTATTCTTGTTTTTA
* * *
601232 TTTA--TTTATTATATATGTTGTTATTA
1 TTTATTTTTATTTTAT-TCTTGTTTTTA
*
601258 TTTTATTTATT-TTTTA-TCTTTATTTTTA
1 -TTTATTT-TTATTTTATTC-TTGTTTTTA
601286 TTCT-TTTTTATTTTATT
1 TT-TATTTTTATTTTATT
601303 TTCTTTATCT
Statistics
Matches: 55, Mismatches: 7, Indels: 17
0.70 0.09 0.22
Matches are distributed among these distances:
25 9 0.16
26 11 0.20
27 19 0.35
28 9 0.16
29 5 0.09
30 2 0.04
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.76
Consensus pattern (27 bp):
TTTATTTTTATTTTATTCTTGTTTTTA
Found at i:601324 original size:80 final size:77
Alignment explanation
Indices: 601176--601333 Score: 178
Period size: 77 Copynumber: 2.0 Consensus size: 77
601166 ATTTCCTCTA
* * *
601176 TATTCATTTTATTTCTTTATTTCTTTATTTTTATTTTTATTTTATTCTTGTTTTTATTTATTTAT
1 TATTCATTTTATTTATTTATTTCTTTATTTTTATTCTTATTTTATTCTTGTTTTTATTCATTTAT
601241 TATA-TATGTTGT
66 TATATTAT-TTGT
* * *
601253 TATT-ATTTTATTTATTTTTTATCTTTATTTTTATTCTT-TTTTATTTTATTTTCTTTATCTCAT
1 TATTCATTTTATTTATTTATT-TCTTTATTTTTATTCTTATTTTATTCT-TGTT-TTTAT-TCA-
*
601316 TTTTTTATATTATTTGT
61 TTTATTATATTATTTGT
601333 T
1 T
601334 TTCTTATCTT
Statistics
Matches: 68, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
76 22 0.32
77 23 0.34
78 5 0.07
79 2 0.03
80 13 0.19
81 3 0.04
ACGTcount: A:0.18, C:0.06, G:0.03, T:0.74
Consensus pattern (77 bp):
TATTCATTTTATTTATTTATTTCTTTATTTTTATTCTTATTTTATTCTTGTTTTTATTCATTTAT
TATATTATTTGT
Found at i:601335 original size:14 final size:13
Alignment explanation
Indices: 601174--601335 Score: 50
Period size: 14 Copynumber: 12.1 Consensus size: 13
601164 TTATTTCCTC
601174 TATATTCATTTTATT
1 TATATT-ATTTT-TT
* *
601189 TCT-TTATTTCTT
1 TATATTATTTTTT
*
601201 TATTTTTATTTTTAT
1 TA-TATTATTTTT-T
* *
601216 TTTATTCTTGTTTT
1 TATATTATT-TTTT
*
601230 TAT-TTA-TTTAT
1 TATATTATTTTTT
601241 TATA-TATGTTGTTAT
1 TATATTAT-TT-TT-T
* *
601256 TATTTTATTTATT
1 TATATTATTTTTT
601269 T-T-TTATCTTTATT
1 TATATTAT-TTT-TT
* *
601282 TTTATT-CTTTTT
1 TATATTATTTTTT
*
601294 TATTTTATTTTCTT
1 TATATTATTTT-TT
* *
601308 TATCTCATTTTTT
1 TATATTATTTTTT
601321 TATATTATTTGTTT
1 TATATTATTT-TTT
601335 T
1 T
601336 CTTATCTTCC
Statistics
Matches: 108, Mismatches: 22, Indels: 35
0.65 0.13 0.21
Matches are distributed among these distances:
11 12 0.11
12 13 0.12
13 30 0.28
14 35 0.32
15 15 0.14
16 3 0.03
ACGTcount: A:0.18, C:0.06, G:0.02, T:0.74
Consensus pattern (13 bp):
TATATTATTTTTT
Found at i:601366 original size:14 final size:14
Alignment explanation
Indices: 601349--601375 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
601339 ATCTTCCTTA
601349 CTTTATTTTATTTG
1 CTTTATTTTATTTG
601363 CTTTATTTTATTT
1 CTTTATTTTATTT
601376 ATTTTCATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.07, G:0.04, T:0.74
Consensus pattern (14 bp):
CTTTATTTTATTTG
Found at i:606282 original size:18 final size:18
Alignment explanation
Indices: 606261--606300 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
606251 CAATTTAGTC
606261 ATTTTCTTATTT-TTATTT
1 ATTTT-TTATTTGTTATTT
*
606279 ATTTTTTATTTGTTGTTT
1 ATTTTTTATTTGTTATTT
606297 ATTT
1 ATTT
606301 GTTTTATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.15, C:0.03, G:0.05, T:0.78
Consensus pattern (18 bp):
ATTTTTTATTTGTTATTT
Found at i:606286 original size:11 final size:11
Alignment explanation
Indices: 606270--606312 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
606260 CATTTTCTTA
*
606270 TTTTTATTTAT
1 TTTTTATTTGT
606281 TTTTTATTTGT
1 TTTTTATTTGT
*
606292 TGTTTATTTGT
1 TTTTTATTTGT
606303 TTTATTATTT
1 TTT-TTATTT
606313 TTATCTAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
11 22 0.79
12 6 0.21
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (11 bp):
TTTTTATTTGT
Found at i:606345 original size:2 final size:2
Alignment explanation
Indices: 606338--606390 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
606328 TTTACATGTT
606338 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
606380 TA TA TA TA TA T
1 TA TA TA TA TA T
606391 TATTTTATTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:606545 original size:22 final size:23
Alignment explanation
Indices: 606520--606562 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
606510 CTCTATATTC
*
606520 ATTTTTTTCTT-TATTTATTTTT
1 ATTTTATTCTTGTATTTATTTTT
*
606542 ATTTTATTCTTGTTTTTATTT
1 ATTTTATTCTTGTATTTATTT
606563 ATTTATTGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.14, C:0.05, G:0.02, T:0.79
Consensus pattern (23 bp):
ATTTTATTCTTGTATTTATTTTT
Found at i:606595 original size:9 final size:9
Alignment explanation
Indices: 606529--606639 Score: 50
Period size: 9 Copynumber: 11.8 Consensus size: 9
606519 CATTTTTTTC
606529 TTTATTTATT
1 TTTATTTA-T
606539 TTTATTTTAT
1 TTTA-TTTAT
* *
606549 TCTTGTTTTT
1 T-TTATTTAT
606559 ATTTATTTAT
1 -TTTATTTAT
* *
606569 TGTA-TAAGT
1 TTTATTTA-T
606578 TGTTA-TTAT
1 T-TTATTTAT
606587 TTTATTTAT
1 TTTATTTAT
*
606596 TTTCTTTAT
1 TTTATTTAT
606605 TTT-TCTCTAT
1 TTTAT-T-TAT
*
606615 ATT-TTTAT
1 TTTATTTAT
*
606623 TCTTATTTCT
1 T-TTATTTAT
606633 TTTATTT
1 TTTATTT
606640 TCTTTATCTC
Statistics
Matches: 79, Mismatches: 12, Indels: 21
0.71 0.11 0.19
Matches are distributed among these distances:
8 9 0.11
9 32 0.41
10 31 0.39
11 7 0.09
ACGTcount: A:0.18, C:0.05, G:0.04, T:0.73
Consensus pattern (9 bp):
TTTATTTAT
Found at i:606643 original size:10 final size:10
Alignment explanation
Indices: 606591--606678 Score: 51
Period size: 10 Copynumber: 8.5 Consensus size: 10
606581 TATTATTTTA
606591 TTTATTTTC-
1 TTTATTTTCT
606600 TTTATTTTTCT
1 TTTA-TTTTCT
* *
606611 CTATATTTTTAT
1 -TTTA-TTTTCT
606623 TCTTA-TTTCT
1 T-TTATTTTCT
606633 TTTATTTTC-
1 TTTATTTTCT
606642 TTTATCTCATT-T
1 TTTAT-T--TTCT
606654 TTTATTTTCT
1 TTTATTTTCT
606664 TTTATTCTT-T
1 TTTATT-TTCT
606674 TTTAT
1 TTTAT
606679 ATAACTCTTT
Statistics
Matches: 64, Mismatches: 4, Indels: 21
0.72 0.04 0.24
Matches are distributed among these distances:
9 14 0.22
10 28 0.44
11 4 0.06
12 18 0.28
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.75
Consensus pattern (10 bp):
TTTATTTTCT
Found at i:606645 original size:9 final size:9
Alignment explanation
Indices: 606583--606665 Score: 50
Period size: 9 Copynumber: 9.2 Consensus size: 9
606573 TAAGTTGTTA
*
606583 TTATTTTAT
1 TTATTTTCT
606592 TTATTTTCT
1 TTATTTTCT
606601 TTATTTTTCT
1 TTA-TTTTCT
* *
606611 CTATATT-T
1 TTATTTTCT
606619 TTA--TTC-
1 TTATTTTCT
606625 TTA-TTTCTT
1 TTATTTTC-T
606634 TTATTTTCT
1 TTATTTTCT
*
606643 TTATCTCATTTT
1 TTAT-T--TTCT
606655 TTATTTTCT
1 TTATTTTCT
606664 TT
1 TT
606666 TATTCTTTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 18
0.71 0.07 0.22
Matches are distributed among these distances:
6 5 0.08
7 3 0.05
8 3 0.05
9 27 0.46
10 13 0.22
11 1 0.02
12 7 0.12
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.75
Consensus pattern (9 bp):
TTATTTTCT
