Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008822.1 Hibiscus syriacus cultivar Beakdansim tig00111990_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: 699754
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:587848 original size:19 final size:19
Alignment explanation
Indices: 587824--587861 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
587814 ATGTCACTCA
587824 TTGTTTGTAATATTAGAAT
1 TTGTTTGTAATATTAGAAT
587843 TTGTTTGTAATATTAGAAT
1 TTGTTTGTAATATTAGAAT
587862 GGTTATAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.53
Consensus pattern (19 bp):
TTGTTTGTAATATTAGAAT
Found at i:587994 original size:2 final size:2
Alignment explanation
Indices: 587987--588023 Score: 58
Period size: 2 Copynumber: 18.5 Consensus size: 2
587977 TATAATGTTA
587987 AT AT AT AT -T GAT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT A
588024 ATTTTTAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 31 0.94
3 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:591239 original size:47 final size:47
Alignment explanation
Indices: 591170--591265 Score: 192
Period size: 47 Copynumber: 2.0 Consensus size: 47
591160 TGTTGCAGAA
591170 TTCATGCCTTGGTTCACTGCATCTATTCTCTTCTCTGCTTAAAGGAC
1 TTCATGCCTTGGTTCACTGCATCTATTCTCTTCTCTGCTTAAAGGAC
591217 TTCATGCCTTGGTTCACTGCATCTATTCTCTTCTCTGCTTAAAGGAC
1 TTCATGCCTTGGTTCACTGCATCTATTCTCTTCTCTGCTTAAAGGAC
591264 TT
1 TT
591266 TTACATGGTA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.17, C:0.27, G:0.15, T:0.42
Consensus pattern (47 bp):
TTCATGCCTTGGTTCACTGCATCTATTCTCTTCTCTGCTTAAAGGAC
Found at i:593606 original size:3 final size:3
Alignment explanation
Indices: 593598--593672 Score: 122
Period size: 3 Copynumber: 26.3 Consensus size: 3
593588 AATTTTTATT
593598 TAA TAA TAA TAA TAA TAA TAA -AA TAA T-A TAA TAA TAA TAA TAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
593643 TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
593673 GAAAAAAATT
Statistics
Matches: 68, Mismatches: 0, Indels: 8
0.89 0.00 0.11
Matches are distributed among these distances:
2 8 0.12
3 60 0.88
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:593629 original size:25 final size:25
Alignment explanation
Indices: 593600--593668 Score: 129
Period size: 25 Copynumber: 2.8 Consensus size: 25
593590 TTTTTATTTA
593600 ATAATAATAATAATAATAAAATAAT
1 ATAATAATAATAATAATAAAATAAT
*
593625 ATAATAATAATAATAATATAATAAT
1 ATAATAATAATAATAATAAAATAAT
593650 ATAATAATAATAATAATAA
1 ATAATAATAATAATAATAA
593669 TAATGAAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (25 bp):
ATAATAATAATAATAATAAAATAAT
Found at i:593965 original size:45 final size:45
Alignment explanation
Indices: 593875--594382 Score: 727
Period size: 45 Copynumber: 11.4 Consensus size: 45
593865 TTGTCATGTA
* *
593875 GAAGGGCTTATAGATGACCCGAAGGTTTTTGAAAACATCATGCACT
1 GAAGGGCTTACAGATGACCCGAAGG-TTTTGAAAACATCAAGCACT
* *
593921 GAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACT
1 GAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAGCACT
*
593966 GAAGGGCTTACAGATGA-CCGAAGGTTTTGAAAACATCATGCACT
1 GAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAGCACT
* ** * *
594010 GAAGGACTTACTTATGACCTGAAGGTTTTGAGAACATCAAGCACT
1 GAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAGCACT
* * *
594055 GAAGGACTTACAGATGACCCAAAGGTTTTGAGAACATCAAGCACT
1 GAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAGCACT
594100 GAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAGCACT
1 GAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAGCACT
* * *
594145 GAAGGGCTTACAGGTGACCCGAAGGTTTTGAAGACATCAAGAACT
1 GAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAGCACT
* * * *
594190 GAAGGGCTTACAGATGACCTGAAGGTTTTGAAGACATCATGCAAT
1 GAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAGCACT
*
594235 GAAGGGCTTACAGATGACCCGAAGGTTTTGAAGACATCAAGCACT
1 GAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAGCACT
* * *
594280 GAA-GGCTTACATATGACCCGAAGGTTTTGAAGACATCATGCACT
1 GAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAGCACT
* * *
594324 GAA-GACTTACAGATGACCCAAAGGTTTTGAAGACATC-AGCACT
1 GAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAGCACT
*
594367 GAAGGACTTACAGATG
1 GAAGGGCTTACAGATG
594383 TGGGAAATAG
Statistics
Matches: 427, Mismatches: 33, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
43 8 0.02
44 126 0.30
45 270 0.63
46 23 0.05
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.22
Consensus pattern (45 bp):
GAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAGCACT
Found at i:594013 original size:25 final size:25
Alignment explanation
Indices: 593941--594014 Score: 70
Period size: 25 Copynumber: 3.2 Consensus size: 25
593931 CAGATGACCC
593941 GAAGGTTTTGAAAACATCATGCACT
1 GAAGGTTTTGAAAACATCATGCACT
** * *
593966 GAAGGGCTT----ACA-GATG-ACC
1 GAAGGTTTTGAAAACATCATGCACT
593985 GAAGGTTTTGAAAACATCATGCACT
1 GAAGGTTTTGAAAACATCATGCACT
594010 GAAGG
1 GAAGG
594015 ACTTACTTAT
Statistics
Matches: 35, Mismatches: 8, Indels: 12
0.64 0.15 0.22
