Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008621.1 Hibiscus syriacus cultivar Beakdansim tig00111584_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: 1991651
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 11
Found at i:753291 original size:32 final size:32
Alignment explanation
Indices: 753254--753330 Score: 154
Period size: 32 Copynumber: 2.4 Consensus size: 32
753244 ATTAAAATTA
753254 AATTTGAAAGTTAGAGTGACTGAATTAAGAGT
1 AATTTGAAAGTTAGAGTGACTGAATTAAGAGT
753286 AATTTGAAAGTTAGAGTGACTGAATTAAGAGT
1 AATTTGAAAGTTAGAGTGACTGAATTAAGAGT
753318 AATTTGAAAGTTA
1 AATTTGAAAGTTA
753331 AGCAATTAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.42, C:0.03, G:0.23, T:0.32
Consensus pattern (32 bp):
AATTTGAAAGTTAGAGTGACTGAATTAAGAGT
Found at i:753293 original size:16 final size:16
Alignment explanation
Indices: 753274--753325 Score: 54
Period size: 15 Copynumber: 3.2 Consensus size: 16
753264 TTAGAGTGAC
753274 TGAATTAAGAGTAATT
1 TGAATTAAGAGTAATT
* *
753290 TGAAAGTT-AGAGTGA-C
1 TG-AA-TTAAGAGTAATT
753306 TGAATTAAGAGTAATT
1 TGAATTAAGAGTAATT
753322 TGAA
1 TGAA
753326 AGTTAAGCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 8
0.70 0.10 0.20
Matches are distributed among these distances:
14 2 0.07
15 8 0.29
16 8 0.29
17 8 0.29
18 2 0.07
ACGTcount: A:0.42, C:0.02, G:0.23, T:0.33
Consensus pattern (16 bp):
TGAATTAAGAGTAATT
Found at i:760809 original size:14 final size:14
Alignment explanation
Indices: 760786--760815 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
760776 TTACATTGAG
760786 TTTCTCAATAAAAC
1 TTTCTCAATAAAAC
*
760800 TTTCTTAATAAAAC
1 TTTCTCAATAAAAC
760814 TT
1 TT
760816 AAAAGATCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.43
Consensus pattern (14 bp):
TTTCTCAATAAAAC
Found at i:763776 original size:35 final size:35
Alignment explanation
Indices: 763726--763798 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 35
763716 AAACAATCTC
* * *
763726 CAATTTCATTTTAAACCCTAAATTCCAAAATAATT
1 CAATTACATTCTAAACCCCAAATTCCAAAATAATT
* *
763761 CAATTACATTCTAAACCCCAAATTCTAAAATACTT
1 CAATTACATTCTAAACCCCAAATTCCAAAATAATT
763796 CAA
1 CAA
763799 AATAATATTG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.44, C:0.23, G:0.00, T:0.33
Consensus pattern (35 bp):
CAATTACATTCTAAACCCCAAATTCCAAAATAATT
Found at i:764380 original size:35 final size:35
Alignment explanation
Indices: 764334--764401 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
764324 TATTATTTTG
*
764334 ATTATTTTGGAATTTAGGGTTTAGAATGTAATTGA
1 ATTATTTTGGAATTTAGGGTTTAGAATGAAATTGA
*
764369 ATTATTTTGGAATTTGGGGTTTAGAATGAAATT
1 ATTATTTTGGAATTTAGGGTTTAGAATGAAATT
764402 AAGGATTGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.31, C:0.00, G:0.24, T:0.46
Consensus pattern (35 bp):
ATTATTTTGGAATTTAGGGTTTAGAATGAAATTGA
Found at i:765211 original size:17 final size:17
Alignment explanation
Indices: 765176--765223 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
765166 GAAGTTTATT
*
765176 TTAATTTAAATGATAAAA
1 TTAATTTAAATAAT-AAA
* *
765194 TTATTTTGAATAATAAA
1 TTAATTTAAATAATAAA
765211 TTAATTTAAATAA
1 TTAATTTAAATAA
765224 AATTGGTAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 14 0.56
18 11 0.44
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (17 bp):
TTAATTTAAATAATAAA
Found at i:786037 original size:16 final size:16
Alignment explanation
Indices: 786009--786055 Score: 78
Period size: 16 Copynumber: 3.0 Consensus size: 16
785999 CTTTGGTAAG
*
786009 AGTC-GACCATTGACC
1 AGTCAGACCGTTGACC
786024 AGTCAGACCGTTGACC
1 AGTCAGACCGTTGACC
786040 AGTCAGACCGTTGACC
1 AGTCAGACCGTTGACC
786056 GTTGACTTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
15 4 0.13
16 26 0.87
ACGTcount: A:0.26, C:0.32, G:0.23, T:0.19
Consensus pattern (16 bp):
AGTCAGACCGTTGACC
Found at i:790907 original size:21 final size:20
Alignment explanation
Indices: 790867--790908 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
790857 CCAACTTACA
*
790867 ATGCATTATGAACCATTATT
1 ATGCATTATCAACCATTATT
*
790887 ATGCATTATACAACTATTATT
1 ATGCATTAT-CAACCATTATT
790908 A
1 A
790909 GTTGTATGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.40
Consensus pattern (20 bp):
ATGCATTATCAACCATTATT
Found at i:795568 original size:21 final size:20
Alignment explanation
Indices: 795528--795569 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
795518 CCAACTTACA
*
795528 ATGCATTATGAACCATTATT
1 ATGCATTATCAACCATTATT
*
795548 ATGCATTATACAACTATTATT
1 ATGCATTAT-CAACCATTATT
795569 A
1 A
795570 GTTGTATGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.40
Consensus pattern (20 bp):
ATGCATTATCAACCATTATT
Found at i:799003 original size:28 final size:28
Alignment explanation
Indices: 798951--799005 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
798941 TCGTTGTTGC
* * *
798951 TTTTAAGTACTAGCTCGATGGCATAATG
1 TTTTAAGCACTAGCTCGACGACATAATG
*
798979 TTTTAAGCACTAGCTTGACGACATAAT
1 TTTTAAGCACTAGCTCGACGACATAAT
799006 TTTAATGGAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (28 bp):
TTTTAAGCACTAGCTCGACGACATAATG
Found at i:799211 original size:31 final size:31
Alignment explanation
Indices: 799173--799274 Score: 97
Period size: 31 Copynumber: 3.4 Consensus size: 31
799163 GTAACTTTTA
799173 ATAGTCGGGGAACTCAACGAAACAATGTTCT