Found at i:606655 original size:20 final size:21
Alignment explanation
Indices: 606632--606701 Score: 72
Period size: 21 Copynumber: 3.2 Consensus size: 21
606622 TTCTTATTTC
606632 TTTTATTTTC-TTTATCTCATT
1 TTTTATTTTCTTTTAT-TCATT
606653 TTTTATTTTCTTTTATTC-TT
1 TTTTATTTTCTTTTATTCATT
* *
606673 TTTTATATAACTCTTTTATTGATT
1 TTTTAT-T--TTCTTTTATTCATT
606697 TTTTA
1 TTTTA
606702 AGGGGTACGT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
20 8 0.19
21 13 0.31
22 5 0.12
23 9 0.21
24 7 0.17
ACGTcount: A:0.17, C:0.10, G:0.01, T:0.71
Consensus pattern (21 bp):
TTTTATTTTCTTTTATTCATT
Found at i:607859 original size:15 final size:15
Alignment explanation
Indices: 607839--607877 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
607829 TATTATAATA
607839 AAAACTAAATTATAT
1 AAAACTAAATTATAT
607854 AAAACTAAATTATAT
1 AAAACTAAATTATAT
607869 AAAACTAAA
1 AAAACTAAA
607878 GAAAATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (15 bp):
AAAACTAAATTATAT
Found at i:608438 original size:54 final size:54
Alignment explanation
Indices: 608356--608460 Score: 210
Period size: 54 Copynumber: 1.9 Consensus size: 54
608346 GGAAAAAATA
608356 TGTCTTCCCTTTAAGTTGTGCATATCATCTTCAATCTCTTACATTACACACATT
1 TGTCTTCCCTTTAAGTTGTGCATATCATCTTCAATCTCTTACATTACACACATT
608410 TGTCTTCCCTTTAAGTTGTGCATATCATCTTCAATCTCTTACATTACACAC
1 TGTCTTCCCTTTAAGTTGTGCATATCATCTTCAATCTCTTACATTACACAC
608461 CCCTTTCATC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.24, C:0.27, G:0.08, T:0.42
Consensus pattern (54 bp):
TGTCTTCCCTTTAAGTTGTGCATATCATCTTCAATCTCTTACATTACACACATT
Found at i:608498 original size:32 final size:32
Alignment explanation
Indices: 608434--608503 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
608424 GTTGTGCATA
* * *
608434 TCATCTTCAATCTCTTACATTACACACCCCTT
1 TCATCTTCAATCTCCTACAATACAAACCCCTT
*
608466 TCATCTTCAATCTCCTACACATA-AAACTCCTT
1 TCATCTTCAATCTCCTACA-ATACAAACCCCTT
608498 TCATCT
1 TCATCT
608504 AACCAAAAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 31 0.94
33 2 0.06
ACGTcount: A:0.27, C:0.36, G:0.00, T:0.37
Consensus pattern (32 bp):
TCATCTTCAATCTCCTACAATACAAACCCCTT
Found at i:613166 original size:5 final size:5
Alignment explanation
Indices: 613158--613182 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
613148 TAAAAATAAA
613158 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
613183 GAGTATTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:613553 original size:20 final size:21
Alignment explanation
Indices: 613520--613561 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
613510 AAGTTATTTG
*
613520 TATATAAATTTTATTGAATATA
1 TATATAAA-TTTATAGAATATA
613542 TATATAAA-TTATAGAATATA
1 TATATAAATTTATAGAATATA
613562 AAATTGTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 11 0.58
22 8 0.42
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (21 bp):
TATATAAATTTATAGAATATA
Found at i:616210 original size:54 final size:54
Alignment explanation
Indices: 616094--616211 Score: 130
Period size: 54 Copynumber: 2.2 Consensus size: 54
616084 ATTGCACTGA
* * ** *
616094 AGTGCCGAAATGGAGATTCGTAAACTTATTATGAATTCCATGGATTACACACAT
1 AGTGCCGAAATGGACATTCATAAACACATTATGAATACCATGGATTACACACAT
* * * **
616148 AGTACCGAAATGGTCATTCATAAACACATTATGAATACCATGCG-TTGCACATTT
1 AGTGCCGAAATGGACATTCATAAACACATTATGAATACCATG-GATTACACACAT
616202 AGTGCCGAAA
1 AGTGCCGAAA
616212 ATGCACCGTT
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
54 51 0.98
55 1 0.02
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.28
Consensus pattern (54 bp):
AGTGCCGAAATGGACATTCATAAACACATTATGAATACCATGGATTACACACAT
Found at i:617489 original size:11 final size:11
Alignment explanation
Indices: 617475--617507 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
617465 GTTTTAATCA
*
617475 TCCTTTAACCT
1 TCCTTAAACCT
617486 TCCTTAAACCT
1 TCCTTAAACCT
617497 TCCTTAAACCT
1 TCCTTAAACCT
617508 CTATATCACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.24, C:0.36, G:0.00, T:0.39
Consensus pattern (11 bp):
TCCTTAAACCT
Found at i:618561 original size:12 final size:13
Alignment explanation
Indices: 618543--618625 Score: 79
Period size: 12 Copynumber: 6.8 Consensus size: 13
618533 AACAACAATA
618543 AATATAA-ACTAT
1 AATATAATACTAT
* *
618555 TATATAATACAAT
1 AATATAATACTAT
618568 -ATATAATA-TAT
1 AATATAATACTAT
618579 AATATAATACTAT
1 AATATAATACTAT
618592 AATAT-ATA-TAAT
1 AATATAATACT-AT
**
618604 AATATGCTA-TAT
1 AATATAATACTAT
618616 AATATAATAC
1 AATATAATAC
618626 ATACTATATA
Statistics
Matches: 59, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
11 3 0.05
12 41 0.69
13 15 0.25
ACGTcount: A:0.54, C:0.06, G:0.01, T:0.39
Consensus pattern (13 bp):
AATATAATACTAT
Found at i:618597 original size:37 final size:36
Alignment explanation
Indices: 618543--618659 Score: 114
Period size: 37 Copynumber: 3.2 Consensus size: 36
618533 AACAACAATA
*
618543 AATATAA-ACTATTATATAATACAATATATAATATAT
1 AATATAATACTATAATAT-ATACAATATATAATATAT
* **
618579 AATATAATACTATAATATATATAATAATATGCTATAT
1 AATATAATACTATAATATATACAAT-ATATAATATAT
* *
618616 AATATAATAC-ATACTATATACCATATA-AATGTTATAT
1 AATATAATACTATAATATATACAATATATAA---TATAT
618653 AATATAA
1 AATATAA
618660 CATAATATGT
Statistics
Matches: 67, Mismatches: 9, Indels: 9
0.79 0.11 0.11
Matches are distributed among these distances:
35 3 0.04
36 24 0.36
37 40 0.60
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.38
Consensus pattern (36 bp):
AATATAATACTATAATATATACAATATATAATATAT
Found at i:618602 original size:17 final size:18
Alignment explanation
Indices: 618539--618625 Score: 74
Period size: 17 Copynumber: 4.8 Consensus size: 18
618529 TAATAACAAC
618539 AATA-AATATAA-ACTAT
1 AATATAATATAATACTAT
* *
618555 TATATAATACAATA-TAT
1 AATATAATATAATACTAT
618572 AATATATAATATAATACTAT
1 -A-ATATAATATAATACTAT
*
618592 AATAT-ATATAATAATAT
1 AATATAATATAATACTAT
*
618609 GCTATATAATATAATAC
1 --AATATAATATAATAC
618626 ATACTATATA
Statistics
Matches: 56, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
16 3 0.05
17 20 0.36
18 5 0.09
19 17 0.30
20 11 0.20
ACGTcount: A:0.55, C:0.06, G:0.01, T:0.38
Consensus pattern (18 bp):
AATATAATATAATACTAT
Found at i:618636 original size:7 final size:7
Alignment explanation
Indices: 618565--618621 Score: 53
Period size: 7 Copynumber: 7.9 Consensus size: 7
618555 TATATAATAC
618565 AATATAT
1 AATATAT
618572 AATATAT
1 AATATAT
618579 AATATAAT
1 AATAT-AT
*
618587 ACTATA-
1 AATATAT
618593 ATATATAT
1 A-ATATAT
618601 AATAATAT
1 AAT-ATAT
**
618609 GCTATAT
1 AATATAT
618616 AATATA
1 AATATA
618622 ATACATACTA
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
6 1 0.03
7 27 0.68
8 12 0.30
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (7 bp):
AATATAT
Found at i:622996 original size:19 final size:19
Alignment explanation
Indices: 622972--623016 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
622962 TAAATTCCTC