Matches are distributed among these distances:
19 9 0.26
20 3 0.09
21 3 0.09
23 3 0.09
24 3 0.09
25 14 0.40
ACGTcount: A:0.35, C:0.16, G:0.26, T:0.23
Consensus pattern (25 bp):
GAAGGTTTTGAAAACATCATGCACT
Found at i:595070 original size:22 final size:22
Alignment explanation
Indices: 595045--595123 Score: 122
Period size: 22 Copynumber: 3.6 Consensus size: 22
595035 AATAAAGCTT
*
595045 TCATCTTTGAAAATAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
* *
595067 TCATCTTTAAAAAGAGAATATA
1 TCATCTTTGAAAAGAGAATCTA
*
595089 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
595111 TCATCTTTGAAAA
1 TCATCTTTGAAAA
595124 ATGTAGATGT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:595567 original size:50 final size:51
Alignment explanation
Indices: 595473--595628 Score: 190
Period size: 54 Copynumber: 3.0 Consensus size: 51
595463 AATAACTGGT
* * * *
595473 TCGTAAAACATTTGACAACACATGCAT-CATCTCATGTGGTTTCTGCTCAGA
1 TCGTAAAACATTTGACAACACATTCATCCTTTTC-TGTGGCTTCTGCTCAGA
* *
595524 T-GTAAAACACTTGACAACACATTCATCCTTTTCTATGGCTTCTGCTCAGA
1 TCGTAAAACATTTGACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAGA
**
595574 TGTTCGTAAAGTATTTGACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAGA
1 ---TCGTAAAACATTTGACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAGA
595628 T
1 T
595629 TTCTCAATCA
Statistics
Matches: 90, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
50 38 0.42
51 6 0.07
53 1 0.01
54 45 0.50
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (51 bp):
TCGTAAAACATTTGACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAGA
Found at i:596637 original size:76 final size:76
Alignment explanation
Indices: 596500--596646 Score: 197
Period size: 76 Copynumber: 1.9 Consensus size: 76
596490 ATGATGATGT
* * *
596500 GGGCCTTCAGCATGCCCCAGCATTTGCTAATACAAATATTCAAAAATGCATCAACAGTCCTGATT
1 GGGCCTTCAACATGCCCCAGCATTTACTAATACAAATATTCAAAAATACATCAACAGTCCTGATT
596565 CTGATTGAAAG
66 CTGATTGAAAG
* * * * * *
596576 GGGCTTTCAACATGCCCCAGCATTTTACTAATATAAATATTC-AGAATACTTCAATATTCCTGAT
1 GGGCCTTCAACATGCCCCAGCA-TTTACTAATACAAATATTCAAAAATACATCAACAGTCCTGAT
596640 TCTGATT
65 TCTGATT
596647 AAAAATGGTT
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
76 44 0.72
77 17 0.28
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.31
Consensus pattern (76 bp):
GGGCCTTCAACATGCCCCAGCATTTACTAATACAAATATTCAAAAATACATCAACAGTCCTGATT
CTGATTGAAAG
Found at i:596670 original size:76 final size:77
Alignment explanation
Indices: 596500--596676 Score: 196
Period size: 76 Copynumber: 2.3 Consensus size: 77
596490 ATGATGATGT
* * *
596500 GGGCCTTCAGCATGCCCCAGCA-TTTGCTAATACAAATATTCAAAAATGCATCAACAGTCCTGAT
1 GGGCTTTCAGCATGCCCCAGCATTTTACTAATACAAATATTCAAAAATACATCAACAGTCCTGAT
* *
596564 TCTGATTGAAAG
66 TCTGATTAAAAA
* * * * * *
596576 GGGCTTTCAACATGCCCCAGCATTTTACTAATATAAATATTC-AGAATACTTCAATATTCCTGAT
1 GGGCTTTCAGCATGCCCCAGCATTTTACTAATACAAATATTCAAAAATACATCAACAGTCCTGAT
596640 TCTGATTAAAAA
66 TCTGATTAAAAA
* * * * *
596652 TGGTTTTTAGCATACCCCAACATTT
1 GGGCTTTCAGCATGCCCCAGCATTT
596677 GCTTCTTGTT
Statistics
Matches: 83, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
76 66 0.80
77 17 0.20
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.32
Consensus pattern (77 bp):
GGGCTTTCAGCATGCCCCAGCATTTTACTAATACAAATATTCAAAAATACATCAACAGTCCTGAT
TCTGATTAAAAA
Found at i:596922 original size:109 final size:109
Alignment explanation
Indices: 596691--596929 Score: 297
Period size: 109 Copynumber: 2.2 Consensus size: 109
596681 CTTGTTAATT
* * * *
596691 TGAGCCTTCAAAATGCCCCACCATTTGCTGATACAGATTTTAAAAGTGTATTCACATTATTTCTT
1 TGAGCCTTCAAAATGCCCCAACATTTGCTGATACAGATGTTAAAAGTGTACTCACATTACTTCTT
* * *
596756 GTTGATATGAGCCTCCAAGAATGCCCCACATGGATCTGTCTGAAG
66 GTTGAGATGAGCCTCCAAGAATGCCCCAAAT-GATCTATCTGAAG
* * *
596801 -GAACCTTTAAAATGCCCCAACATTTGCTGATACAGATGTTAAAAGTGTGCTCAACATTACTTCT
1 TGAGCCTTCAAAATGCCCCAACATTTGCTGATACAGATGTTAAAAGTGTACTC-ACATTACTTCT
* **
596865 TGTTGAGATGAGTCTCCAAGAATG-CCCAAAT-ATTCATAT-TGTTG
65 TGTTGAGATGAGCCTCCAAGAATGCCCCAAATGA-TC-TATCTGAAG
596909 TGAGCCTTCAAAATGCCCCAA
1 TGAGCCTTCAAAATGCCCCAA
596930 TATTCTATTT
Statistics
Matches: 110, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
107 1 0.01
108 5 0.05
109 72 0.65
110 32 0.29
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (109 bp):
TGAGCCTTCAAAATGCCCCAACATTTGCTGATACAGATGTTAAAAGTGTACTCACATTACTTCTT
GTTGAGATGAGCCTCCAAGAATGCCCCAAATGATCTATCTGAAG
Found at i:600072 original size:16 final size:16
Alignment explanation
Indices: 600048--600080 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
600038 TTTCAATTTC
600048 TCCTCTTTTTCTTTTT
1 TCCTCTTTTTCTTTTT
*
600064 TCCTTTTTTTCTTTTT
1 TCCTCTTTTTCTTTTT
600080 T
1 T
600081 TTTTTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (16 bp):
TCCTCTTTTTCTTTTT
Found at i:600073 original size:9 final size:9
Alignment explanation
Indices: 600059--600101 Score: 59
Period size: 9 Copynumber: 4.7 Consensus size: 9
600049 CCTCTTTTTC
*
600059 TTTTTTCCT
1 TTTTTTCTT
600068 TTTTTTCTT