1 ATAGTCGGGGAACTCAACGAAACAATGTTCT
* ***
799204 ATAGTCGGGGGACT-ATTTTATAAC--T-TT-T
1 ATAGTCGGGGAACTCA-ACGA-AACAATGTTCT
799232 AATAGTCGGGGAACTCAACGAAACAATGTTCT
1 -ATAGTCGGGGAACTCAACGAAACAATGTTCT
*
799264 ATAGTCAGGGA
1 ATAGTCGGGGA
799275 CCATTTATGT
Statistics
Matches: 54, Mismatches: 9, Indels: 16
0.68 0.11 0.20
Matches are distributed among these distances:
28 4 0.07
29 16 0.30
30 4 0.07
31 26 0.48
32 4 0.07
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (31 bp):
ATAGTCGGGGAACTCAACGAAACAATGTTCT
Found at i:807414 original size:22 final size:23
Alignment explanation
Indices: 807378--807447 Score: 108
Period size: 22 Copynumber: 3.1 Consensus size: 23
807368 CTTTTTTCTG
*
807378 TTATTTTCTTTTCAAACATTTTTT
1 TTATTTT-TTTTCAATCATTTTTT
807402 TTA-TTTTTTTCAATCA-TTTTT
1 TTATTTTTTTTCAATCATTTTTT
807423 TTATTTTTTTTCAATCATTTTTT
1 TTATTTTTTTTCAATCATTTTTT
807446 TT
1 TT
807448 CGTGGAACAA
Statistics
Matches: 43, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
21 8 0.19
22 22 0.51
23 10 0.23
24 3 0.07
ACGTcount: A:0.19, C:0.10, G:0.00, T:0.71
Consensus pattern (23 bp):
TTATTTTTTTTCAATCATTTTTT
Found at i:807422 original size:14 final size:13
Alignment explanation
Indices: 807404--807446 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
807394 CATTTTTTTT
807404 ATTTTTTTCAATC
1 ATTTTTTTCAATC
807417 ATTTTTTT--AT-
1 ATTTTTTTCAATC
807427 -TTTTTTTCAATC
1 ATTTTTTTCAATC
807439 ATTTTTTT
1 ATTTTTTT
807447 TCGTGGAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
9 7 0.27
11 4 0.15
13 15 0.58
ACGTcount: A:0.19, C:0.09, G:0.00, T:0.72
Consensus pattern (13 bp):
ATTTTTTTCAATC
Found at i:811214 original size:35 final size:35
Alignment explanation
Indices: 811166--811236 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
811156 TTTTCTTGCA
*
811166 GGTCCTTATTTTCTAAAATTACTGGTAAAATGGAC
1 GGTCCTTACTTTCTAAAATTACTGGTAAAATGGAC
811201 GGTCCTTACTTTCTAAAATTACTGGTAAAATGGAC
1 GGTCCTTACTTTCTAAAATTACTGGTAAAATGGAC
811236 G
1 G
811237 TATTCTTTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.35
Consensus pattern (35 bp):
GGTCCTTACTTTCTAAAATTACTGGTAAAATGGAC
Found at i:812500 original size:19 final size:20
Alignment explanation
Indices: 812460--812497 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
812450 TAAATGACTA
812460 GGGGTATCGGTACCCATAAG
1 GGGGTATCGGTACCCATAAG
812480 GGGGTATCGGTACCCATA
1 GGGGTATCGGTACCCATA
812498 GGGCATTCTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.21, G:0.34, T:0.21
Consensus pattern (20 bp):
GGGGTATCGGTACCCATAAG
Found at i:812898 original size:12 final size:12
Alignment explanation
Indices: 812883--812913 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
812873 CAAAAATAAT
812883 TTTTGAAATCAA
1 TTTTGAAATCAA
812895 TTTTG-AATCAA
1 TTTTGAAATCAA
812906 TTTTGAAA
1 TTTTGAAA
812914 AATTACTCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.39, C:0.06, G:0.10, T:0.45
Consensus pattern (12 bp):
TTTTGAAATCAA
Found at i:813184 original size:18 final size:17
Alignment explanation
Indices: 813153--813202 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
813143 TCAAATAACT
* *
813153 AATAACCATTCAAACCAA
1 AATAAACATCCAAA-CAA
813171 AATAAACATCCAAACAA
1 AATAAACATCCAAACAA
*
813188 ATTCAAACATCCAAA
1 AAT-AAACATCCAAA
813203 ATAAAACAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 5 0.18
18 23 0.82
ACGTcount: A:0.58, C:0.26, G:0.00, T:0.16
Consensus pattern (17 bp):
AATAAACATCCAAACAA
Found at i:814647 original size:13 final size:13
Alignment explanation
Indices: 814629--814663 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
814619 AATAGGCAAT
814629 TTTGAAAACT-ATG
1 TTTGAAAA-TAATG
814642 TTTGAAAATAATG
1 TTTGAAAATAATG
814655 TTTGAAAAT
1 TTTGAAAAT
814664 CAATATGTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 1 0.05
13 20 0.95
ACGTcount: A:0.43, C:0.03, G:0.14, T:0.40
Consensus pattern (13 bp):
TTTGAAAATAATG
Found at i:814701 original size:19 final size:20
Alignment explanation
Indices: 814677--814724 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
814667 TATGTAGTTT
814677 TCAAAACAAC-ATAATT-AAA
1 TCAAAACAACAAT-ATTAAAA
*
814696 TCAAAACAACAATTTTAAAA
1 TCAAAACAACAATATTAAAA
814716 TCAAAACAA
1 TCAAAACAA
814725 TTTTTTTTCG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.62, C:0.17, G:0.00, T:0.21
Consensus pattern (20 bp):
TCAAAACAACAATATTAAAA
Found at i:820982 original size:19 final size:20
Alignment explanation
Indices: 820942--820979 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
820932 CAAATTACTA
*
820942 GGGGCATCGGTACCCATAAG
1 GGGGCATCGATACCCATAAG
*
820962 GGGGTATCGATACCCATA
1 GGGGCATCGATACCCATA
820980 GGGCATTCTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.24, G:0.32, T:0.18
Consensus pattern (20 bp):
GGGGCATCGATACCCATAAG
Found at i:827708 original size:18 final size:19
Alignment explanation
Indices: 827685--827721 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
827675 CTGCGCTTAT
827685 TTTTCAAAATCAAA-ACAG
1 TTTTCAAAATCAAAGACAG
827703 TTTTCAAAATCAAAGACAG
1 TTTTCAAAATCAAAGACAG
827722 ACTTTGGTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.49, C:0.16, G:0.08, T:0.27
Consensus pattern (19 bp):
TTTTCAAAATCAAAGACAG
Found at i:836023 original size:20 final size:19
Alignment explanation