622972 AGTGCATCGGTGCATGGTA
1 AGTGCATCGGTGCATGGTA
622991 AGTGCATCGGTGCATGGTA
1 AGTGCATCGGTGCATGGTA
623010 AGTGCAT
1 AGTGCAT
623017 GGATGTATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.22, C:0.16, G:0.36, T:0.27
Consensus pattern (19 bp):
AGTGCATCGGTGCATGGTA
Found at i:622996 original size:65 final size:64
Alignment explanation
Indices: 622862--623005 Score: 175
Period size: 65 Copynumber: 2.2 Consensus size: 64
622852 GTGCACTAAG
* * *
622862 AGTGAATCGATGCATCAAGTGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGCT
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGGCT
* * * *
622926 GGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAT-TCCTCAGTGCATCGGTGCATGG-
1 AGTGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATAGCCACAGTGCATCGATGCATGGC
622989 T
64 T
*
622990 AAGTGCATCGGTGCAT
1 -AGTGCATCGATGCAT
623006 GGTAAGTGCA
Statistics
Matches: 68, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
64 28 0.41
65 36 0.53
66 4 0.06
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.29
Consensus pattern (64 bp):
AGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGGCT
Found at i:623052 original size:84 final size:82
Alignment explanation
Indices: 622907--623071 Score: 181
Period size: 84 Copynumber: 2.0 Consensus size: 82
622897 AAATAGCCAG
* *
622907 AGTGCATCGATGCATGGCTGGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAATTCCTC
1 AGTGCATCGATGCATGGCTAGTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAATTCAT-
*
622972 AGTGCATCGGTGCATGGTA
64 AGTGCATCGATGCATGGTA
* * * * * *
622991 AGTGCATCGGTGCATGG-TAAGTGCATGGATGTATGATATGCATTCGATG-TTCAATTTAATTCA
1 AGTGCATCGATGCATGGCT-AGTGCATCGATGCATCAAATGCATTCGATGTTTC-A-TAAATTCA
*
623054 TGGTGCATCGATGCATGG
63 TAGTGCATCGATGCATGG
623072 ATTGGTTCAG
Statistics
Matches: 68, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
82 3 0.04
83 17 0.25
84 48 0.71
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (82 bp):
AGTGCATCGATGCATGGCTAGTGCATCGATGCATCAAATGCATTCGATGTTTCATAAATTCATAG
TGCATCGATGCATGGTA
Found at i:624177 original size:14 final size:14
Alignment explanation
Indices: 624158--624189 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
624148 GAGAGGAGCT
*
624158 AGGAGCAGCTCGTG
1 AGGAGCAACTCGTG
624172 AGGAGCAACTCGTG
1 AGGAGCAACTCGTG
624186 AGGA
1 AGGA
624190 ACTAGCTCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.28, C:0.19, G:0.41, T:0.12
Consensus pattern (14 bp):
AGGAGCAACTCGTG
Found at i:625241 original size:14 final size:14
Alignment explanation
Indices: 625206--625246 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
625196 ATGAGCAATG
*
625206 TTTTGAAAA-ACTA
1 TTTTGAAAATAATA
625219 -TTTGAAAATAATA
1 TTTTGAAAATAATA
*
625232 TTTTGTAAATAATA
1 TTTTGAAAATAATA
625246 T
1 T
625247 GTATAGTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 8 0.33
13 3 0.12
14 13 0.54
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.44
Consensus pattern (14 bp):
TTTTGAAAATAATA
Found at i:629619 original size:22 final size:21
Alignment explanation
Indices: 629577--629616 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
629567 AAGAATATTT
629577 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
**
629598 TCATTTTTGTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
629617 ATAGAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:631505 original size:29 final size:29
Alignment explanation
Indices: 631460--631526 Score: 116
Period size: 29 Copynumber: 2.3 Consensus size: 29
631450 GCAGTTGGGA
*
631460 GCATCAGTACATCGATGCATACCCATGGT
1 GCATCAGTGCATCGATGCATACCCATGGT
*
631489 GCGTCAGTGCATCGATGCATACCCATGGT
1 GCATCAGTGCATCGATGCATACCCATGGT
631518 GCATCAGTG
1 GCATCAGTG
631527 TAAAATTCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.24, C:0.27, G:0.25, T:0.24
Consensus pattern (29 bp):
GCATCAGTGCATCGATGCATACCCATGGT
Found at i:631716 original size:65 final size:64
Alignment explanation
Indices: 631584--631742 Score: 180
Period size: 65 Copynumber: 2.5 Consensus size: 64
631574 TAAGAGTGCA
* * *
631584 TGCATCGATGCATCAAGTGCATTTGATG-TTTCAAACTAGCCAGAGTGCATCGATGCATGGCTGG
1 TGCATCGATGCATCAAATGCATTTGATGTTTTCAAAATAGCCA-AGTGCATCGATGCATGGCTAG
* * * *
631648 TGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCGTC-AGTGCATCGGTGCATGG-TA
1 TGCATCGATGCATCAAATGCATTTGATGTTTTC--AAAATAGCCAAGTGCATCGATGCATGGCT-
631711 AG
63 AG
* *
631713 TGCATCGATACATGAAATGCATTTGATGTT
1 TGCATCGATGCATCAAATGCATTTGATGTT
631743 CAATTTAATT
Statistics
Matches: 81, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
64 27 0.33
65 48 0.59
67 6 0.07
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (64 bp):
TGCATCGATGCATCAAATGCATTTGATGTTTTCAAAATAGCCAAGTGCATCGATGCATGGCTAG
Found at i:636246 original size:25 final size:25
Alignment explanation
Indices: 636218--636271 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
636208 TACTTAACTC
*
636218 GATCAGATACGGATTTGATTGTTAA
1 GATCAAATACGGATTTGATTGTTAA
636243 GATCAAATACGGATTTGATTGTTAA
1 GATCAAATACGGATTTGATTGTTAA
636268 GATC
1 GATC
636272 TTAACTTAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.33, C:0.09, G:0.22, T:0.35
Consensus pattern (25 bp):
GATCAAATACGGATTTGATTGTTAA
Found at i:637563 original size:24 final size:24
Alignment explanation
Indices: 637535--637642 Score: 69
Period size: 24 Copynumber: 4.5 Consensus size: 24
637525 GAATATTTTA
637535 TCTGATTTCTGACTTGAATTATGT
1 TCTGATTTCTGACTTGAATTATGT
* * *
637559 TCTGA-TACATTACCTGAATTATGT
1 TCTGATTTC-TGACTTGAATTATGT
* * *
637583 TCTGATTTGTGATCTAG-ATTATTT
1 TCTGATTTCTGA-CTTGAATTATGT
* * **
637607 TATGATATCTGA-TCTGAATTCCGT
1 TCTGATTTCTGACT-TGAATTATGT
*
637631 TTTGATTTCTGA
1 TCTGATTTCTGA
637643 TATCTTCGTT
Statistics
Matches: 61, Mismatches: 18, Indels: 10
0.69 0.20 0.11
Matches are distributed among these distances:
22 1 0.02
23 3 0.05
24 54 0.89
25 3 0.05
ACGTcount: A:0.23, C:0.13, G:0.16, T:0.48
Consensus pattern (24 bp):
TCTGATTTCTGACTTGAATTATGT
Found at i:651652 original size:24 final size:24
Alignment explanation
Indices: 651601--651652 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
651591 AATCCTGTTG
* * *
651601 TGATTTCTTATCTGGATTCTCTTC
1 TGATATCTTATCTGAATTCGCTTC
651625 TGATATCTTATCTGAATTCAGCTT-
1 TGATATCTTATCTGAATTC-GCTTC
651649 TGAT
1 TGAT
651653 TTCTGATATC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 21 0.88
25 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.13, T:0.50
Consensus pattern (24 bp):
TGATATCTTATCTGAATTCGCTTC
Found at i:656124 original size:12 final size:13
Alignment explanation
Indices: 656107--656202 Score: 96
Period size: 12 Copynumber: 7.7 Consensus size: 13
656097 TAATAAAAAC
656107 ATAATAATA-ATA
1 ATAATAATATATA
656119 ATAATAATA-ATA
1 ATAATAATATATA
*
656131 A-ACTAATATATA
1 ATAATAATATATA
656143 AT-ATAATATATA
1 ATAATAATATATA
* **
656155 AT-ACAATATGCA
1 ATAATAATATATA
656167 ATATATAATATATA