1 TTTTTTCTT
*
600077 TTTTTTTTT
1 TTTTTTCTT
600086 TTTTTGTCTT
1 TTTTT-TCTT
600096 TTTTTT
1 TTTTTT
600102 TTGCTGGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
9 22 0.73
10 8 0.27
ACGTcount: A:0.00, C:0.09, G:0.02, T:0.88
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:600081 original size:8 final size:8
Alignment explanation
Indices: 600053--600088 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
600043 ATTTCTCCTC
600053 TTTTTCTT
1 TTTTTCTT
*
600061 TTTTCCTT
1 TTTTTCTT
600069 TTTTTCTT
1 TTTTTCTT
600077 TTTTT-TT
1 TTTTTCTT
600084 TTTTT
1 TTTTT
600089 TTGTCTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
7 7 0.27
8 19 0.73
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTTCTT
Found at i:600086 original size:16 final size:16
Alignment explanation
Indices: 600053--600103 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
600043 ATTTCTCCTC
**
600053 TTTTTCTTTTTTCCTT
1 TTTTTCTTTTTTTTTT
600069 TTTTTCTTTTTTTTTT
1 TTTTTCTTTTTTTTTT
*
600085 TTTTT-TGTCTTTTTTT
1 TTTTTCT-TTTTTTTTT
600101 TTT
1 TTT
600104 GCTGGATGAG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
15 1 0.03
16 30 0.97
ACGTcount: A:0.00, C:0.10, G:0.02, T:0.88
Consensus pattern (16 bp):
TTTTTCTTTTTTTTTT
Found at i:607032 original size:17 final size:17
Alignment explanation
Indices: 607005--607043 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
606995 AAATTACAAT
607005 TAATT-TAAATAATATC
1 TAATTATAAATAATATC
*
607021 TAATTATAAATAATATT
1 TAATTATAAATAATATC
607038 TAATTA
1 TAATTA
607044 ATTTGATTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (17 bp):
TAATTATAAATAATATC
Found at i:607701 original size:31 final size:31
Alignment explanation
Indices: 607663--607730 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
607653 TTATAATACA
607663 GTCCCCCAACATTTAGT-TCATTTGCAATATG
1 GTCCCCCAACATTTAGTCT-ATTTGCAATATG
*
607694 GTCCCCCAACATTTAGTCTGTTTGCAATATG
1 GTCCCCCAACATTTAGTCTATTTGCAATATG
607725 GTCCCC
1 GTCCCC
607731 GATCATTTGA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
31 34 0.97
32 1 0.03
ACGTcount: A:0.22, C:0.29, G:0.15, T:0.34
Consensus pattern (31 bp):
GTCCCCCAACATTTAGTCTATTTGCAATATG
Found at i:609747 original size:31 final size:31
Alignment explanation
Indices: 609674--609735 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
609664 ACGGTCGGGA
*
609674 ACCATATTGCAAACAGACTAAATGTTGGGGG
1 ACCATATTGCAAACAGACTAAATGTAGGGGG
*
609705 ACCATATTGCAAACGGACTAAATGTAGGGGG
1 ACCATATTGCAAACAGACTAAATGTAGGGGG
609736 TCTGTATTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.35, C:0.16, G:0.27, T:0.21
Consensus pattern (31 bp):
ACCATATTGCAAACAGACTAAATGTAGGGGG
Found at i:614248 original size:37 final size:35
Alignment explanation
Indices: 614171--614251 Score: 90
Period size: 35 Copynumber: 2.3 Consensus size: 35
614161 AACACAGTCA
* * * * **
614171 TCAATTACATTCTAAACCTCAACTTTCAAAATGTT
1 TCAATTACACTCAAAACCTCAAATTCCAAAATACT
614206 TCAATTACACTCAAAACCTCAAATTCCAAAAAATACT
1 TCAATTACACTCAAAACCTCAAATTCC--AAAATACT
614243 TCAATTACA
1 TCAATTACA
614252 TGATCAACCC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
35 23 0.61
37 15 0.39
ACGTcount: A:0.43, C:0.25, G:0.01, T:0.31
Consensus pattern (35 bp):
TCAATTACACTCAAAACCTCAAATTCCAAAATACT
Found at i:615010 original size:145 final size:143
Alignment explanation
Indices: 614745--615030 Score: 418
Period size: 145 Copynumber: 2.0 Consensus size: 143
614735 AAACTATTTA
*
614745 AATTAGAATCAAAAATAATATATATAGTATAAATATTATAATTAAATTTAAACAGAACTCGAAAA
1 AATTAGAAT-AAAAATAATATATATAGTATAAATATTATAATTAAATTTAAACAGAACTAGAAAA
* * **
614810 ATTCAATTCAATTCGATTGATTTAAATTTTATAAACTCAAATTGAAAAATTTCGAGTCAACTATT
65 ATTCAATTCAATTCGATTGATTTAAATTTCATAAACTCAAATTAAAAAAAATCGAGTCAACTATT
*
614875 TTATAAATTGAACTG
130 TT-TAAACTGAACTG
*
614890 AATTAGAAT-AAAATAATATTATATA-TGATAAATATTTATAATTAAATTTAAATAGAAACTAG-
1 AATTAGAATAAAAATAATA-TATATAGT-ATAAATA-TTATAATTAAATTTAAACAG-AACTAGA
614952 AAAATTCAATTCAATTCGACTTGATTTAAATTTCATAAACTCAAA-TAAAAAAAATCGAGTCAAC
62 AAAATTCAATTCAATTCGA-TTGATTTAAATTTCATAAACTCAAATTAAAAAAAATCGAGTCAAC
615016 TATTTTTAAACTGAA
126 TATTTTTAAACTGAA
615031 TTGAGTATTT
Statistics
Matches: 129, Mismatches: 7, Indels: 11
0.88 0.05 0.07
Matches are distributed among these distances:
143 10 0.08
144 21 0.16
145 69 0.53
146 29 0.22
ACGTcount: A:0.49, C:0.09, G:0.07, T:0.35
Consensus pattern (143 bp):
AATTAGAATAAAAATAATATATATAGTATAAATATTATAATTAAATTTAAACAGAACTAGAAAAA
TTCAATTCAATTCGATTGATTTAAATTTCATAAACTCAAATTAAAAAAAATCGAGTCAACTATTT
TTAAACTGAACTG
Found at i:615228 original size:174 final size:175
Alignment explanation
Indices: 614934--615284 Score: 679
Period size: 174 Copynumber: 2.0 Consensus size: 175
614924 TTTATAATTA
614934 AATTTAAATAGAAACTAGAAAATTCAATTCAATTCGACTTGATTTAAATTTCATAAACTCAAATA
1 AATTTAAATAGAAACTAGAAAATTCAATTCAATTCGACTTGATTTAAATTTCATAAACTCAAATA
614999 AAAAAAATCGAGTCAACTATTTTTAAACTGAATTGAGTATTTAGGTCCAAACATAACCCTAAG-C
66 AAAAAAATCGAGTCAACTATTTTTAAACTGAATTGAGTATTTAGGTCCAAACATAACCCTAAGCC