Indices: 836000--836166 Score: 106
Period size: 20 Copynumber: 8.4 Consensus size: 19
835990 GTTTCTACAA
*
836000 TCGCAACGCGAATTTCTTT
1 TCGCAACGCGAATTTCTAT
* *
836019 CTCGCAACGCGATTTTCAAAT
1 -TCGCAACGCGAATTTC-TAT
*
836040 TCGCAACTCG-ATTTCTAAAT
1 TCGCAACGCGAATTTCT--AT
*
836060 TCGCAACTCG-ATTTCTAAAT
1 TCGCAACGCGAATTTCT--AT
*
836080 TCGCAACGCGAATTTCTTTT
1 TCGCAACGCGAATTTC-TAT
*
836100 TCGCAACGCGAATTTCTTTT
1 TCGCAACGCGAATTTC-TAT
**
836120 TCGCAACATGAATTTTGCT-T
1 TCGCAACGCGAA-TTT-CTAT
* * *
836140 TCGCAACTCGATTTTCAAAT
1 TCGCAACGCGAATTTC-TAT
836160 TCGCAAC
1 TCGCAAC
836167 ACAAATTTTA
Statistics
Matches: 124, Mismatches: 14, Indels: 18
0.79 0.09 0.12
Matches are distributed among these distances:
18 1 0.01
19 7 0.06
20 104 0.84
21 10 0.08
22 2 0.02
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.35
Consensus pattern (19 bp):
TCGCAACGCGAATTTCTAT
Found at i:836093 original size:80 final size:79
Alignment explanation
Indices: 835914--836166 Score: 230
Period size: 80 Copynumber: 3.1 Consensus size: 79
835904 AATGACCAAC
* * * * * * *
835914 AAATTCGCAACGCGAACTCCAATTTCGCAACAC-AGTTTCCAAATTCGCAACGCGATTTTCCCAA
1 AAATTCGCAACGCGAATTTC-TTTTCGCAACGCGA-TTTTCAAATTCGCAACTCGA-TTT-CTAA
*
835978 ATTCGCAACT-TAGTTTCT
62 ATTCGCAACTCGA-TTTCT
835996 ACAA-TCGCAACGCGAATTTCTTTCTCGCAACGCGATTTTCAAATTCGCAACTCGATTTCTAAAT
1 A-AATTCGCAACGCGAATTTCTTT-TCGCAACGCGATTTTCAAATTCGCAACTCGATTTCTAAAT
836060 TCGCAACTCGATTTCT
64 TCGCAACTCGATTTCT
* *** ***
836076 AAATTCGCAACGCGAATTTCTTTTTCGCAACGCGAATTTCTTTTTCGCAACAT-GAATTT-TGCT
1 AAATTCGCAACGCGAATTTC-TTTTCGCAACGCGATTTTCAAATTCGCAAC-TCG-ATTTCTAAA
836139 TTCGCAACTCGATTT-T
63 TTCGCAACTCGATTTCT
836155 CAAATTCGCAAC
1 -AAATTCGCAAC
836167 ACAAATTTTA
Statistics
Matches: 147, Mismatches: 15, Indels: 20
0.81 0.08 0.11
Matches are distributed among these distances:
79 3 0.02
80 86 0.59
81 14 0.10
82 41 0.28
83 3 0.02
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.32
Consensus pattern (79 bp):
AAATTCGCAACGCGAATTTCTTTTCGCAACGCGATTTTCAAATTCGCAACTCGATTTCTAAATTC
GCAACTCGATTTCT
Found at i:836103 original size:40 final size:40
Alignment explanation
Indices: 835914--836186 Score: 179
Period size: 40 Copynumber: 6.8 Consensus size: 40
835904 AATGACCAAC
* * * * *
835914 AAATTCGCAACGCGAACTCCAATTTCGCAACAC-AGTTTCC
1 AAATTCGCAACGCGAATTTCTATTTCGCAACTCGA-TTTCT
* * * *
835954 AAATTCGCAACGCGATTTTCCCAAATTCGCAACT-TAGTTTCT
1 AAATTCGCAACGCGAATTT--CTATTTCGCAACTCGA-TTTCT
*
835996 ACAA-TCGCAACGCGAATTTCT-TTCTCGCAACGCGATTT-T
1 A-AATTCGCAACGCGAATTTCTATT-TCGCAACTCGATTTCT
* *
836035 CAAATTCGCAACTCG-ATTTCTAAATTCGCAACTCGATTTCT
1 -AAATTCGCAACGCGAATTTCT-ATTTCGCAACTCGATTTCT
* *
836076 AAATTCGCAACGCGAATTTCTTTTTCGCAACGCGAATTTCT
1 AAATTCGCAACGCGAATTTCTATTTCGCAACTCG-ATTTCT
** ** *
836117 -TTTTCGCAACATGAATTT-TGCTTTCGCAACTCGATTT-T
1 AAATTCGCAACGCGAATTTCT-ATTTCGCAACTCGATTTCT
* *
836155 CAAATTCGCAACACAAATTT-TAATTTCGCAAC
1 -AAATTCGCAACGCGAATTTCT-ATTTCGCAAC
836187 AGCTTTTATT
Statistics
Matches: 187, Mismatches: 30, Indels: 32
0.75 0.12 0.13
Matches are distributed among these distances:
38 1 0.01
39 15 0.08
40 122 0.65
41 15 0.08
42 32 0.17
43 2 0.01
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (40 bp):
AAATTCGCAACGCGAATTTCTATTTCGCAACTCGATTTCT
Found at i:836182 original size:20 final size:19
Alignment explanation
Indices: 836020--836208 Score: 71
Period size: 20 Copynumber: 9.6 Consensus size: 19
836010 AATTTCTTTC
* * *
836020 TCGCAACGCGATTTTCAAAT
1 TCGCAACACAATTTT-AATT
* * *
836040 TCGCAACTCGATTTCTAAAT
1 TCGCAACACAATTT-TAATT
* * *
836060 TCGCAACTCGATTTCTAAAT
1 TCGCAACACAATTT-TAATT
* *
836080 TCGCAACGCGAATTTCT-TTT
1 TCGCAACAC-AATTT-TAATT
* *
836100 TCGCAACGCGAATTTCT-TTT
1 TCGCAACAC-AATTT-TAATT
* **
836120 TCGCAACATGAATTTTGCTT
1 TCGCAACA-CAATTTTAATT
* * *
836140 TCGCAACTCGATTTTCAAAT
1 TCGCAACACAATTTT-AATT
836160 TCGCAACACAAATTTTAATT
1 TCGCAACAC-AATTTTAATT
*
836180 TCGCAACAGC--TTTTATTT
1 TCGCAACA-CAATTTTAATT
836198 TCGCAACACAA
1 TCGCAACACAA
836209 ATGTTTTGGG
Statistics
Matches: 142, Mismatches: 18, Indels: 19
0.79 0.10 0.11
Matches are distributed among these distances:
17 1 0.01
18 15 0.11
19 6 0.04
20 107 0.75
21 13 0.09
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (19 bp):
TCGCAACACAATTTTAATT
Found at i:836216 original size:80 final size:78
Alignment explanation
Indices: 836059--836210 Score: 177
Period size: 80 Copynumber: 1.9 Consensus size: 78
836049 GATTTCTAAA
* * *
836059 TTCGCAACTCGATTTCTAAATTCGCAACGCGAATTTCTTTTTCGCAACGCGAATTTCTTTTTCGC
1 TTCGCAACTCGATTTCTAAATTCGCAACACAAATTTCTATTTCGCAACGC--ATTTCTTTTTCGC
**
836124 AACATGAATTTTGCT
64 AACACAAATTTTGCT
836139 TTCGCAACTCGATTT-TCAAATTCGCAACACAAATTT-TAATTTCGCAACAGC-TTT-TATTTTC
1 TTCGCAACTCGATTTCT-AAATTCGCAACACAAATTTCT-ATTTCGCAAC-GCATTTCT-TTTTC
836200 GCAACACAAAT
62 GCAACACAAAT
836211 GTTTTGGGTA
Statistics
Matches: 63, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
77 1 0.02
78 17 0.27
79 2 0.03
80 41 0.65
81 2 0.03
ACGTcount: A:0.28, C:0.24, G:0.11, T:0.37
Consensus pattern (78 bp):
TTCGCAACTCGATTTCTAAATTCGCAACACAAATTTCTATTTCGCAACGCATTTCTTTTTCGCAA
CACAAATTTTGCT
Found at i:837045 original size:24 final size:24
Alignment explanation
Indices: 837013--837066 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
837003 GTATTCGAAA