1 ATA-ATAATATATA
656181 ATATATAATATATA
1 ATA-ATAATATATA
656195 AT-ATAATA
1 ATAATAATA
656203 GTATTTTTGA
Statistics
Matches: 72, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
11 6 0.08
12 43 0.60
14 23 0.32
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.36
Consensus pattern (13 bp):
ATAATAATATATA
Found at i:656146 original size:7 final size:7
Alignment explanation
Indices: 656107--656199 Score: 93
Period size: 7 Copynumber: 13.1 Consensus size: 7
656097 TAATAAAAAC
656107 ATAATA-
1 ATAATAT
656113 ATAATA-
1 ATAATAT
656119 ATAATA-
1 ATAATAT
*
656125 ATAATAA
1 ATAATAT
656132 ACTAATAT
1 A-TAATAT
656140 ATAATAT
1 ATAATAT
656147 AATATATAAT
1 -ATA-AT-AT
*
656157 ACAATAT
1 ATAATAT
**
656164 GCAATAT
1 ATAATAT
656171 ATAATAT
1 ATAATAT
656178 ATAATAT
1 ATAATAT
656185 ATAATAT
1 ATAATAT
656192 ATAATAT
1 ATAATAT
656199 A
1 A
656200 ATAGTATTTT
Statistics
Matches: 77, Mismatches: 5, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
6 18 0.23
7 42 0.55
8 11 0.14
9 4 0.05
10 2 0.03
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (7 bp):
ATAATAT
Found at i:656156 original size:33 final size:32
Alignment explanation
Indices: 656107--656197 Score: 96
Period size: 33 Copynumber: 2.8 Consensus size: 32
656097 TAATAAAAAC
656107 ATAATAATAATA-ATAATAATAATAAACTAATAT
1 ATAAT-ATAATATATAATAATAATAAAC-AATAT
* **
656140 ATAATATAATATATAAT-ACAATATGCAATAT
1 ATAATATAATATATAATAATAATAAACAATAT
656171 ATAATATATAATATATAATATATAATA
1 AT-A-ATATAATATATAATA-ATAATA
656198 TAATAGTATT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
31 7 0.14
32 13 0.27
33 24 0.49
35 5 0.10
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.36
Consensus pattern (32 bp):
ATAATATAATATATAATAATAATAAACAATAT
Found at i:657117 original size:65 final size:65
Alignment explanation
Indices: 656919--657127 Score: 219
Period size: 65 Copynumber: 3.2 Consensus size: 65
656909 GTGCACTAAG
* * *
656919 AGTGCATCGATGCATGAAATGCATTCGATGTTTCAAAAT-AGCCA-GAGTGCATCGATGCATGGC
1 AGTGCATCGATGCATGAAATGCATTCGATGTTTCAATATAATCCATG-GTGCATCGATGCATGGT
656982 T
65 T
* * * * * * ** *
656983 GGTGCATCGATGCATCAAATGTATTCCATGTTTTC-ATAAAATCCTTATTGCATCGGTGCATGGT
1 AGTGCATCGATGCATGAAATGCATTCGATG-TTTCAATATAATCCATGGTGCATCGATGCATGGT
*
657047 A
65 T
* *
657048 AGTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATGGTGCATCGATGCATGGAT
1 AGTGCATCGATGCATGAAATGCATTCGATGTTTCAATATAATCCATGGTGCATCGATGCATGG-T
657112 T
65 T
*
657113 AGTGCATCGGTGCAT
1 AGTGCATCGATGCAT
657128 CACTTTGAAA
Statistics
Matches: 114, Mismatches: 26, Indels: 9
0.77 0.17 0.06
Matches are distributed among these distances:
63 3 0.03
64 49 0.43
65 62 0.54
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (65 bp):
AGTGCATCGATGCATGAAATGCATTCGATGTTTCAATATAATCCATGGTGCATCGATGCATGGTT
Found at i:659221 original size:13 final size:14
Alignment explanation
Indices: 659200--659229 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
659190 TAATTAAATC
659200 AGAACATCAAATTT
1 AGAACATCAAATTT
659214 AGAA-ATCAAATTT
1 AGAACATCAAATTT
659227 AGA
1 AGA
659230 TTTTCGAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.53, C:0.10, G:0.10, T:0.27
Consensus pattern (14 bp):
AGAACATCAAATTT
Found at i:659681 original size:23 final size:22
Alignment explanation
Indices: 659651--659732 Score: 85
Period size: 23 Copynumber: 3.6 Consensus size: 22
659641 GTATGGCCTT
659651 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
659673 CGTGCATCGATGCACCTT-TATG
1 -GTGCATCGATGCACATTCAAGG
*
659695 GTGTATCGATGCACATTCAAAGG
1 GTGCATCGATGCACATTC-AAGG
*
659718 GATACATCGATGCAC
1 G-TGCATCGATGCAC
659733 TATTAAGTGT
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
21 15 0.32
22 2 0.04
23 19 0.40
24 11 0.23
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.26
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:659708 original size:44 final size:44
Alignment explanation
Indices: 659655--659751 Score: 128
Period size: 44 Copynumber: 2.2 Consensus size: 44
659645 GGCCTTGTGC
* *
659655 ATCGATGCACATTC-AAGGCG-TGCATCGATGCACCT-TTATGGTGT
1 ATCGATGCACATTCAAAGG-GATACATCGATGCA-CTATTA-AGTGT
659699 ATCGATGCACATTCAAAGGGATACATCGATGCACTATTAAGTGT
1 ATCGATGCACATTCAAAGGGATACATCGATGCACTATTAAGTGT
659743 ATCGATGCA
1 ATCGATGCA
659752 TGAAGCACAA
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
44 30 0.62
45 18 0.38
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.28
Consensus pattern (44 bp):
ATCGATGCACATTCAAAGGGATACATCGATGCACTATTAAGTGT
Found at i:665694 original size:65 final size:65
Alignment explanation
Indices: 665494--665704 Score: 214
Period size: 65 Copynumber: 3.3 Consensus size: 65
665484 CGTTGGACCC
* *
665494 TTAGTGCATCGATGCATGAAATGCATTCAATGTTTCAAAAT-AGCCA-GAGTGCATCGATGCATG
1 TTAGTGCATCGATGCATGAAATGCATTCAATGTTTCAATATAATCCATG-GTGCATCGATGCATG
665557 G
65 G
* * * * * * ** * *
665558 TTGGTGCATCGATGCATCAAATGTATTCCATGTTTTC-ATAAAATCCTTATTGCATTGGTGCATG
1 TTAGTGCATCGATGCATGAAATGCATTCAATG-TTTCAATATAATCCATGGTGCATCGATGCATG
665622 G
65 G
* * * *
665623 TAAGTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATGGTGCATCGATGCATGG
1 TTAGTGCATCGATGCATGAAATGCATTCAATGTTTCAATATAATCCATGGTGCATCGATGCATGG
*
665687 ATTAGTGCATCGGTGCAT
1 -TTAGTGCATCGATGCAT
665705 CACTTTGAAA
Statistics
Matches: 115, Mismatches: 27, Indels: 9
0.76 0.18 0.06
Matches are distributed among these distances:
63 3 0.03
64 50 0.43
65 62 0.54
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (65 bp):
TTAGTGCATCGATGCATGAAATGCATTCAATGTTTCAATATAATCCATGGTGCATCGATGCATGG
Found at i:665966 original size:7 final size:7
Alignment explanation
Indices: 665960--666184 Score: 110
Period size: 7 Copynumber: 31.0 Consensus size: 7
665950 CAAGTATAAT
665960 ATATAATA
1 ATAT-ATA
665968 ATATATA
1 ATATATA
665975 ATATAT-
1 ATATATA
665981 A-ATATA
1 ATATATA
665987 ATATATA
1 ATATATA
* *
665994 TTATGTA
1 ATATATA
**
666001 CCATATA
1 ATATATA
666008 A-ATAT-
1 ATATATA
666013 -TATATA
1 ATATATA
666019 ATATATA
1 ATATATA
* *
666026 CTACATA
1 ATATATA
666033 ATATACT-
1 ATATA-TA
666040 ATAATTATA
1 AT-A-TATA
666049 ATATATA
1 ATATATA
*
666056 CTATATA
1 ATATATA
666063 ATATAACATA
1 ATAT---ATA
666073 ATATATA
1 ATATATA
666080 ATACTATA
1 ATA-TATA
666088 TACTATATAA
1 -A-TATAT-A
666098 ATATTATA
1 ATA-TATA
666106 ATATATA
1 ATATATA
* *
666113 TGTTGTATA
1 --ATATATA
*
666122 ATGTACCATA
1 A--TA-TATA
*
666132 CTATATA
1 ATATATA
666139 ATATATA
1 ATATATA
*
666146 CTATATA
1 ATATATA
666153 A-A-ATA
1 ATATATA
666158 ATATATA
1 ATATATA
666165 ATATAGT-
1 ATATA-TA
666172 ATA-ATA
1 ATATATA
666178 ATATATA
1 ATATATA
666185 TAAATAGAAA
Statistics
Matches: 168, Mismatches: 22, Indels: 55
0.69 0.09 0.22
Matches are distributed among these distances:
5 13 0.08
6 12 0.07
7 91 0.54
8 21 0.12
9 18 0.11
10 13 0.08
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.41
Consensus pattern (7 bp):
ATATATA
Found at i:665978 original size:5 final size:5