615063 CAACAAAATCACTTGTTGTTCACTTATAGTTGGTTAAATGTTTTG
131 CAACAAAATCACTTGTTGTTCACTTATAGTTGGTTAAATGTTTTG
615108 AATTTAAATAGAAACTAGAAAATTCAATTCAATTCGACTTGATTTAAATTTCATAAACTCAAATA
1 AATTTAAATAGAAACTAGAAAATTCAATTCAATTCGACTTGATTTAAATTTCATAAACTCAAATA
615173 AAAAAAATCGAGTCAACTATTTTATAAACTGAATTGAGTATTTAGGTCC-AACATAACCCTAAGC
66 AAAAAAATCGAGTCAACTATTTT-TAAACTGAATTGAGTATTTAGGTCCAAACATAACCCTAAGC
615237 CCAACAAAATCACTTGTTGTTCACTTATAGTTGGTTAAATGTTTTG
130 CCAACAAAATCACTTGTTGTTCACTTATAGTTGGTTAAATGTTTTG
615283 AA
1 AA
615285 ACGATTATGT
Statistics
Matches: 175, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
174 102 0.58
175 73 0.42
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.34
Consensus pattern (175 bp):
AATTTAAATAGAAACTAGAAAATTCAATTCAATTCGACTTGATTTAAATTTCATAAACTCAAATA
AAAAAAATCGAGTCAACTATTTTTAAACTGAATTGAGTATTTAGGTCCAAACATAACCCTAAGCC
CAACAAAATCACTTGTTGTTCACTTATAGTTGGTTAAATGTTTTG
Found at i:615417 original size:35 final size:35
Alignment explanation
Indices: 615378--615449 Score: 90
Period size: 35 Copynumber: 2.1 Consensus size: 35
615368 GTTGGGCATA
* *
615378 TAATTAAAGTATTTTAGAATTTGAGGTTTAGGATG
1 TAATTAAAGCATTTTAGAATTTGAGGTTTAGAATG
* * * *
615413 TAATTGAAGCATTTTGGATTTTGGGGTTTAGAATG
1 TAATTAAAGCATTTTAGAATTTGAGGTTTAGAATG
615448 TA
1 TA
615450 GTTGATGATT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.31, C:0.01, G:0.25, T:0.43
Consensus pattern (35 bp):
TAATTAAAGCATTTTAGAATTTGAGGTTTAGAATG
Found at i:630584 original size:12 final size:12
Alignment explanation
Indices: 630567--630591 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
630557 TTCCAACCAC
630567 TTACCACGTTTG
1 TTACCACGTTTG
630579 TTACCACGTTTG
1 TTACCACGTTTG
630591 T
1 T
630592 AGGATCTGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.16, T:0.44
Consensus pattern (12 bp):
TTACCACGTTTG
Found at i:634243 original size:19 final size:17
Alignment explanation
Indices: 634216--634250 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 17
634206 TTCCCTTAAC
634216 AAAAACAAATAATCAATA
1 AAAAACAAATAA-CAATA
634234 AAAAATCAAATAACAAT
1 AAAAA-CAAATAACAAT
634251 GTCAAAGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.71, C:0.11, G:0.00, T:0.17
Consensus pattern (17 bp):
AAAAACAAATAACAATA
Found at i:641114 original size:59 final size:59
Alignment explanation
Indices: 641016--641662 Score: 940
Period size: 59 Copynumber: 11.0 Consensus size: 59
641006 ATTAATTCCC
* * * * * *
641016 ATATGGAAATTCATACACTTAGTATGAATTTCTTATCATTTTGGCACAC-AAGGTACCCA
1 ATATGGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAA-GTGCCCT
* * * * * * * *
641075 ATACGAAAATTCAAACACTTAGTATGAATTTCTTATCATTTTAGAACACGAAGCGCCCT
1 ATATGGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCT
** * * * * * *
641134 ATACAGAAATTCCTACACTTAATATGAATTTCTTATCATTTTAGCACACGAAGCGCCCT
1 ATATGGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCT
* * * * *
641193 ATACGGAAATTCATACGCTTAATATGAATTTCTTCTCATGTTAGCAAACGAAGTGCCCT
1 ATATGGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCT
*
641252 ATATGGAAATTCATACAC-TAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCTCT
1 ATATGGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCT
* * * *
641310 ATATGGGAATTCATACACTTAGTATGAATTCCTTCTCATGTCAACACACGAAGTTCCCT
1 ATATGGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCT
641369 ATATGGAAATTCATACACTT-GTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCT
1 ATATGGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCT
*
641427 ATATGGTAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCT
1 ATATGGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCT
*
641486 ATATGGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAGGTGCCCT
1 ATATGGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCT
* *
641545 ATATGGAAATTCATACACTTAGTATGAATTCCTTCTCATGCTAGCACACGAAGAGCCCT
1 ATATGGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCT
641604 ATATGGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCT
1 ATATGGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCT
641663 TCTGGTAATC
Statistics
Matches: 541, Mismatches: 44, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
58 107 0.20
59 432 0.80
60 2 0.00
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (59 bp):
ATATGGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCT
Found at i:642212 original size:21 final size:21
Alignment explanation
Indices: 642186--642260 Score: 132
Period size: 21 Copynumber: 3.6 Consensus size: 21
642176 CCCTTACCAT
642186 GGTATCGATACTACCTCGTTC
1 GGTATCGATACTACCTCGTTC
642207 GGTATCGATACTACCTCGTTC
1 GGTATCGATACTACCTCGTTC
*
642228 GGTATCGATACTACCTCATTC
1 GGTATCGATACTACCTCGTTC
*
642249 AGTATCGATACT
1 GGTATCGATACT
642261 TCTCATCTAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.33
Consensus pattern (21 bp):
GGTATCGATACTACCTCGTTC
Found at i:647228 original size:25 final size:25
Alignment explanation
Indices: 647194--647242 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
647184 CAGCTCCACC
*
647194 CAGTTTCTCATGATTAGAGCACTGA