837013 TTTGATCTTGGTCAATACTCGGAC
1 TTTGATCTTGGTCAATACTCGGAC
*
837037 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACTCGGAC
837061 TTTGAT
1 TTTGAT
837067 GATGTTTCAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACTCGGAC
Found at i:838599 original size:158 final size:155
Alignment explanation
Indices: 838312--838624 Score: 574
Period size: 158 Copynumber: 2.0 Consensus size: 155
838302 TGCTTTCATG
838312 GACTTTGTGGTGTCATTTATAGAAATCTAAAATCAAGGTCTGTTGGTATAAAAATCACAAATGGA
1 GACTTTGTGGTGTCATTTATAGAAATCTAAAATCAAGGTCTGTTGGTATAAAAATCACAAATGGA
838377 CAACTGGAAGGCTGTAAAGCTTATCGGGAAGTGGATTTTAATAAGCATATAAATTGTTTAAGACG
66 CAACTGGAAGGCTGTAAAGCTTATCGGGAAGTGGATTTTAATAAGCATATAAATTGTTTAAGACG
838442 TGTTTTGGCTCAATGTGCTCAAACA
131 TGTTTTGGCTCAATGTGCTCAAACA
*
838467 GACTTTGTGGTGT-TTTGTATAGAAATCTAAAATCAAGGTCTGTTGGTATAAAAAATCACAAATG
1 GACTTTGTGGTGTCATT-TATAGAAATCTAAAATCAAGGTCTGTTGGTAT-AAAAATCACAAATG
838531 GACAAACTGGAAGGCTGTAAAAGCTTATCGGGAAGTGGATTTTAATAAGCATATAAATTGTTTAA
64 GAC-AACTGGAAGGCTGT-AAAGCTTATCGGGAAGTGGATTTTAATAAGCATATAAATTGTTTAA
838596 GACGTGTTTTGGCTCAATGTGCTCAAACA
127 GACGTGTTTTGGCTCAATGTGCTCAAACA
838625 CTAGAAGATG
Statistics
Matches: 153, Mismatches: 1, Indels: 5
0.96 0.01 0.03
Matches are distributed among these distances:
154 2 0.01
155 45 0.29
156 17 0.11
157 14 0.09
158 75 0.49
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.32
Consensus pattern (155 bp):
GACTTTGTGGTGTCATTTATAGAAATCTAAAATCAAGGTCTGTTGGTATAAAAATCACAAATGGA
CAACTGGAAGGCTGTAAAGCTTATCGGGAAGTGGATTTTAATAAGCATATAAATTGTTTAAGACG
TGTTTTGGCTCAATGTGCTCAAACA
Found at i:839491 original size:18 final size:18
Alignment explanation
Indices: 839468--839503 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
839458 AAGCAAAAGG
* *
839468 AAATCATAATCGCAATCA
1 AAATCAAAATCCCAATCA
839486 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
839504 CAAAAGGCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.25, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:839744 original size:14 final size:14
Alignment explanation
Indices: 839725--839758 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
839715 GAAAGTCAAA
*
839725 TTTGCGTTGTGATT
1 TTTGCGTTGCGATT
839739 TTTGCGTTGCGATT
1 TTTGCGTTGCGATT
*
839753 GTTGCG
1 TTTGCG
839759 AAAGTTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.12, G:0.32, T:0.50
Consensus pattern (14 bp):
TTTGCGTTGCGATT
Found at i:839863 original size:20 final size:20
Alignment explanation
Indices: 839840--839878 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
839830 ATCGCAATGC
839840 GAATTTGACTTTCGCGTTGT
1 GAATTTGACTTTCGCGTTGT
* *
839860 GAATTTGATTTTTGCGTTG
1 GAATTTGACTTTCGCGTTG
839879 CGAAACTTTT
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:0.15, C:0.10, G:0.26, T:0.49
Consensus pattern (20 bp):
GAATTTGACTTTCGCGTTGT
Found at i:841305 original size:21 final size:20
Alignment explanation
Indices: 841277--841396 Score: 111
Period size: 21 Copynumber: 5.8 Consensus size: 20
841267 CATGTGAATC
* *
841277 GGGCTCTTGAACGGTGGGAG
1 GGGCTCTTGAACGATGAGAG
841297 GGGCGTCTTGAACGATGAGAG
1 GGGC-TCTTGAACGATGAGAG
*
841318 GGGTCTCTTGAACAATGAGA-
1 GGG-CTCTTGAACGATGAGAG
*
841338 GGCCTCTTGAACGAT-ATGAG
1 GGGCTCTTGAACGATGA-GAG
*
841358 GGGCCTCTTGAATGAT-ATGAG
1 GGG-CTCTTGAACGATGA-GAG
*
841379 GGGCCTCTTGAATGATGA
1 GGG-CTCTTGAACGATGA
841397 CAGGTGAATC
Statistics
Matches: 87, Mismatches: 7, Indels: 10
0.84 0.07 0.10
Matches are distributed among these distances:
18 1 0.01
19 13 0.15
20 8 0.09
21 63 0.72
22 2 0.02
ACGTcount: A:0.23, C:0.16, G:0.37, T:0.24
Consensus pattern (20 bp):
GGGCTCTTGAACGATGAGAG
Found at i:841350 original size:40 final size:43
Alignment explanation
Indices: 841302--841396 Score: 126
Period size: 40 Copynumber: 2.3 Consensus size: 43
841292 GGGAGGGGCG
*
841302 TCTTGAACGATGA-GAGGGGTCTCTTGAA-CA-ATGAGAGGCC
1 TCTTGAACGATGATGAGGGGCCTCTTGAATCATATGAGAGGCC
* *
841342 TCTTGAACGAT-ATGAGGGGCCTCTTGAATGATATGAGGGGCC
1 TCTTGAACGATGATGAGGGGCCTCTTGAATCATATGAGAGGCC
*
841384 TCTTGAATGATGA
1 TCTTGAACGATGA
841397 CAGGTGAATC
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
39 1 0.02
40 25 0.53
41 1 0.02
42 19 0.40
43 1 0.02
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (43 bp):
TCTTGAACGATGATGAGGGGCCTCTTGAATCATATGAGAGGCC
Found at i:841561 original size:4 final size:4
Alignment explanation
Indices: 841540--841581 Score: 66
Period size: 4 Copynumber: 10.5 Consensus size: 4
841530 AGGCCGCTAA
* *
841540 AAAT AAAT TAAT ACAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
841582 TATCAAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:841702 original size:21 final size:21
Alignment explanation
Indices: 841678--841729 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
841668 TAAAATAATC
* * *
841678 TCACGTAGAGTGGCTACCTCA
1 TCACGTAAAGTAGATACCTCA
841699 TCACGTAAAGTAGATACCTCA
1 TCACGTAAAGTAGATACCTCA
*
841720 CCACGTAAAG
1 TCACGTAAAG
841730 CACCATTTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.21
Consensus pattern (21 bp):
TCACGTAAAGTAGATACCTCA
Found at i:841828 original size:21 final size:21
Alignment explanation
Indices: 841804--841853 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
841794 ACCATTGTTG
841804 TCACGTAAAGTACCGACCTCA