Alignment explanation
Indices: 665954--666110 Score: 68
Period size: 5 Copynumber: 31.8 Consensus size: 5
665944 TTTCAACAAG
* *
665954 TATAA TAT-A TAATAA TAT-A TA-ATA TATAA TATAA TAT-A TATTA TGTACCA
1 TATAA TATAA T-ATAA TATAA TATA-A TATAA TATAA TATAA TATAA TATA--A
* * *
666004 TATAAA TATTA TATAA TAT-A TACT-A CATAA TATAC TATAA TTATAA
1 TAT-AA TATAA TATAA TATAA TA-TAA TATAA TATAA TATAA -TATAA
* *
666050 TAT-A TACT-A TATAA TATAA CATAA TAT-A TAATAC TAT-A TACT-A
1 TATAA TA-TAA TATAA TATAA TATAA TATAA T-ATAA TATAA TA-TAA
*
666093 TATAA -ATAT TATAA TATA
1 TATAA TATAA TATAA TATA
666111 TATGTTGTAT
Statistics
Matches: 118, Mismatches: 15, Indels: 38
0.69 0.09 0.22
Matches are distributed among these distances:
4 25 0.21
5 76 0.64
6 13 0.11
7 3 0.03
8 1 0.01
ACGTcount: A:0.52, C:0.06, G:0.01, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:666054 original size:37 final size:36
Alignment explanation
Indices: 665955--666187 Score: 114
Period size: 37 Copynumber: 6.4 Consensus size: 36
665945 TTCAACAAGT
*
665955 ATAATATA-TAATAATATATAATATATAATATAATATAT
1 ATAATATACT-ATAAT-TATAATATATAATAT-ATATAC
* * *
665993 ATTATGTACCATATAA--ATATTATATAATATATACTAC
1 ATAATATA-C-TATAATTATAATATATAATATATA-TAC
666030 ATAATATACTATAATTATAATATATACTATATAATATAAC
1 ATAATATACTATAATTATAATATATA--ATAT-ATAT-AC
* *
666070 ATAATATA-TAATACTATATACTATATAA-ATAT-T--
1 ATAATATACT-ATAAT-TATAATATATAATATATATAC
** * **
666103 ATAATATA-TATGTTGTATAATGTACCATACTATATA-
1 ATAATATACTATAAT-TATAATATATAATA-TATATAC
**
666139 AT-ATATACTATATAAAATAATATATAATATAGTATA-
1 ATAATATACTATA-ATTATAATATATAATATA-TATAC
666175 ATAATATA-TATAA
1 ATAATATACTATAA
666188 ATAGAAACCC
Statistics
Matches: 152, Mismatches: 23, Indels: 43
0.70 0.11 0.20
Matches are distributed among these distances:
32 11 0.07
33 10 0.07
34 3 0.02
35 14 0.09
36 30 0.20
37 37 0.24
38 8 0.05
39 7 0.05
40 21 0.14
41 11 0.07
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.41
Consensus pattern (36 bp):
ATAATATACTATAATTATAATATATAATATATATAC
Found at i:666190 original size:10 final size:11
Alignment explanation
Indices: 665958--666190 Score: 118
Period size: 12 Copynumber: 20.9 Consensus size: 11
665948 AACAAGTATA
665958 ATATATAATA-
1 ATATATAATAT
665968 ATATATAATAT
1 ATATATAATAT
665979 ATAATATAATAT
1 AT-ATATAATAT
*
665991 ATAT-T-ATGT
1 ATATATAATAT
*
666000 ACCATATAA-AT
1 A-TATATAATAT
666011 ATTATATAATAT
1 A-TATATAATAT
666023 ATACTACATAATAT
1 ATA-T--ATAATAT
*
666037 A-CTATAAT-T
1 ATATATAATAT
666046 ATA-AT-ATAT
1 ATATATAATAT
666055 ACTATATAATAT
1 A-TATATAATAT
*
666067 A-ACATAATAT
1 ATATATAATAT
666077 ATA-ATACTATAT
1 ATATATA--ATAT
666089 ACTATATAA-AT
1 A-TATATAATAT
666100 AT-TATAATAT
1 ATATATAATAT
* **
666110 ATATGTTGTAT
1 ATATATAATAT
*
666121 A-ATGTACCATACT
1 ATATATA--ATA-T
666134 ATATA-ATATAT
1 ATATATA-ATAT
*
666145 ACTATATAAAAT
1 A-TATATAATAT
666157 AATATATAATAT
1 -ATATATAATAT
666169 AGTATAATAATAT
1 A-TAT-ATAATAT
666182 ATATA-AATA
1 ATATATAATA
666191 GAAACCCAGA
Statistics
Matches: 176, Mismatches: 17, Indels: 60
0.70 0.07 0.24
Matches are distributed among these distances:
8 2 0.01
9 15 0.09
10 45 0.26
11 31 0.18
12 55 0.31
13 15 0.09
14 13 0.07
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.41
Consensus pattern (11 bp):
ATATATAATAT
Found at i:669266 original size:25 final size:26
Alignment explanation
Indices: 669221--669280 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 26
669211 CATAAATTAT
* *
669221 AAAATTTTATATTAAATTATTCT-AA
1 AAAATTTTATATTAAAATATTATGAA
669246 AAAATTTTAT-TTAAAAATATTATGAA
1 AAAATTTTATATT-AAAATATTATGAA
*
669272 AATATTTTA
1 AAAATTTTA
669281 AATAATTATA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
24 2 0.07
25 18 0.60
26 10 0.33
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (26 bp):
AAAATTTTATATTAAAATATTATGAA
Found at i:669309 original size:21 final size:22
Alignment explanation
Indices: 669253--669310 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
669243 TAAAAAATTT
669253 TATTTAAAA-ATATTATGAAAA
1 TATTTAAAATATATTATGAAAA
*
669274 TATTTTAAATA-ATTAT-AAAA
1 TATTTAAAATATATTATGAAAA
669294 T-TTTAAAATCATATTAT
1 TATTTAAAAT-ATATTAT
669311 TTATTTACTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
19 7 0.22
20 6 0.19
21 18 0.56
22 1 0.03
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (22 bp):
TATTTAAAATATATTATGAAAA
Found at i:669453 original size:19 final size:21
Alignment explanation
Indices: 669419--669465 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
669409 CTTTAAATTT
*
669419 AAATAATATATAATTTTAAAA
1 AAATAATATATAATTTCAAAA
*
669440 AAATAATAT-T-ATTTCAAAT
1 AAATAATATATAATTTCAAAA
669459 AAATAAT
1 AAATAAT
669466 TAATTAGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 14 0.58
20 1 0.04
21 9 0.38
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
AAATAATATATAATTTCAAAA
Found at i:669536 original size:25 final size:23
Alignment explanation
Indices: 669489--669549 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 23
669479 AAAATAGATA
669489 AATATTTTTATAATATTATATAT
1 AATATTTTTATAATATTATATAT
669512 -ATACCTTTTTATAATTATT-TCATAT
1 AATA--TTTTTATAA-TATTAT-ATAT
669537 AATATTTTTATAA
1 AATATTTTTATAA
669550 AATATATGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
22 3 0.09
24 19 0.58
25 8 0.24
26 3 0.09
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (23 bp):
AATATTTTTATAATATTATATAT
Found at i:669544 original size:24 final size:21
Alignment explanation
Indices: 669473--669549 Score: 68
Period size: 24 Copynumber: 3.5 Consensus size: 21
669463 AATTAATTAG
* *
669473 ATTTTTAAAATA-GATA-AAT
1 ATTTTTATAATATTATATAAT
669492 ATTTTTATAATATTATATATAT
1 ATTTTTATAATATTATATA-AT
669514 ACCTTTTTATAATTATTTCATATAAT
1 A--TTTTTATAA-TA-TT-ATATAAT
669540 ATTTTTATAA
1 ATTTTTATAA
669550 AATATATGAA
Statistics
Matches: 48, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
19 11 0.23
20 3 0.06
21 1 0.02
22 3 0.06
24 18 0.38
25 2 0.04
26 5 0.10
27 5 0.10
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.53
Consensus pattern (21 bp):
ATTTTTATAATATTATATAAT
Found at i:673148 original size:216 final size:216
Alignment explanation
Indices: 672494--673401 Score: 1484
Period size: 215 Copynumber: 4.2 Consensus size: 216
672484 AGGTCTTATG
672494 GATGACCCGAAGGATTTAAGCAT-ATGCTCAAAAGACTTACTGATGGCCAGAAGGACTTATAAAT
1 GATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCAGAAGGACTTATAAAT
* * *
672558 TGTGAAATTTTGAAAATATCATTCTTTGTTTTCAAAAATTTCATCTTCTCAAAGCATC-TTTTTT
66 TGTGAAATTTTGAAAATAGCATTCTTCGTTTTCAAAAATTTCATCTTCTCAAAACATCATTTTTT
* * *
672622 TCATTTTCAAATTCATGTGAAAACATCCTACCCGCAGGTCTTATGGATGGCCCGAAGAACTTATC
131 TCATTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATC
672687 ATCTTGCTCTAAAGGCTTACA
196 ATCTTGCTCTAAAGGCTTACA
* * *
672708 GATGACCCGAAGGATTTAAGCATCATGCTCGAAATACTTACTGATGGCCCGAAGGACTTATAAAT