1 CAGTTTCTCATGATCAGAGCACTGA
647219 CAGTTTCTCATGATCAGAGCACTG
1 CAGTTTCTCATGATCAGAGCACTG
647243 CAAACTTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (25 bp):
CAGTTTCTCATGATCAGAGCACTGA
Found at i:648217 original size:59 final size:59
Alignment explanation
Indices: 648100--648620 Score: 661
Period size: 59 Copynumber: 8.8 Consensus size: 59
648090 TCCCATATAA
** * * * * * *
648100 TCATACACTTAGTATGAATTTATTATCATTTTGGCACAC-AAGGTACCCAATACGGAAAT
1 TCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAA-GTGCCCTATATGGAAAT
* * * * * ** * **
648159 TCATACACTTAGTATGAATTTCTTATCATTTTAGCAAATGAAGCACCCTCTACAGAAAT
1 TCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTATATGGAAAT
* * * * * *
648218 TCCTACACTTAGTATGAATTTCTTATTATTTTAGCACACGAAGCGCCCTATATGGAAAT
1 TCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTATATGGAAAT
* * * * *
648277 CCATACACTTTGTATGAATTTCTTCTCAAGTTAGCACACGAAATGCCCTATATGGAAAT
1 TCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTATATGGAAAT
* * *
648336 TCATACACATAGTATGAATTCCTTCTTATGTTAGCACACGAAGTGCTCTATATGGAAAT
1 TCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTATATGGAAAT
648395 TCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTATATGGAAAT
1 TCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTATATGGAAAT
648454 TCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTATATGGAAAT
1 TCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTATATGGAAAT
* *
648513 TCATACACCTT-GTTTGAATTCCTTCTCATGTTAGCATACGAAGTTG-CCTATATGGAAAT
1 TCATACA-CTTAGTATGAATTCCTTCTCATGTTAGCACACGAAG-TGCCCTATATGGAAAT
* * *
648572 TCATACATTTAGCATGAATTCATTCTCATGTTAGCACACGAAGTGCCCT
1 TCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCT
648621 TCTAGTAATC
Statistics
Matches: 414, Mismatches: 43, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
58 4 0.01
59 403 0.97
60 7 0.02
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (59 bp):
TCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTATATGGAAAT
Found at i:649159 original size:20 final size:20
Alignment explanation
Indices: 649131--649182 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
649121 CGATGTTACT
649131 TGATATCGATACCCTTACCA
1 TGATATCGATACCCTTACCA
*
649151 TGGTATCGATACCCTTACCA
1 TGATATCGATACCCTTACCA
649171 TGATATCGATAC
1 TGATATCGATAC
649183 TACCTCATTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (20 bp):
TGATATCGATACCCTTACCA
Found at i:650776 original size:4 final size:4
Alignment explanation
Indices: 650767--650822 Score: 69
Period size: 4 Copynumber: 13.8 Consensus size: 4
650757 CTGAAATGGT
* *
650767 TAAA TAAA TAAA TAAA TAAAA TAAA TACA TACA T-AA TAAA TAAA TAATA
1 TAAA TAAA TAAA TAAA T-AAA TAAA TAAA TAAA TAAA TAAA TAAA TAA-A
650816 TAAA TAA
1 TAAA TAA
650823 TCGTAACAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
3 2 0.04
4 37 0.79
5 8 0.17
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.27
Consensus pattern (4 bp):
TAAA
Found at i:650882 original size:37 final size:37
Alignment explanation
Indices: 650841--651172 Score: 366
Period size: 37 Copynumber: 8.8 Consensus size: 37
650831 ATAATAATGA
*
650841 AAAAATATTTTTTAAAAACTATATATTATACGTTTTTA
1 AAAAATATTTTTTAAAAACTATATATTATACG-TTTTC
*
650879 AAAATATATTTTTTAAAAACTATATATTATATGTTTTC
1 AAAA-ATATTTTTTAAAAACTATATATTATACGTTTTC
***
650917 AAAAATATTTAAAAAAAACTATATATTATACGTTTTC
1 AAAAATATTTTTTAAAAACTATATATTATACGTTTTC
* * *
650954 AAAAATATTTTTAAAAAATTATATATTATACTTTTTC
1 AAAAATATTTTTTAAAAACTATATATTATACGTTTTC
****
650991 AAAAA-AAAAATTAAAAACTATATATTATACGTTTTC
1 AAAAATATTTTTTAAAAACTATATATTATACGTTTTC
* *
651027 AAAAATATTTTTTTAAAAAAAACTATATATTATACATCTTC
1 AAAAATA-TTTTTT---AAAAACTATATATTATACGTTTTC
* * * *
651068 AAAACTA-TTTTAAAAAATTATATATTATACATTTTC
1 AAAAATATTTTTTAAAAACTATATATTATACGTTTTC
651104 AAAAATATTTTTTTAATAAAGGCTATATATTATACGTTTTC
1 AAAAATA-TTTTTTAA-AAA--CTATATATTATACGTTTTC
* *
651145 -AAAAT-TATTTTAAAAACTATACATTATA
1 AAAAATATTTTTTAAAAACTATATATTATA
651173 TAGTTATATA
Statistics
Matches: 250, Mismatches: 33, Indels: 25
0.81 0.11 0.08
Matches are distributed among these distances:
35 11 0.04
36 57 0.23
37 71 0.28
38 27 0.11
39 34 0.14
40 5 0.02
41 45 0.18
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.43
Consensus pattern (37 bp):
AAAAATATTTTTTAAAAACTATATATTATACGTTTTC
Found at i:650892 original size:16 final size:16
Alignment explanation
Indices: 650873--650903 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
650863 ATATTATACG
650873 TTTTTAAAAA-TATAT
1 TTTTTAAAAACTATAT
650888 TTTTTAAAAACTATAT
1 TTTTTAAAAACTATAT
650904 ATTATATGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTTTAAAAACTATAT
Found at i:651069 original size:77 final size:75
Alignment explanation
Indices: 650852--651172 Score: 359
Period size: 77 Copynumber: 4.3 Consensus size: 75
650842 AAAATATTTT
* *
650852 TTAAAAACTATATATTATACGTTTTTAAAAATATATTTTTT-AAAAACTATATATTATATGTTTT
1 TTAAAAACTATATATTATACGTTTTCAAAAATAT-TTTTTTAAAAAACTATATATTATACGTTTT
650916 CAAAAATATTTAAA
65 CAAAAA-A--TAAA
* *