1 TCACGTAAAGTACCGACCTCA
*
841825 TCACGTAAAGTACTGACCTCA
1 TCACGTAAAGTACCGACCTCA
841846 TCACGTAA
1 TCACGTAA
841854 CTCCCCTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.34, C:0.30, G:0.14, T:0.22
Consensus pattern (21 bp):
TCACGTAAAGTACCGACCTCA
Found at i:843613 original size:19 final size:20
Alignment explanation
Indices: 843553--843616 Score: 94
Period size: 20 Copynumber: 3.2 Consensus size: 20
843543 AAACTTAAAT
*
843553 TCGCAACACGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
843573 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
* *
843593 TCGTAACGCGAAACT-AAAA
1 TCGCAACGCGAAAATGAAAA
843612 TCGCA
1 TCGCA
843617 TTGCGATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
19 8 0.20
20 32 0.80
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.12
Consensus pattern (20 bp):
TCGCAACGCGAAAATGAAAA
Found at i:843647 original size:20 final size:20
Alignment explanation
Indices: 843622--843660 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
843612 TCGCATTGCG
*
843622 ATTTTCGTGTTGTGAATTTC
1 ATTTTCGTGTTGCGAATTTC
843642 ATTTTCGTGTTGCGAATTT
1 ATTTTCGTGTTGCGAATTT
843661 AAGTTTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.10, G:0.21, T:0.54
Consensus pattern (20 bp):
ATTTTCGTGTTGCGAATTTC
Found at i:843667 original size:20 final size:20
Alignment explanation
Indices: 843624--843667 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
843614 GCATTGCGAT
* * *
843624 TTTCGTGTTGTGAATTTCAT
1 TTTCGTGTTGCGAATTTAAG
843644 TTTCGTGTTGCGAATTTAAG
1 TTTCGTGTTGCGAATTTAAG
843664 TTTC
1 TTTC
843668 AAAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.16, C:0.11, G:0.20, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGAATTTAAG
Found at i:844019 original size:22 final size:22
Alignment explanation
Indices: 843991--844038 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
843981 ATAGAGGGGG
* *
843991 GTCGTCGGATATGGGGACGGAT
1 GTCGTCGAAGATGGGGACGGAT
*
844013 GTCGTCGAAGATGGGGATGGAT
1 GTCGTCGAAGATGGGGACGGAT
844035 GTCG
1 GTCG
844039 CCGTAGAGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.19, C:0.12, G:0.46, T:0.23
Consensus pattern (22 bp):
GTCGTCGAAGATGGGGACGGAT
Found at i:846701 original size:521 final size:515
Alignment explanation
Indices: 845726--846701 Score: 1311
Period size: 521 Copynumber: 1.9 Consensus size: 515
845716 TATAAATTTA
* * * * *
845726 AAAATAAGTCAGATTGAATTGAGTGATCAAAATGGAACAAAAACTTATGTTTAATTATGATTTTG
1 AAAATAAATCAGATTGAATTGAGTGATCAAAACGAAACAAAAACTTAAGTTTAATGATGATTTTG
845791 AAAAGAAAAATAGTTTGAAGACCAAAATAGAATCGCATGAAAAGTTGAGTGACTAAATATGTAAT
66 AAAAGAAAAATAGTTTGAAGACCAAAATAGAATCGCATGAAAAGTTGAGTGACTAAATATGTAAT
*
845856 TTACCCACGTGGGTTTTAGAGTTAATTATTTGGGCAAATGAGGTAACAAATTAAACTTTAGGGCA
131 TTACCCACGTGGGTTTTAGAGTTAATTATTTGGGCAAATGAGGAAACAAATTAAACTTTAGGGCA
* * *
845921 AATTGTCTCAAAAAAATATTCTTAGAGGACAACTCAATATAAATGGTATAGTTTAGGGGACAAAT
196 AATCGTCTCAAAAAAATACTCTTAGAGGACAACTCAATACAAATGGTATAGTTTAGGGGACAAAT
*
845986 GCACCATTAAGTTATCATATATTTTAGGATAAACTATACCATTGACCATCCAACTATTTAGCCAT
261 GCACCATTAAGTTATCATATATTATAGGATAAACTATACCATTGACCATCCAACTATTTAGCCAT
* * * *
846051 TTTATTATTATCACTGATCATTCAATTTTGTCAATCAAACCATATAACTATTTAATTGTATTCAA
326 TTTATTATTATCACCGATCATTCAATTTTGTCAAACAAACCACATAACTATTTAATTGTATCCAA
** * * * * *
846116 TCAAACCACTAGTCGTTAACATTTATCAGAAATGGTGACATGGTAGTTATAGATTTTGGTATAAT
391 TCAAACCACTAGTCGAAAACAGTTAACAGAAATGGTGACATGGCAGTTAAAAATTTTGGTATAAT
846181 TACACGTCCGGTCACTCTTACTTGCATATTATATTAATTTGGTCCTTATTTTAATAAATG
456 TACACGTCCGGTCACTCTTACTTGCATATTATATTAATTTGGTCCTTATTTTAATAAATG
* *
846241 AAAATAAATTAGATTGAATTTAGTGATCAAAACGAAACAAAAACTTAAGTTTAATGATGATTTTG
1 AAAATAAATCAGATTGAATTGAGTGATCAAAACGAAACAAAAACTTAAGTTTAATGATGATTTTG
* * *
846306 CAAAGAAAAA-AGTTTGAAGACCAAAATAGAATCGTATGAATAGTTGAGTGACTAAATATGTAAT
66 AAAAGAAAAATAGTTTGAAGACCAAAATAGAATCGCATGAAAAGTTGAGTGACTAAATATGTAAT
* * * ** *
846370 TTACCCACGT-GTTTTTGATGGAGTTTATTGTTTGGGCAAATGAGGAAATTATTTAAACTTTAGG
131 TTACCCACGTGGGTTTT-A--GAGTTAATTATTTGGGCAAATGAGGAAACAAATTAAACTTTA-G
** * * * ***
846434 AGGCAAA-CGTC-CCGAAGAATACT-TTAG-GGGCATCTTGGTACAAATGGTATAGTTTAGGGGA
192 -GGCAAATCGTCTCAAAAAAATACTCTTAGAGGACAACTCAATACAAATGGTATAGTTTAGGGGA
* * * * *
846495 CAATGGTGCATTTAAGCCTTTAAGTTGTCATATATTATAGGGTAAACTATACTATTGACCA-CTC
256 CAA--ATGC-----A-CCATTAAGTTATCATATATTATAGGATAAACTATACCATTGACCATC-C
* * * ***
846559 AACTATTTAGTCGTTTTATT-TTATCACCGATCTTTCAATTTTGTCAAACAGGGCACATAACTAT
312 AACTATTTAGCCATTTTATTATTATCACCGATCATTCAATTTTGTCAAACAAACCACATAACTAT
846623 TTAATTGTATCCAATCAAACCACTAGTCGAAAACAGTTAACAGAAATGGTGACATGGCAGTTAAA
377 TTAATTGTATCCAATCAAACCACTAGTCGAAAACAGTTAACAGAAATGGTGACATGGCAGTTAAA
846688 AATTTTGGTATAAT
442 AATTTTGGTATAAT
846702 CACAAATTTG
Statistics
Matches: 396, Mismatches: 51, Indels: 22
0.84 0.11 0.05
Matches are distributed among these distances:
513 5 0.01
514 94 0.24
515 71 0.18
516 47 0.12
517 4 0.01
518 6 0.02
521 110 0.28
522 59 0.15
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (515 bp):
AAAATAAATCAGATTGAATTGAGTGATCAAAACGAAACAAAAACTTAAGTTTAATGATGATTTTG
AAAAGAAAAATAGTTTGAAGACCAAAATAGAATCGCATGAAAAGTTGAGTGACTAAATATGTAAT
TTACCCACGTGGGTTTTAGAGTTAATTATTTGGGCAAATGAGGAAACAAATTAAACTTTAGGGCA
AATCGTCTCAAAAAAATACTCTTAGAGGACAACTCAATACAAATGGTATAGTTTAGGGGACAAAT