1 GATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCAGAAGGACTTATAAAT
* * * *
672773 TGTGAAATTTTGAAAATAGCATTCTTTGTTTTTAAAATTTTCATCTTCTCAAATCATCA-TTTTT
66 TGTGAAATTTTGAAAATAGCATTCTTCGTTTTCAAAAATTTCATCTTCTCAAAACATCATTTTTT
672837 TCATTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATC
131 TCATTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATC
*
672902 ATCTTTCTCTAAAGGCTTACA
196 ATCTTGCTCTAAAGGCTTACA
* *
672923 GATGACCCGAATGATTTAAGCATCATGCTCAAAAGACTTATTGATGGCCAGAAGGACTTATAAAT
1 GATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCAGAAGGACTTATAAAT
* * * * *
672988 CGTGAAATTTTGAAAATCGCATTCTTCATTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTT
66 TGTGAAATTTTGAAAATAGCATTCTTCGTTTTCAAAAATTTCATCTTCTCAAAACATCATTTTTT
673053 TCATTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATC
131 TCATTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATC
* *
673118 ATCTTTCTCTAAAGGCTTACG
196 ATCTTGCTCTAAAGGCTTACA
* * * *
673139 GATGACCCGAAGGATTTTAGCATCATGCTCGAAAGACTTACTGAAT-TCCCGAAGGACTTATAAA
1 GATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTG-ATGGCCAGAAGGACTTATAAA
* * *
673203 TTGTGAAAATTTGAAAATCGCATTCTTCG-TTTCAAAAATTTCATCTTCTTAAAACATCATTTTT
65 TTGTGAAATTTTGAAAATAGCATTCTTCGTTTTCAAAAATTTCATCTTCTCAAAACATCA-TTTT
*
673267 TTTCATTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTTTTATGGATGGCTCGAAGGACTTA
129 TTTCATTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTA
673332 TCATCTTGCTCTAAAGGCTTACA
194 TCATCTTGCTCTAAAGGCTTACA
673355 GATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGG
1 GATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGG
673402 GTTTGATTCA
Statistics
Matches: 646, Mismatches: 42, Indels: 10
0.93 0.06 0.01
Matches are distributed among these distances:
214 23 0.04
215 320 0.50
216 301 0.47
217 2 0.00
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.34
Consensus pattern (216 bp):
GATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCAGAAGGACTTATAAAT
TGTGAAATTTTGAAAATAGCATTCTTCGTTTTCAAAAATTTCATCTTCTCAAAACATCATTTTTT
TCATTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATC
ATCTTGCTCTAAAGGCTTACA
Found at i:673517 original size:37 final size:37
Alignment explanation
Indices: 673426--673577 Score: 191
Period size: 37 Copynumber: 4.1 Consensus size: 37
673416 CTTAAGGTGG
* * *
673426 TGCTTCACTACTCTTCGGTGAAGGATTAAGA-TGGTT
1 TGCTTCACTCCTCTTCGGTGAAGGCTTAAGATTGATT
* * *
673462 TGTTTCACTCCTCTTTGGTGAAGGCTTCAGATTGATT
1 TGCTTCACTCCTCTTCGGTGAAGGCTTAAGATTGATT
673499 TGCTTCACTCCTTCTT-GGTGAAGGCTTAAGATTGATT
1 TGCTTCACTCC-TCTTCGGTGAAGGCTTAAGATTGATT
* * *
673536 TGCTTCAGTCCTTTTCGATGAAGGCTTAAGATTGACTT
1 TGCTTCACTCCTCTTCGGTGAAGGCTTAAGATTGA-TT
673574 TGCT
1 TGCT
673578 CCAATCTCAT
Statistics
Matches: 101, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
36 29 0.29
37 62 0.61
38 10 0.10
ACGTcount: A:0.19, C:0.18, G:0.22, T:0.40
Consensus pattern (37 bp):
TGCTTCACTCCTCTTCGGTGAAGGCTTAAGATTGATT
Found at i:679844 original size:24 final size:24
Alignment explanation
Indices: 679790--679845 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 24
679780 TGGTCTTCAA
* *
679790 GTCCTTGG--TGAATGGTCTTCTC
1 GTCCTTGGTATGAACGGTCGTCTC
679812 GT-CTT--TATGAACGGTCGTCTC
1 GTCCTTGGTATGAACGGTCGTCTC
679833 GTCCTTGGTATGA
1 GTCCTTGGTATGA
679846 TTGTATCTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
21 17 0.63
22 5 0.19
24 5 0.19
ACGTcount: A:0.12, C:0.21, G:0.27, T:0.39
Consensus pattern (24 bp):
GTCCTTGGTATGAACGGTCGTCTC
Found at i:687546 original size:12 final size:12
Alignment explanation
Indices: 687510--687721 Score: 63
Period size: 12 Copynumber: 17.2 Consensus size: 12
687500 TGGACCTGAA
*
687510 AATAATAAA-AA
1 AATAATAAATAT
*
687521 AAT-ATTAATAAT
1 AATAATAAAT-AT
687533 AATAATAAATAT
1 AATAATAAATAT
*
687545 AA-ACT-AATAT
1 AATAATAAATAT
687555 -ATAATATAATAT
1 AATAATA-AATAT
687567 -ATAATACAATAT
1 AATAATA-AATAT
687579 -ATAATTCAATATAT
1 AATAA-T-AA-ATAT
687593 AAT-ATATAATAT
1 AATAATA-AATAT
687605 ATATATATAAATAT
1 A-ATA-ATAAATAT
*
687619 -ATATATATATAT
1 AATA-ATAAATAT
*
687631 ACTACAT-AATAT
1 AATA-ATAAATAT
*
687643 ACTATATAAATATT
1 AATA-ATAAATA-T
* *
687657 ACTATATAATGTAT
1 AATA-ATAA-ATAT
*
687671 ACT-ATAATATAT
1 AATAATAA-ATAT
687683 ACTATAAT-AATAT
1 A--ATAATAAATAT
*
687696 -ATAATATATTAT
1 AATAATA-AATAT
*
687708 AATAATATATAT
1 AATAATAAATAT
687720 AA
1 AA
687722 ATAGAAACCC
Statistics
Matches: 160, Mismatches: 17, Indels: 47
0.71 0.08 0.21
Matches are distributed among these distances:
9 1 0.01
10 16 0.10
11 5 0.03
12 73 0.46
13 29 0.18
14 27 0.17
15 9 0.06
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.39
Consensus pattern (12 bp):
AATAATAAATAT
Found at i:687561 original size:36 final size:37
Alignment explanation
Indices: 687521--687621 Score: 120
Period size: 36 Copynumber: 2.7 Consensus size: 37
687511 ATAATAAAAA
687521 AATATTAATAATAATAATAAATATA-AACT-AATATAT
1 AATATTAAT-ATAATAATAAATATATAACTCAATATAT
*
687557 AATA-TAATAT-ATAATACAATATATAATTCAATATAT
1 AATATTAATATAATAATA-AATATATAACTCAATATAT
687593 AATATATAATATATATATATAAATATATA
1 AATAT-TAATATA-ATA-ATAAATATATA
687622 TATATATATA
Statistics
Matches: 56, Mismatches: 1, Indels: 12
0.81 0.01 0.17
Matches are distributed among these distances:
33 6 0.11
34 8 0.14
35 7 0.12
36 15 0.27
38 6 0.11
40 11 0.20
41 3 0.05
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (37 bp):
AATATTAATATAATAATAAATATATAACTCAATATAT
Found at i:687568 original size:2 final size:2
Alignment explanation
Indices: 687551--687720 Score: 108
Period size: 2 Copynumber: 91.5 Consensus size: 2
687541 ATATAAACTA
*
687551 AT AT AT A- AT AT A- AT AT AT A- AT AC A- AT AT AT A- AT -T CA-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT
*
687587 AT AT AT A- AT AT AT A- AT AT AT AT AT AT AA AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
687627 AT AT ACT AC AT A- AT AT ACT AT AT AA AT AT -T ACT AT AT A- AT
1 AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT AT A-T AT AT AT AT
*
687667 GT AT ACT AT A- AT AT AT ACT AT A- AT A- AT AT AT A- AT AT AT -T
1 AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
687706 AT A- AT A- AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
687721 AATAGAAACC
Statistics
Matches: 134, Mismatches: 9, Indels: 50
0.69 0.05 0.26
Matches are distributed among these distances:
1 19 0.14
2 105 0.78
3 10 0.07
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.42
Consensus pattern (2 bp):
AT
Found at i:688549 original size:23 final size:23
Alignment explanation
Indices: 688488--688549 Score: 56
Period size: 23 Copynumber: 2.8 Consensus size: 23
688478 ACTCGTAAGC
688488 TACCA-AAA-GCAGAGAAAAACG
1 TACCACAAAGGCAGAGAAAAACG
* * * *
688509 TGCCACAAAGACAAAGAAAAATG
1 TACCACAAAGGCAGAGAAAAACG
* *
688532 TATCATAAAGGCAGAGAA
1 TACCACAAAGGCAGAGAA
688550 CATGTCACAA
Statistics