650930 --AAAAACTATATATTATACGTTTTCAAAAATA--TTTTTAAAAAATTATATATTATACTTTTTC
1 TTAAAAACTATATATTATACGTTTTCAAAAATATTTTTTTAAAAAACTATATATTATACGTTTTC
*
650991 AAAAAAAAAA
66 AAAAAATAAA
* *
651001 TTAAAAACTATATATTATACGTTTTCAAAAATATTTTTTTAAAAAAAACTATATATTATACATCT
1 TTAAAAACTATATATTATACGTTTTCAAAAATATTTTTTT--AAAAAACTATATATTATACGTTT
* **
651066 TC-AAAACTATT
64 TCAAAAAATAAA
* * *
651077 TTAAAAAATTATATATTATACATTTTCAAAAATATTTTTTTAATAAAGGCTATATATTATACGTT
1 TT-AAAAACTATATATTATACGTTTTCAAAAATATTTTTTTAA-AAA-ACTATATATTATACGTT
* **
651142 TTC-AAAATTATT
63 TTCAAAAAATAAA
*
651154 TTAAAAACTATACATTATA
1 TTAAAAACTATATATTATA
651173 TAGTTATATA
Statistics
Matches: 213, Mismatches: 20, Indels: 22
0.84 0.08 0.09
Matches are distributed among these distances:
71 3 0.01
73 37 0.17
74 26 0.12
75 7 0.03
76 55 0.26
77 85 0.40
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.43
Consensus pattern (75 bp):
TTAAAAACTATATATTATACGTTTTCAAAAATATTTTTTTAAAAAACTATATATTATACGTTTTC
AAAAAATAAA
Found at i:664419 original size:18 final size:18
Alignment explanation
Indices: 664396--664446 Score: 93
Period size: 18 Copynumber: 2.8 Consensus size: 18
664386 TGATGGACAA
*
664396 TTGGACTGTTGGACCCAG
1 TTGGACTATTGGACCCAG
664414 TTGGACTATTGGACCCAG
1 TTGGACTATTGGACCCAG
664432 TTGGACTATTGGACC
1 TTGGACTATTGGACC
664447 TGGACCCTGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (18 bp):
TTGGACTATTGGACCCAG
Found at i:664489 original size:4 final size:4
Alignment explanation
Indices: 664480--664536 Score: 62
Period size: 4 Copynumber: 13.8 Consensus size: 4
664470 CTGAAATGGT
* *
664480 TAAA TAAA TAAA TAAAA TAAA TACA T-AA TAAA TAAT TAAA TATAA TAAA
1 TAAA TAAA TAAA T-AAA TAAA TAAA TAAA TAAA TAAA TAAA TA-AA TAAA
664529 TAATA TAA
1 TAA-A TAA
664537 TAACAATAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
3 2 0.04
4 31 0.69
5 12 0.27
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (4 bp):
TAAA
Found at i:664511 original size:11 final size:9
Alignment explanation
Indices: 664480--664545 Score: 57
Period size: 9 Copynumber: 7.3 Consensus size: 9
664470 CTGAAATGGT
664480 TAAAT-AAA
1 TAAATAAAA
664488 TAAATAAAA
1 TAAATAAAA
664497 TAAATACATAA
1 TAAATA-A-AA
*
664508 TAAAT-AAT
1 TAAATAAAA
*
664516 TAAATATAA
1 TAAATAAAA
*
664525 TAAATAATA
1 TAAATAAAA
664534 T-AATAACAA
1 TAAATAA-AA
664543 TAA
1 TAA
664546 TAACGAAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
8 16 0.35
9 21 0.46
10 2 0.04
11 7 0.15
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (9 bp):
TAAATAAAA
Found at i:664512 original size:28 final size:29
Alignment explanation
Indices: 664480--664539 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 29
664470 CTGAAATGGT
664480 TAAATAAATAAATAAAATAAAT-ACATAA
1 TAAATAAATAAATAAAATAAATAACATAA
* * *
664508 TAAATAATTAAATATAATAAATAATATAA
1 TAAATAAATAAATAAAATAAATAACATAA
664537 TAA
1 TAA
664540 CAATAATAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 20 0.71
29 8 0.29
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (29 bp):
TAAATAAATAAATAAAATAAATAACATAA
Found at i:664513 original size:24 final size:25
Alignment explanation
Indices: 664482--664539 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 25
664472 GAAATGGTTA
*
664482 AATAAATAAATAAAATA-AATACAT
1 AATAAATAAATAAAATATAATAAAT
*
664506 AATAAAT-AATTAAATATAATAAAT
1 AATAAATAAATAAAATATAATAAAT
664530 AATATAATAA
1 AATA-AATAA
664540 CAATAATAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 8 0.28
24 17 0.59
25 3 0.10
26 1 0.03
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (25 bp):
AATAAATAAATAAAATATAATAAAT
Found at i:664538 original size:17 final size:18
Alignment explanation
Indices: 664480--664536 Score: 73
Period size: 17 Copynumber: 3.2 Consensus size: 18
664470 CTGAAATGGT
*
664480 TAAATA-AATAAATAAAA
1 TAAATATAATAAATAATA
664497 TAAATACATAATAAATAAT-
1 TAAAT--ATAATAAATAATA
664516 TAAATATAATAAATAATA
1 TAAATATAATAAATAATA
664534 TAA
1 TAA
664537 TAACAATAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
17 17 0.49
18 3 0.09
19 6 0.17
20 9 0.26
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (18 bp):
TAAATATAATAAATAATA
Found at i:664595 original size:38 final size:38
Alignment explanation
Indices: 664552--664896 Score: 444
Period size: 38 Copynumber: 9.3 Consensus size: 38
664542 ATAATAACGA
664552 AAAAATATTTTTTAAAAAACTATATATTATACGTTTTC
1 AAAAATATTTTTTAAAAAACTATATATTATACGTTTTC
*
664590 AAAAATATTTTTAAAAAAACTATATATTATACGTTTTC
1 AAAAATATTTTTTAAAAAACTATATATTATACGTTTTC
* *
664628 AAAAATATTTTTAAAAAAACTATATATTATATGTTTTC
1 AAAAATATTTTTTAAAAAACTATATATTATACGTTTTC
*
664666 AAAAATATTTTTTAAAAAAAACTATATATTATACTTTTTC
1 AAAAATATTTTTT--AAAAAACTATATATTATACGTTTTC
664706 AAAAATA-TTTTTAAAAAACTATATATTATACGTTTTC
1 AAAAATATTTTTTAAAAAACTATATATTATACGTTTTC
* *
664743 ---AAT-TTTTTT-TAAAAC--TATATTATATG-TTTC
1 AAAAATATTTTTTAAAAAACTATATATTATACGTTTTC
* *
664773 CAAAATAATTTTTTAAAAAACTATATATTATAC-TTTTGT
1 AAAAAT-ATTTTTTAAAAAACTATATATTATACGTTTT-C
* **
664812 AAAACTA--TTTTAAAAAACTATATATTATATATTTTC
1 AAAAATATTTTTTAAAAAACTATATATTATACGTTTTC