GCACCATTAAGTTATCATATATTATAGGATAAACTATACCATTGACCATCCAACTATTTAGCCAT
TTTATTATTATCACCGATCATTCAATTTTGTCAAACAAACCACATAACTATTTAATTGTATCCAA
TCAAACCACTAGTCGAAAACAGTTAACAGAAATGGTGACATGGCAGTTAAAAATTTTGGTATAAT
TACACGTCCGGTCACTCTTACTTGCATATTATATTAATTTGGTCCTTATTTTAATAAATG
Found at i:846761 original size:73 final size:73
Alignment explanation
Indices: 846642--846787 Score: 283
Period size: 73 Copynumber: 2.0 Consensus size: 73
846632 TCCAATCAAA
846642 CCACTAGTCGAAAACAGTTAACAGAAATGGTGACATGGCAGTTAAAAATTTTGGTATAATCACAA
1 CCACTAGTCGAAAACAGTTAACAGAAATGGTGACATGGCAGTTAAAAATTTTGGTATAATCACAA
846707 ATTTGGTC
66 ATTTGGTC
846715 CCACTAGTCGAAAACAGTTAACAGAAATGGTGACATGGCAGTTAAAAATTTTGGTATAATCACAA
1 CCACTAGTCGAAAACAGTTAACAGAAATGGTGACATGGCAGTTAAAAATTTTGGTATAATCACAA
*
846780 GTTTGGTC
66 ATTTGGTC
846788 ACTCTTACTT
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 72 1.00
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (73 bp):
CCACTAGTCGAAAACAGTTAACAGAAATGGTGACATGGCAGTTAAAAATTTTGGTATAATCACAA
ATTTGGTC
Found at i:847071 original size:18 final size:18
Alignment explanation
Indices: 847043--847089 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
847033 TTTATATATT
847043 TAAATTTAAATTCACATAC
1 TAAA-TTAAATTCACATAC
* *
847062 TAAATTAAATTTACATTC
1 TAAATTAAATTCACATAC
847080 TAATATTAAA
1 TAA-ATTAAA
847090 AATTCTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 15 0.60
19 10 0.40
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (18 bp):
TAAATTAAATTCACATAC
Found at i:847139 original size:31 final size:30
Alignment explanation
Indices: 847104--847220 Score: 112
Period size: 29 Copynumber: 3.9 Consensus size: 30
847094 CTATTACATT
* *
847104 TTATTGTTAACTTATTAAATATATATTATTT
1 TTATT-TTAACTTATAAAATATATATTATTC
* * * *
847135 TTATTTCAACTTAAGAAAATATATTTTAATC
1 TTATTTTAACTT-ATAAAATATATATTATTC
*
847166 TTATTTTAACTTA-AAAATATATTTTATTC
1 TTATTTTAACTTATAAAATATATATTATTC
* * *
847195 TTATCTTAATTTTTAAAA-ATATATTA
1 TTATTTTAACTTATAAAATATATATTA
847221 AATTTAAAAA
Statistics
Matches: 72, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
29 32 0.44
30 11 0.15
31 29 0.40
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.53
Consensus pattern (30 bp):
TTATTTTAACTTATAAAATATATATTATTC
Found at i:847182 original size:29 final size:30
Alignment explanation
Indices: 847104--847203 Score: 112
Period size: 31 Copynumber: 3.3 Consensus size: 30
847094 CTATTACATT
** * *
847104 TTATTGTTAACTTATTAAATATATATTATTT
1 TTATT-TTAACTTAGAAAATATATTTTATTC
* *
847135 TTATTTCAACTTAAGAAAATATATTTTAATC
1 TTATTTTAACTT-AGAAAATATATTTTATTC
847166 TTATTTTAACTTA-AAAATATATTTTATTC
1 TTATTTTAACTTAGAAAATATATTTTATTC
*
847195 TTATCTTAA
1 TTATTTTAA
847204 TTTTTAAAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
29 23 0.39
30 7 0.12
31 29 0.49
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.53
Consensus pattern (30 bp):
TTATTTTAACTTAGAAAATATATTTTATTC
Found at i:847216 original size:29 final size:29
Alignment explanation
Indices: 847110--847219 Score: 96
Period size: 31 Copynumber: 3.6 Consensus size: 29
847100 CATTTTATTG
* * * *
847110 TTAACTTATTAAATATATATTATTTTTAT-
1 TTAACTTA-AAAATATATTTTAATCTTATC
*
847139 TTCAACTTAAGAAAATATATTTTAATCTTATT
1 TT-AACTT-A-AAAATATATTTTAATCTTATC
*
847171 TTAACTTAAAAATATATTTTATTCTTATC
1 TTAACTTAAAAATATATTTTAATCTTATC
*
847200 TTAATTTTTAAAAATATATT
1 TTAA--CTTAAAAATATATT
847220 AAATTTAAAA
Statistics
Matches: 68, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
29 25 0.37
30 6 0.09
31 35 0.51
32 2 0.03
ACGTcount: A:0.40, C:0.06, G:0.01, T:0.53
Consensus pattern (29 bp):
TTAACTTAAAAATATATTTTAATCTTATC
Found at i:847268 original size:30 final size:30
Alignment explanation
Indices: 847227--847510 Score: 156
Period size: 30 Copynumber: 9.6 Consensus size: 30
847217 ATTAAATTTA
*
847227 AAAAAGTAAAATATATTTCATAAGTTAAGAT
1 AAAAA-TAAAATATATTTAATAAGTTAAGAT
* *
847258 AAAAATAAAATAT-TTTTA-AAGTTAAAAT
1 AAAAATAAAATATATTTAATAAGTTAAGAT
** * * * *
847286 ATGACTAAATATATATTT--TAAATAAAAAT
1 AAAAATAAA-ATATATTTAATAAGTTAAGAT
* *
847315 AAAAATAATATATATTTAATAATTTAAGAT
1 AAAAATAAAATATATTTAATAAGTTAAGAT
*** *
847345 AAAATATATTTTTAAATTTTAATAAG-TAA-AT
1 AAAA-ATA-AAATATA-TTTAATAAGTTAAGAT
* ** ** * *
847376 TAATTTAAAA-ATATTTTTTAAATAAAGAT
1 AAAAATAAAATATATTTAATAAGTTAAGAT
*
847405 AAGAATAAAATATATTT-ATAAGTTCAA-AT
1 AAAAATAAAATATATTTAATAAGTT-AAGAT
* * ** *
847434 AAGATTAAAATATATTTTTTAAGTTAAAAT
1 AAAAATAAAATATATTTAATAAGTTAAGAT
* *
847464 AAAATTAAAATATATTTAATAAGTTATGA-
1 AAAAATAAAATATATTTAATAAGTTAAGAT
*
847493 AAACAATAAATTATATTT
1 AAA-AATAAAATATATTT
847511 TTTTAATAAT
Statistics
Matches: 193, Mismatches: 45, Indels: 31
0.72 0.17 0.12
Matches are distributed among these distances:
27 6 0.03
28 27 0.14
29 56 0.29
30 77 0.40
31 12 0.06
32 7 0.04
33 8 0.04
ACGTcount: A:0.55, C:0.01, G:0.05, T:0.39
Consensus pattern (30 bp):
AAAAATAAAATATATTTAATAAGTTAAGAT
Found at i:847510 original size:60 final size:59
Alignment explanation
Indices: 847381--847519 Score: 153
Period size: 59 Copynumber: 2.4 Consensus size: 59
847371 TAAATTAATT
* *
847381 TAAAA-ATATTTTTTAAATAAAGATAAGAATAAAATATATTTATAAGTTCAAATAAGAT
1 TAAAATATATTTTTTAAATAAAGATAAGAATAAAATATATTTATAAGTTCAAATAACAA
*
847439 TAAAATATATTTTTTAAGTTAAA-ATAA-AATTAAAATATATTTAATAAGTT-ATGAA-AACAA