Matches: 30, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
21 4 0.13
22 3 0.10
23 23 0.77
ACGTcount: A:0.55, C:0.16, G:0.19, T:0.10
Consensus pattern (23 bp):
TACCACAAAGGCAGAGAAAAACG
Found at i:695688 original size:30 final size:29
Alignment explanation
Indices: 695644--695966 Score: 230
Period size: 30 Copynumber: 11.0 Consensus size: 29
695634 ATTTTACATG
695644 TTAACATTAAAAATATATTTTATTTTTATA
1 TTAAC-TTAAAAATATATTTTATTTTTATA
* * *
695674 TTAACTTATTAAATATATTTTATTTTTGTC
1 TTAACTTA-AAAATATATTTTATTTTTATA
* * *
695704 TAAACCTAAAAATATATTTTAGTCTTTA-A
1 TTAACTTAAAAATATATTTTA-TTTTTATA
*
695733 CTTAACTTAAAAATATATTTTAGTCTTTA-A
1 -TTAACTTAAAAATATATTTTA-TTTTTATA
* *
695763 CTTAACTTAAAAATATATTTTATTCTTATC
1 -TTAACTTAAAAATATATTTTATTTTTATA
* * * *
695793 TTAACTTATAACATAAATTATATTCTTA-A
1 TTAACTTA-AAAATATATTTTATTTTTATA
* * ** * * *
695822 CTTAAATTATTAAATATAAATAATTGTTATT
1 -TTAACTTA-AAAATATATTTTATTTTTATA
*
695853 TTAACTTAAAACATA-ACTTTTATTCTTATA
1 TTAACTTAAAA-ATATA-TTTTATTTTTATA
*
695883 TTAACTTAAAAA-ATA---TATTTTTATT
1 TTAACTTAAAAATATATTTTATTTTTATA
* *
695908 TTAACTAAAAAATATATTTTATTTTTATC
1 TTAACTTAAAAATATATTTTATTTTTATA
* * *
695937 TTAAATACAAAAAATATATTATATTTTTAT
1 TTAACT--TAAAAATATATTTTATTTTTAT
695967 TTTTATTTTA
Statistics
Matches: 236, Mismatches: 41, Indels: 31
0.77 0.13 0.10
Matches are distributed among these distances:
25 19 0.08
26 3 0.01
28 1 0.00
29 46 0.19
30 146 0.62
31 21 0.09
ACGTcount: A:0.42, C:0.08, G:0.01, T:0.49
Consensus pattern (29 bp):
TTAACTTAAAAATATATTTTATTTTTATA
Found at i:695723 original size:59 final size:60
Alignment explanation
Indices: 695651--695803 Score: 186
Period size: 59 Copynumber: 2.6 Consensus size: 60
695641 ATGTTAACAT
* * **
695651 TAAAAATATATTTTATTTTTATATTAACTTATTAAATATATTTTA-TTTTTGTCTAAACC
1 TAAAAATATATTTTATTTTTATATTAACTTATAAAATATATTTTAGTCTTTAACTAAACC
* * *
695710 TAAAAATATATTTTAGTCTTTA-ACTTAACTTA-AAAATATATTTTAGTCTTTAACTTAACT
1 TAAAAATATATTTTA-TTTTTATA-TTAACTTATAAAATATATTTTAGTCTTTAACTAAACC
* *
695770 TAAAAATATATTTTATTCTTATCTTAACTTATAA
1 TAAAAATATATTTTATTTTTATATTAACTTATAA
695804 CATAAATTAT
Statistics
Matches: 79, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
59 40 0.51
60 39 0.49
ACGTcount: A:0.39, C:0.08, G:0.02, T:0.50
Consensus pattern (60 bp):
TAAAAATATATTTTATTTTTATATTAACTTATAAAATATATTTTAGTCTTTAACTAAACC
Found at i:695780 original size:60 final size:59
Alignment explanation
Indices: 695644--695826 Score: 185
Period size: 59 Copynumber: 3.1 Consensus size: 59
695634 ATTTTACATG
* * * **
695644 TTAACATTAAAAATATATTTTATTTTTATA-TTAACTTATTAAATATATTTTATTTTTGTC
1 TTAAC-TTAAAAATATATTTTATCTTTA-ACTTAACTTATAAAATATATTTTATCTTTAAC
* *
695704 TAAACCTAAAAATATATTTTAGTCTTTAACTTAACTTA-AAAATATATTTTAGTCTTTAAC
1 TTAACTTAAAAATATATTTTA-TCTTTAACTTAACTTATAAAATATATTTTA-TCTTTAAC
* * * *
695764 TTAACTTAAAAATATATTTTAT-TCTTATCTTAACTTATAACATAAATTATAT-TCTTAAC
1 TTAACTTAAAAATATATTTTATCT-TTAACTTAACTTATAAAATATATTTTATCT-TTAAC
695823 TTAA
1 TTAA
695827 ATTATTAAAT
Statistics
Matches: 104, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
58 2 0.02
59 51 0.49
60 51 0.49
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (59 bp):
TTAACTTAAAAATATATTTTATCTTTAACTTAACTTATAAAATATATTTTATCTTTAAC
Found at i:695917 original size:23 final size:24
Alignment explanation
Indices: 695873--695941 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 24
695863 ACATAACTTT
* *
695873 TATTCTTATATTAACTTAAAAAATA
1 TATTTTTATTTTAACTTAAAAAA-A
695898 TATTTTTATTTTAAC-T-AAAAAA
1 TATTTTTATTTTAACTTAAAAAAA
*
695920 TATATTTTATTTTTATCTTAAA
1 TAT-TTTTA-TTTTAACTTAAA
695942 TACAAAAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
22 4 0.11
23 10 0.27
24 7 0.19
25 14 0.38
26 2 0.05
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (24 bp):
TATTTTTATTTTAACTTAAAAAAA
Found at i:695921 original size:24 final size:25
Alignment explanation
Indices: 695873--695941 Score: 88
Period size: 24 Copynumber: 2.8 Consensus size: 25
695863 ACATAACTTT
* *
695873 TATTCTTATATTAACTTAAAAAATA
1 TATTTTTATTTTAACTTAAAAAATA
695898 TATTTTTATTTTAAC-TAAAAAATA
1 TATTTTTATTTTAACTTAAAAAATA
*
695922 TA-TTTTATTTTTATCTTAAA
1 TATTTTTA-TTTTAACTTAAA
695942 TACAAAAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
23 5 0.13
24 17 0.44
25 17 0.44
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (25 bp):
TATTTTTATTTTAACTTAAAAAATA
Found at i:695928 original size:54 final size:56
Alignment explanation
Indices: 695839--695956 Score: 145
Period size: 54 Copynumber: 2.2 Consensus size: 56
695829 TATTAAATAT
* * *
695839 AAATA-ATTGTTATTTTAACTTAAAACATAACTTTTATTCTTATATTAACT-TAAA
1 AAATATATTGTTATTTTAACTTAAAAAATAACTTTTATTCTTATATTAAATACAAA
* * *
695893 AAATATATTTTTATTTTAAC-TAAAAAATATA-TTTTATTTTTATCTTAAATACAAA
1 AAATATATTGTTATTTTAACTTAAAAAATA-ACTTTTATTCTTATATTAAATACAAA
695948 AAATATATT
1 AAATATATT
695957 ATATTTTTAT
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
54 29 0.53
55 26 0.47
ACGTcount: A:0.45, C:0.07, G:0.01, T:0.47
Consensus pattern (56 bp):
AAATATATTGTTATTTTAACTTAAAAAATAACTTTTATTCTTATATTAAATACAAA
Found at i:695948 original size:29 final size:30
Alignment explanation
Indices: 695896--695966 Score: 99
Period size: 31 Copynumber: 2.4 Consensus size: 30
695886 ACTTAAAAAA
* *
695896 TATATTTTTATTTTAACT-AAAAAATATAT
1 TATATTTTTATCTTAAATAAAAAAATATAT
*
695925 TTTATTTTTATCTTAAATACAAAAAATATAT
1 TATATTTTTATCTTAAATA-AAAAAATATAT
695956 TATATTTTTAT
1 TATATTTTTAT
695967 TTTTATTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
29 15 0.42
31 21 0.58
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (30 bp):
TATATTTTTATCTTAAATAAAAAAATATAT
Found at i:696046 original size:29 final size:29
Alignment explanation
Indices: 695987--696157 Score: 174
Period size: 29 Copynumber: 6.0 Consensus size: 29
695977 ATATATTATT
*
695987 AGAATAAAATATAAATATTTAAGTTAAGATA
1 AGAATAAAATAT--ATTTTTAAGTTAAGATA
*
696018 AGAATAAAATATATTTTTAATTTAAGATA
1 AGAATAAAATATATTTTTAAGTTAAGATA
* *
696047 AGAATAAAATATATTTTTAAATTAAAATA
1 AGAATAAAATATATTTTTAAGTTAAGATA
* * * * *
696076 AGAAGAAAATATATTTCTAGGTTATGAAA
1 AGAATAAAATATATTTTTAAGTTAAGATA
696105 AGAATAAAATATA--TTTAA---AAGATA
1 AGAATAAAATATATTTTTAAGTTAAGATA
*
696129 AG-ATAAAAAATATTTTTTAATGTTAAGAT
1 AGAATAAAATATA-TTTTTAA-GTTAAGAT
696158 GTAAAATTAA
Statistics
Matches: 116, Mismatches: 17, Indels: 15
0.78 0.11 0.10
Matches are distributed among these distances:
23 9 0.08
24 6 0.05
26 5 0.04
27 3 0.03
29 76 0.66
30 5 0.04
31 12 0.10
ACGTcount: A:0.54, C:0.01, G:0.09, T:0.36
Consensus pattern (29 bp):
AGAATAAAATATATTTTTAAGTTAAGATA
Found at i:696185 original size:18 final size:18
Alignment explanation
Indices: 696144--696198 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
696134 AAAAATATTT
696144 TTTAATGTTAAGATGTAAA
1 TTTAAT-TTAAGATGTAAA
* * *
696163 ATTAATTTAATATGTGAA
1 TTTAATTTAAGATGTAAA
* *
696181 TTTAAGTTAAGATATAAA