* *
664848 AAAAATATTTTTAAAAAAACTATATATTATACGTTTAC
1 AAAAATATTTTTTAAAAAACTATATATTATACGTTTTC
*
664886 AAAATTATTTT
1 AAAAATATTTT
664897 AAAAATATAC
Statistics
Matches: 270, Mismatches: 21, Indels: 32
0.84 0.07 0.10
Matches are distributed among these distances:
30 4 0.01
31 10 0.04
33 8 0.03
34 8 0.03
35 6 0.02
36 33 0.12
37 28 0.10
38 134 0.50
39 9 0.03
40 30 0.11
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.45
Consensus pattern (38 bp):
AAAAATATTTTTTAAAAAACTATATATTATACGTTTTC
Found at i:671381 original size:29 final size:29
Alignment explanation
Indices: 671356--671536 Score: 272
Period size: 29 Copynumber: 6.2 Consensus size: 29
671346 TTTTTTTAAA
671356 AAATTACAATAAATACCATAACTTTTTTAT
1 AAATTACAATAAATACCATAAC-TTTTTAT
*
671386 AAATTGCAATAAATACCATAACTTTTTAT
1 AAATTACAATAAATACCATAACTTTTTAT
* * * *
671415 AAATTAAAATAAATATCAAAACTTTCTAT
1 AAATTACAATAAATACCATAACTTTTTAT
671444 AAATTACAATAAATACCATAACTTTTTAT
1 AAATTACAATAAATACCATAACTTTTTAT
*
671473 AAATTACAATAAATACCATAACATTTTAT
1 AAATTACAATAAATACCATAACTTTTTAT
* * *
671502 AAATTACAATAAATAACAAAACTATTTAT
1 AAATTACAATAAATACCATAACTTTTTAT
671531 AAATTA
1 AAATTA
671537 AAATCAAAGA
Statistics
Matches: 136, Mismatches: 15, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
29 115 0.85
30 21 0.15
ACGTcount: A:0.51, C:0.12, G:0.01, T:0.36
Consensus pattern (29 bp):
AAATTACAATAAATACCATAACTTTTTAT
Found at i:671493 original size:87 final size:88
Alignment explanation
Indices: 671356--671536 Score: 303
Period size: 87 Copynumber: 2.1 Consensus size: 88
671346 TTTTTTTAAA
* *
671356 AAATTACAATAAATACCATAACTTTTTTATAAATTGCAATAAATACCATAACTTTTTATAAATTA
1 AAATTACAATAAATACCATAACTTTTTTATAAATTACAATAAATACCATAACATTTTATAAATTA
*
671421 AAATAAATATCAAAACT-TTCTAT
66 AAATAAATAACAAAACTATT-TAT
671444 AAATTACAATAAATACCATAAC-TTTTTATAAATTACAATAAATACCATAACATTTTATAAATTA
1 AAATTACAATAAATACCATAACTTTTTTATAAATTACAATAAATACCATAACATTTTATAAATTA
*
671508 CAATAAATAACAAAACTATTTAT
66 AAATAAATAACAAAACTATTTAT
671531 AAATTA
1 AAATTA
671537 AAATCAAAGA
Statistics
Matches: 88, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
87 64 0.73
88 24 0.27
ACGTcount: A:0.51, C:0.12, G:0.01, T:0.36
Consensus pattern (88 bp):
AAATTACAATAAATACCATAACTTTTTTATAAATTACAATAAATACCATAACATTTTATAAATTA
AAATAAATAACAAAACTATTTAT
Found at i:674394 original size:13 final size:13
Alignment explanation
Indices: 674378--674405 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
674368 GAATGTGAAA
674378 GATAGCCATTTTG
1 GATAGCCATTTTG
674391 GATAGCCATTTTG
1 GATAGCCATTTTG
674404 GA
1 GA
674406 AATTTGGCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (13 bp):
GATAGCCATTTTG
Found at i:675242 original size:21 final size:22
Alignment explanation
Indices: 675217--675257 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
675207 TTTTCGTAAG
675217 AGTACTTTGTGTACT-TGGAGT
1 AGTACTTTGTGTACTATGGAGT
675238 AGTACTTTGTGTACTATGGA
1 AGTACTTTGTGTACTATGGA
675258 ACTTTGTGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.22, C:0.10, G:0.27, T:0.41
Consensus pattern (22 bp):
AGTACTTTGTGTACTATGGAGT
Found at i:675812 original size:2 final size:2
Alignment explanation
Indices: 675805--675845 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
675795 TAAATGTTAT
675805 TA TA TA TA TA 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 TA TA TA TA TA T
675846 GTATGTATGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:681255 original size:228 final size:229
Alignment explanation
Indices: 680858--681317 Score: 841
Period size: 228 Copynumber: 2.0 Consensus size: 229
680848 TTCAGGTTTA
* **
680858 AGGTGTTACTGTTATGCCATATTGATTGGAATATTTATAATTTTATGCTAATGCATGATTATACT
1 AGGTGTTACAGTTATGCCATATTGATTGGAATATTTATAATTTTATAATAATGCATGATTATACT
*
680923 TAAAAAGAACAAAATTAGTAAAGTTGTGATGGTTGAGTACAAAACAAAATTAAAAAGTGTGTTGA
66 TAAAAAGAACAAAATTAGTAAAGTTGTGATGGTTGAGTACAAAACAAAATTAAAAAGTGTGATGA
680988 AAAAGAGAAAGTTAAGAGTTGAATTTGGTTATTGTAAGATTATACAATTGTAAAGTAGGCCAAAG
131 AAAAGAGAAAGTTAAGAGTTGAATTTGGTTATTGTAAGATTATACAATTGTAAAGTAGGCCAAAG
*
681053 TTTATAAACCTAAAGGAGTAGAATTTAAAAA-AT
196 TTTATAAACCTAAAGGAGTAAAATTTAAAAACAT
*
681086 AGGTGTTACAGTTATGCCATGTTGATTGGAATATTTATAATTTTATAATAATGCATGATTATACT
1 AGGTGTTACAGTTATGCCATATTGATTGGAATATTTATAATTTTATAATAATGCATGATTATACT
681151 TAAAAAGAACAAAATTAGTAAAGTTGTGATGGTTGAGTACAAAACAAAATTAAAAAGTGTGATGA
66 TAAAAAGAACAAAATTAGTAAAGTTGTGATGGTTGAGTACAAAACAAAATTAAAAAGTGTGATGA
* *
681216 AAAAGAGAAAGTTAGGAGTTGAATTTGGTTATTGTAAGATTATACAATTGTCAAGTAGGCCAAAG
131 AAAAGAGAAAGTTAAGAGTTGAATTTGGTTATTGTAAGATTATACAATTGTAAAGTAGGCCAAAG
681281 TTTATAAACCTAAAGGAGTAAAATTTAAAAACAT
196 TTTATAAACCTAAAGGAGTAAAATTTAAAAACAT
681315 AGG
1 AGG
681318 AATGAGAGGA
Statistics
Matches: 223, Mismatches: 8, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
228 218 0.98
229 5 0.02
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.32
Consensus pattern (229 bp):
AGGTGTTACAGTTATGCCATATTGATTGGAATATTTATAATTTTATAATAATGCATGATTATACT
TAAAAAGAACAAAATTAGTAAAGTTGTGATGGTTGAGTACAAAACAAAATTAAAAAGTGTGATGA