1 TAAAATATATTTTTTAA-ATAAAGATAAGAA-TAAAATATATTT-ATAAGTTCA--AATAACAA
* *
847499 TAAATTATATTTTTTTAATAA
1 TAAAATATATTTTTTAAATAA
847520 TTTTAATACG
Statistics
Matches: 69, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
58 7 0.10
59 31 0.45
60 29 0.42
61 2 0.03
ACGTcount: A:0.53, C:0.01, G:0.05, T:0.40
Consensus pattern (59 bp):
TAAAATATATTTTTTAAATAAAGATAAGAATAAAATATATTTATAAGTTCAAATAACAA
Found at i:847584 original size:31 final size:31
Alignment explanation
Indices: 847543--847616 Score: 107
Period size: 29 Copynumber: 2.5 Consensus size: 31
847533 ATTTAAATTT
* *
847543 AAATTTATTTTTTAAAATTAAGATAAGATTA
1 AAATATATTTTTTAAAATTAAAATAAGATTA
*
847574 AAATATA--TTTTAAAGTTAAAATAAGATTA
1 AAATATATTTTTTAAAATTAAAATAAGATTA
847603 AAATATATTTTTTA
1 AAATATATTTTTTA
847617 TATTAGAACA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 27 0.71
31 11 0.29
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (31 bp):
AAATATATTTTTTAAAATTAAAATAAGATTA
Found at i:847605 original size:162 final size:156
Alignment explanation
Indices: 847233--847678 Score: 491
Period size: 162 Copynumber: 2.9 Consensus size: 156
847223 TTTAAAAAAG
** * * * *
847233 TAAAATATATTTCATAAGTTAAGATAAAAATAAAATAT-TTTTAAAGTTAAAATATGACT-AAAT
1 TAAAA-ATATTTTTTAAATTAAGATAAGAATAAAATATATTTTAAAGTTAAAATAAGATTAAAAT
* * * * *
847296 ATATATTTTAAATAAAAATAAAAATAATATATATTTAATAA-TT-T---AAGATAAA-ATATATT
65 ATAT-TTTTTAATTAAAATAAAAATAAAATATATTTAATAAGTTATGAAAAAATAAATATATTTT
847355 TTT-A-AATTTTAATAAGTAAATTAATT
129 TTTAATAATTTTAATAAGTAAATTAATT
* *
847381 TAAAAATATTTTTTAAATAAAGATAAGAATAAAATATA-TTTATAAGTTCAAATAAGATTAAAAT
1 TAAAAATATTTTTTAAATTAAGATAAGAATAAAATATATTTTA-AAGTTAAAATAAGATTAAAAT
*
847445 ATATTTTTTAAGTTAAAATAAAATTAAAATATATTTAATAAGTTATGAAAACAATAAATTATATT
65 ATATTTTTTAA-TTAAAATAAAAATAAAATATATTTAATAAGTTATGAAAA-AATAAA-TATATT
* *
847510 TTTTTAATAATTTTAATACGTGAATTTAAATT
127 TTTTTAATAATTTTAATAAGT-AAATT-AATT
** *
847542 TAAATTTATTTTTTAAAATTAAGATAAGATTAAAATATATTTTAAAGTTAAAATAAGATTAAAAT
1 TAAAAATATTTTTT-AAATTAAGATAAGAATAAAATATATTTTAAAGTTAAAATAAGATTAAAAT
* * * * * * *
847607 ATATTTTTTATATTAGAACAAAAATAAAATATATCTAATAAGTTAAGAAAAATTAAATACATTTC
65 ATATTTTTTA-ATTAAAATAAAAATAAAATATATTTAATAAGTTATGAAAAAATAAATATATTTT
847672 TTTAATA
129 TTTAATA
847679 TTAAGATGTG
Statistics
Matches: 250, Mismatches: 29, Indels: 26
0.82 0.10 0.09
Matches are distributed among these distances:
147 31 0.12
148 24 0.10
149 34 0.14
150 2 0.01
151 1 0.00
154 2 0.01
155 5 0.02
157 9 0.04
158 1 0.00
159 12 0.05
160 17 0.07
161 21 0.08
162 86 0.34
163 5 0.02
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.41
Consensus pattern (156 bp):
TAAAAATATTTTTTAAATTAAGATAAGAATAAAATATATTTTAAAGTTAAAATAAGATTAAAATA
TATTTTTTAATTAAAATAAAAATAAAATATATTTAATAAGTTATGAAAAAATAAATATATTTTTT
TAATAATTTTAATAAGTAAATTAATT
Found at i:848976 original size:2 final size:2
Alignment explanation
Indices: 848969--849026 Score: 95
Period size: 2 Copynumber: 30.5 Consensus size: 2
848959 GTTACGTAGC
848969 AT AT AT AT AT AT AT AT AT AT -T 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
849010 AT AT A- AT AT -T AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
849027 CACATTACAT
Statistics
Matches: 53, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
1 3 0.06
2 50 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:851589 original size:16 final size:14
Alignment explanation
Indices: 851533--851581 Score: 55
Period size: 13 Copynumber: 3.4 Consensus size: 14
851523 ATACATACTC
851533 TTTATTTATTTA-T
1 TTTATTTATTTATT
*
851546 TTTATTTAATTATT
1 TTTATTTATTTATT
*
851560 TCTATTTTTATTTATT
1 T-T-TATTTATTTATT
851576 TTTATT
1 TTTATT
851582 AATATTTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
13 11 0.38
14 5 0.17
15 2 0.07
16 11 0.38
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTATTTATTTATT
Found at i:851875 original size:6 final size:6
Alignment explanation
Indices: 851851--851907 Score: 52
Period size: 6 Copynumber: 10.2 Consensus size: 6
851841 TATATTCGTC
* *
851851 TATATT TAT-TAT T-TATT TATATT TATA-T TAT-TT TTTATT TCT-TT
1 TATATT TATAT-T TATATT TATATT TATATT TATATT TATATT TATATT
851895 TATATT TATATT T
1 TATATT TATATT T
851908 TTTATTTACT
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
5 15 0.36
6 27 0.64
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (6 bp):
TATATT
Found at i:851890 original size:33 final size:31
Alignment explanation
Indices: 851853--851914 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 31
851843 TATTCGTCTA
851853 TATTTATTATT-TATTTATATTTATATTATTTTT
1 TATTTATT-TTATATTTATATTT-T-TTATTTTT
*
851886 TATTTCTTTTATATTTATATTTTTTATTT
1 TATTTATTTTATATTTATATTTTTTATTT
851915 ACTTTTTATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 6 0.22
32 3 0.11
33 18 0.67
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (31 bp):
TATTTATTTTATATTTATATTTTTTATTTTT
Found at i:851896 original size:27 final size:26
Alignment explanation
Indices: 851827--851921 Score: 93
Period size: 27 Copynumber: 3.5 Consensus size: 26
851817 ATGTATTTAT
*
851827 TTTTTTATTTTTTCTATATTCGTCTA-TA
1 TTTTTTATTTTTT-TATATT--TATATTA
* *
851855 TTTATTATTTATTTATATTTATATTA
1 TTTTTTATTTTTTTATATTTATATTA
*
851881 TTTTTTATTTCTTTTATATTTATATTT
1 TTTTTTATTT-TTTTATATTTATATTA
*
851908 TTTATTTACTTTTT