1 TTTAATTTAAGATGTAAA
696199 AAATATTAAG
Statistics
Matches: 28, Mismatches: 8, Indels: 1
0.76 0.22 0.03
Matches are distributed among these distances:
18 23 0.82
19 5 0.18
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.42
Consensus pattern (18 bp):
TTTAATTTAAGATGTAAA
Found at i:700999 original size:2 final size:2
Alignment explanation
Indices: 700992--701022 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
700982 ATCGTTTGCC
700992 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
701023 TTTCTTATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:703059 original size:379 final size:376
Alignment explanation
Indices: 702319--703083 Score: 1413
Period size: 379 Copynumber: 2.0 Consensus size: 376
702309 ATCTTAAGGA
702319 AACTGTGTCGTTGTAGGCCTCAACTCATTTCAAGTTTACTATTCAAGTTCTTTATACTAAACTGT
1 AACTGTGTCGTTGTAGGCCTCAACTCATTTCAAGTTTACTATTCAAGTTCTTTATACTAAACTGT
702384 ATCTCTTCCATTATAATAAAATTTGTATTTTATTTTTATTTTTATCTTGGATTGTTATACTAACA
66 ATCTCTTCCATTATAATAAAATTTGTATTTTATTTTTATTTTTATCTTGGATTGTTATACTAACA
702449 CACTCTAAACCTTATTAAGCTCCTCCCTTAATACTGATATATAAGTTTGGTCACCCCATAATGAT
131 CACTCTAAACCTTATTAAGCTCCTCCCTTAATACTGATATATAAGTTTGGTCACCCCATAATGAT
702514 AATATGGATGTTCACAGTCAGTTAACAGTACCATTTAATCTAAACAATTAGGTTAACCGTTATAA
196 AATATGGATGTTCACAGTCAGTTAACAGTACCATTTAATCTAAACAATTAGGTTAACCGTTATAA
702579 CGATTGTTGAATTTGCTAACCATAACTAACCTTTAAGAAACAATTAACCGCTAATGGTTAGCCAT
261 CGATTGTTGAATTTGCTAACCATAACTAACCTTTAAGAAACAATTAACCGCTAATGGTTAGCCAT
702644 TACTAACGATTCAATTACACAGTTAACCTATAACCTATTATAATTTTCTTTTTT
326 TACTAACGATTCAATTACAC---TAACCTATAACCTATTATAATTTTCTTTTTT
702698 AACTGTGTCGTTGTAGGCCTCAACTCATTTCAAGTTTACTATTCAAGTTCTTTATACTAAACTGT
1 AACTGTGTCGTTGTAGGCCTCAACTCATTTCAAGTTTACTATTCAAGTTCTTTATACTAAACTGT
702763 ATCTCTTCCATTATAATAAAATTTGTATTTTATTTTTATTTTTATCTTGGATTGTTATACTATAA
66 ATCTCTTCCATTATAATAAAATTTGTATTTTATTTTTATTTTTATCTTGGATTGTTATAC--TAA
702828 CACACTCTAAACCTTATTAAGCTCCTCCCTTAATACTGATATATAAGTATTGGTCACCCCATTAA
129 CACACTCTAAACCTTATTAAGCTCCTCCCTTAATACTGATATATAAGT-TTGGTCACCCCA-TAA
702893 TGATAATATGGATGTTCACAGTCAGTTAACAGTACCATTTAATCTAAACAATTAGGTTAACCGTT
192 TGATAATATGGATGTTCACAGTCAGTTAACAGTACCATTTAATCTAAACAATTAGGTTAACCGTT
702958 ATAACGATTGTTGAATTTTGCTAACCATAACCTAACCTTTAAGAAACAATTAACCGCTAATGGTT
257 ATAACGATTGTTGAA-TTTGCTAACCATAA-CTAACCTTTAAGAAACAATTAACCGCTAATGGTT
703023 AGCCATTACTAACGATTCAATTACACAAGTTAACCTATAACCTATTATAATTTTCTTTTTT
320 AGCCATTACTAACGATTCAATTACAC----TAACCTATAACCTATTATAATTTTCTTTTTT
703084 CATATTTTTG
Statistics
Matches: 379, Mismatches: 0, Indels: 7
0.98 0.00 0.02
Matches are distributed among these distances:
379 125 0.33
381 51 0.13
382 12 0.03
383 83 0.22
384 14 0.04
385 60 0.16
386 34 0.09
ACGTcount: A:0.32, C:0.18, G:0.10, T:0.39
Consensus pattern (376 bp):
AACTGTGTCGTTGTAGGCCTCAACTCATTTCAAGTTTACTATTCAAGTTCTTTATACTAAACTGT
ATCTCTTCCATTATAATAAAATTTGTATTTTATTTTTATTTTTATCTTGGATTGTTATACTAACA
CACTCTAAACCTTATTAAGCTCCTCCCTTAATACTGATATATAAGTTTGGTCACCCCATAATGAT
AATATGGATGTTCACAGTCAGTTAACAGTACCATTTAATCTAAACAATTAGGTTAACCGTTATAA
CGATTGTTGAATTTGCTAACCATAACTAACCTTTAAGAAACAATTAACCGCTAATGGTTAGCCAT
TACTAACGATTCAATTACACTAACCTATAACCTATTATAATTTTCTTTTTT
Found at i:708148 original size:18 final size:18
Alignment explanation
Indices: 708125--708167 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
708115 TCTTGAGATA
*
708125 ACCTAAA-GAAAATAAAAT
1 ACCTAAATG-AAATAAAAC
708143 ACCTAAATGAAATAAAAC
1 ACCTAAATGAAATAAAAC
708161 ACCTAAA
1 ACCTAAA
708168 AATAATCCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 22 0.96
19 1 0.04
ACGTcount: A:0.63, C:0.16, G:0.05, T:0.16
Consensus pattern (18 bp):
ACCTAAATGAAATAAAAC
Found at i:708241 original size:23 final size:23
Alignment explanation
Indices: 708195--708241 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
708185 TCAAATACTT
* *
708195 AAATCCTAATTAATAGCAATATA
1 AAATCCTAAATAATAGCAAGATA
708218 AAATCCTAAATAATAG-ATAGATA
1 AAATCCTAAATAATAGCA-AGATA
708241 A
1 A
708242 TTCCTAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 1 0.05
23 20 0.95
ACGTcount: A:0.55, C:0.11, G:0.06, T:0.28
Consensus pattern (23 bp):
AAATCCTAAATAATAGCAAGATA
Found at i:709718 original size:20 final size:20
Alignment explanation
Indices: 709693--709767 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
709683 TTTAGGATCG
709693 ATATTGTTCTTATAGTATCA
1 ATATTGTTCTTATAGTATCA
* *
709713 ATATTGTTCATCA-AGTATCG
1 ATATTGTTC-TTATAGTATCA
* **
709733 ATACTGTTCTTATAACATCA
1 ATATTGTTCTTATAGTATCA
709753 ATACTT-TTCTTATAG
1 ATA-TTGTTCTTATAG
709768 CATCGTTAGG
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
19 2 0.05
20 38 0.88
21 3 0.07
ACGTcount: A:0.31, C:0.15, G:0.09, T:0.45
Consensus pattern (20 bp):
ATATTGTTCTTATAGTATCA
Found at i:709771 original size:20 final size:20
Alignment explanation
Indices: 709733--709771 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
709723 TCAAGTATCG
709733 ATACTGTTCTTATAACATCA
1 ATACTGTTCTTATAACATCA
* *
709753 ATACTTTTCTTATAGCATC
1 ATACTGTTCTTATAACATC
709772 GTTAGGAGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.21, G:0.05, T:0.44
Consensus pattern (20 bp):
ATACTGTTCTTATAACATCA
Found at i:712431 original size:24 final size:24
Alignment explanation
Indices: 712410--712467 Score: 116
Period size: 24 Copynumber: 2.4 Consensus size: 24
712400 GAGATTATTA
712410 TCGATTCAATTCTCAATTTTATAT
1 TCGATTCAATTCTCAATTTTATAT
712434 TCGATTCAATTCTCAATTTTATAT
1 TCGATTCAATTCTCAATTTTATAT
712458 TCGATTCAAT
1 TCGATTCAAT
712468 CGTTCAAACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.29, C:0.17, G:0.05, T:0.48
Consensus pattern (24 bp):
TCGATTCAATTCTCAATTTTATAT
Found at i:723964 original size:16 final size:16
Alignment explanation
Indices: 723928--723961 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
723918 CACGTGAGGA
723928 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
723944 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
723961 T
1 T
723962 ATTGTCTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:725880 original size:90 final size:89
Alignment explanation
Indices: 725762--725938 Score: 284
Period size: 90 Copynumber: 2.0 Consensus size: 89
725752 AAATCCAGAA
* * *
725762 TATTTAATTTCAATTAATTAGATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATCAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAA-CCCTAATATCAT
725827 TAGGGTAACATGGA-TATAAAAGGAT
65 TAGGGTAAC-TGGACTATAAAAGGAT
*
725852 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATCATT
*
725917 AGGGTAACTTGACTATAAAAGG
66 AGGGTAACTGGACTATAAAAGG
725939 TGTGTTAGGT
Statistics
Matches: 81, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
88 3 0.04
89 29 0.36
90 49 0.60
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.37
Consensus pattern (89 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATCATT
AGGGTAACTGGACTATAAAAGGAT
Done.