AAAAGAGAAAGTTAAGAGTTGAATTTGGTTATTGTAAGATTATACAATTGTAAAGTAGGCCAAAG
TTTATAAACCTAAAGGAGTAAAATTTAAAAACAT
Found at i:686919 original size:69 final size:68
Alignment explanation
Indices: 686800--687059 Score: 215
Period size: 69 Copynumber: 3.8 Consensus size: 68
686790 TCTATGATTG
* * *
686800 ATCATAAATA-TTCTGGGTGACTTGCACGAGAG-CTCTGAAGGGTTAGAGTGTCTCTCACAATAG
1 ATCATCAATATTTC-GGGTGACTCGCACGAGAGCCCCT-AA-GGTTAGAGTGTCTCTCACAATAG
686863 CACCTA
63 CACCTA
* * * *
686869 ATCATTAATATTTCGGGTGACTCGCATGAGAGCCCCTAAGGATTAAAGTG--TCTCACATTGGAG
1 ATCATCAATATTTCGGGTGACTCGCACGAGAGCCCCTAAGG-TTAGAGTGTCTCTCACAAT--AG
**
686932 CATTTA
63 CACCTA
** * * * *** *
686938 ATCATCAATATTTCGGGTGACTCAAACGGGAGCCCCAAAAGGTTAGAGTGTCTCACACGGGAGTA
1 ATCATCAATATTTCGGGTGACTCGCACGAGAGCCCC-TAAGGTTAGAGTGTCTCTCACAATAGCA
687003 CCTA
65 CCTA
* * *
687007 ATCATCAATATTTCAGGTGACTCGCAC-AGGAGCCCCGAAGAGTTAGTGTGTCT
1 ATCATCAATATTTCGGGTGACTCGCACGA-GAGCCCCTAAG-GTTAGAGTGTCT
687060 TGCAAGGGAG
Statistics
Matches: 153, Mismatches: 28, Indels: 20
0.76 0.14 0.10
Matches are distributed among these distances:
67 8 0.05
68 5 0.03
69 125 0.82
70 10 0.07
71 5 0.03
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (68 bp):
ATCATCAATATTTCGGGTGACTCGCACGAGAGCCCCTAAGGTTAGAGTGTCTCTCACAATAGCAC
CTA
Found at i:688123 original size:31 final size:31
Alignment explanation
Indices: 688088--688159 Score: 126
Period size: 31 Copynumber: 2.3 Consensus size: 31
688078 TTAAAAAAAG
* *
688088 TTGGTCACTTACGTTATCGTTTTATTAAGTT
1 TTGGTCACTTACATTATCATTTTATTAAGTT
688119 TTGGTCACTTACATTATCATTTTATTAAGTT
1 TTGGTCACTTACATTATCATTTTATTAAGTT
688150 TTGGTCACTT
1 TTGGTCACTT
688160 GAGCATTGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.21, C:0.14, G:0.14, T:0.51
Consensus pattern (31 bp):
TTGGTCACTTACATTATCATTTTATTAAGTT
Found at i:689738 original size:18 final size:18
Alignment explanation
Indices: 689712--689755 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
689702 ACATCAGCAA
689712 ACCGTTAAAGGTTTAACG
1 ACCGTTAAAGGTTTAACG
*
689730 ACTGTTAAAGGTTTAACG
1 ACCGTTAAAGGTTTAACG
689748 ACCGTTAA
1 ACCGTTAA
689756 CCTTCAGTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (18 bp):
ACCGTTAAAGGTTTAACG
Found at i:695680 original size:3 final size:3
Alignment explanation
Indices: 695672--695728 Score: 54
Period size: 3 Copynumber: 21.0 Consensus size: 3
695662 TTTGTTTTAT
* *
695672 TTA TTA TTA TT- TTA TT- TTA ATA TTA TTA TTA -TA TTA -TA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
695716 TTA TT- TT- TTA TTA
1 TTA TTA TTA TTA TTA
695729 CAGGCCCAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
2 12 0.26
3 34 0.74
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:695695 original size:19 final size:19
Alignment explanation
Indices: 695673--695726 Score: 83
Period size: 19 Copynumber: 2.9 Consensus size: 19
695663 TTGTTTTATT
*
695673 TATTATTATTTTATTTTAA
1 TATTATTATTTTATTATAA
*
695692 TATTATTATTATATTATAA
1 TATTATTATTTTATTATAA
695711 TATTATTATTTT-TTAT
1 TATTATTATTTTATTAT
695727 TACAGGCCCA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
18 4 0.12
19 28 0.88
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TATTATTATTTTATTATAA
Found at i:697358 original size:20 final size:19
Alignment explanation
Indices: 697333--697374 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
697323 CTATTTTATA
697333 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
697353 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
697372 AAT
1 AAT
697375 ATCGAGGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:697476 original size:23 final size:25
Alignment explanation
Indices: 697431--697482 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 25
697421 ATATTTCTAA
*
697431 ATAAATAAATATTTTATTTATAAAT
1 ATAAATAAATATTTTATTAATAAAT
* *
697456 ATAAATATATA-TTT-TTAATAATT
1 ATAAATAAATATTTTATTAATAAAT
697479 ATAA
1 ATAA
697483 TTTTAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 11 0.46
24 3 0.12
25 10 0.42
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
ATAAATAAATATTTTATTAATAAAT
Found at i:699570 original size:8 final size:7
Alignment explanation
Indices: 699546--699587 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
699536 TTTTCATACA
699546 TGCA-TT
1 TGCATTT
699552 TGCATTT
1 TGCATTT
699559 TGCATCTT
1 TGCAT-TT
699567 TGCATTT
1 TGCATTT
* *
699574 TTCATTG
1 TGCATTT
699581 TGCATTT
1 TGCATTT
699588 ATACTCTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 4 0.13
7 19 0.63
8 7 0.23
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (7 bp):
TGCATTT
Found at i:699570 original size:15 final size:14
Alignment explanation
Indices: 699546--699587 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
699536 TTTTCATACA
699546 TGCA-TTTGCATTT
1 TGCATTTTGCATTT
699559 TGCATCTTTGCATTT
1 TGCAT-TTTGCATTT
* *
699574 TTCATTGTGCATTT
1 TGCATTTTGCATTT
699588 ATACTCTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 13 0.52
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (14 bp):
TGCATTTTGCATTT
Done.