1 TTT-TTTATTTTTT
851922 ATCTTCACTC
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
25 3 0.05
26 11 0.19
27 26 0.46
28 17 0.30
ACGTcount: A:0.21, C:0.05, G:0.01, T:0.73
Consensus pattern (26 bp):
TTTTTTATTTTTTTATATTTATATTA
Found at i:851899 original size:44 final size:44
Alignment explanation
Indices: 851815--851912 Score: 112
Period size: 44 Copynumber: 2.3 Consensus size: 44
851805 TATCTACATC
* * *
851815 TTATGTATTTATTTTTTTATTTTTTCTATATTCGTCTATATTTA
1 TTATTTATTTATATTTATATTTTTTCTATATTCGTCTATATTTA
* * *
851859 TTATTTATTTATATTTATATTATTTTTTAT-TTCTTTTATATTTA
1 TTATTTATTTATATTTATATT-TTTTCTATATTCGTCTATATTTA
851903 -TATTT-TTTAT
1 TTATTTATTTAT
851913 TTACTTTTTA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
42 5 0.11
43 5 0.11
44 30 0.64
45 7 0.15
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.71
Consensus pattern (44 bp):
TTATTTATTTATATTTATATTTTTTCTATATTCGTCTATATTTA
Found at i:856072 original size:99 final size:99
Alignment explanation
Indices: 855892--856084 Score: 289
Period size: 99 Copynumber: 1.9 Consensus size: 99
855882 GATTATTATA
*
855892 TATACAATAAAGCTTGAACTATCCCTCTAGAGCAATTGGTTAAACGGCTCGGCTTTATGGATAAG
1 TATACAATAAAGCTTGAACTATCCCTCTAGAGCAATTGGTTAAACGCCTCGGCTTTATGGATAAG
* * *
855957 ATTCAGCTAGCATGATAAAGGTGATTATAATATC
66 ATTCAACCAACATGATAAAGGTGATTATAATATC
* * *
855991 TATACAATAAAGCTTGAGCTGTCCCTCTA-AGGTAATTGGTTAAACGCCTCGGCTTTATGGATAA
1 TATACAATAAAGCTTGAACTATCCCTCTAGA-GCAATTGGTTAAACGCCTCGGCTTTATGGATAA
* *
856055 GATTCAACCAACCTGATAAAGGTGTTTATA
65 GATTCAACCAACATGATAAAGGTGATTATA
856085 TATTGAGTTG
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
98 1 0.01
99 83 0.99
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (99 bp):
TATACAATAAAGCTTGAACTATCCCTCTAGAGCAATTGGTTAAACGCCTCGGCTTTATGGATAAG
ATTCAACCAACATGATAAAGGTGATTATAATATC
Found at i:856199 original size:69 final size:69
Alignment explanation
Indices: 856088--856222 Score: 270
Period size: 69 Copynumber: 2.0 Consensus size: 69
856078 GTTTATATAT
856088 TGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCTGGCTTTATGGATTTAGCAAGCCAGAGAAT
1 TGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCTGGCTTTATGGATTTAGCAAGCCAGAGAAT
856153 GATA
66 GATA
856157 TGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCTGGCTTTATGGATTTAGCAAGCCAGAGAAT
1 TGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCTGGCTTTATGGATTTAGCAAGCCAGAGAAT
856222 G
66 G
856223 GAGAATTAAA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (69 bp):
TGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCTGGCTTTATGGATTTAGCAAGCCAGAGAAT
GATA
Found at i:857160 original size:83 final size:83
Alignment explanation
Indices: 856942--858203 Score: 1429
Period size: 83 Copynumber: 15.1 Consensus size: 83
856932 AAAGCACCTT
* * * * * * *
856942 CAACAAAAGTCCTTTGAGTTCGATTACACTCAGCTCAAAGACGCATCATTTGCAGCACAGCTCAA
1 CAAC-AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAA
*
857007 GG-TGAGAAGGGATATCTGC
65 GGCT-AGAAGGGTTATCTGC
* * * *
857026 CAACAAAATACCTTCGAGTTCAATTACACTCAGCTCAAAAGTACATCATTTACAGCATAACTCAA
1 CAAC-AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAA
* *
857091 GGCTAGAAGGGTTATATGT
65 GGCTAGAAGGGTTATCTGC
* * *
857110 CAACAAAGACCTTCGATTTCGATTACACTCAGCACAAAGGCACATCATTTACAGTATAACTCAAG
1 CAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAAG
**
857175 GCTAGAAGGGTTATCTAT
66 GCTAGAAGGGTTATCTGC
* * * *
857193 CAACAAAGAACTTCGAGTTTGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAG
1 CAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAAG
* *
857258 GCAAGAAGGGCTATCTGC
66 GCTAGAAGGGTTATCTGC
* * * *
857276 CAACAAAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGACACATCATTTGCAGCATAGCTCAA
1 CAAC-AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAA
**
857341 GGAAAGAAGGGTTATCTGC
65 GGCTAGAAGGGTTATCTGC
* * * *
857360 CAACAAAGACCATCAAGTTCGATTACACTTAGCTCAAAGGCACATCATTTACAGCATGACTCAAG
1 CAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAAG
*
857425 GCTAGAAGGGTTATCTGT
66 GCTAGAAGGGTTATCTGC
* * *
857443 CAACAAAGACCTTCGAGTTCGATTATACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAG
1 CAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAAG
* *
857508 GCAAGAAGGGCTATCTGC
66 GCTAGAAGGGTTATCTGC
* * ** * * *
857526 CAACAAAAGACCTTCGGGTTTGATTACACTCAGCTCCGAGACACATCATTTGA-AGAATAGCTCA
1 CAAC-AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTT-ACAGCATAACTCA
* *
857590 AGGCGAGAAGGGCTATCTGC
64 AGGCTAGAAGGGTTATCTGC
* * * * *
857610 CAACAAAATACCTTCGAGTTTGATTACACTTAGCTCAACGGCACTTCATTTACAGCATAACTCAA
1 CAAC-AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAA
* * *
857675 GG-TAAGAAGGGCTATATAC
65 GGCT-AGAAGGGTTATCTGC
* * * ** *
857694 CAATAAAGACTTTCTG-GTTCGATTACACTCAACTCAAATGG-ACATCATTTGTAGTATAACTCA
1 CAACAAAGACCTTC-GAGTTCGATTACACTCAGCTCAAA-GGCACATCATTTACAGCATAACTCA
**
857757 AGGCTAGAAGGGTTATCTAT
64 AGGCTAGAAGGGTTATCTGC
* ** *
857777 CAACAAAGACCTTCGAGTTCGATTACACTCTGCTCAAAGGCACATCATTTGTAGCATAGCTCAAG
1 CAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAAG
* *
857842 GCAAGAAGGGTTATCTAC
66 GCTAGAAGGGTTATCTGC
* * * *
857860 CAATAAAGAGCATCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAACATAACTCAAG
1 CAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAAG
**
857925 GCTAGAAGGGTTATCTAT
66 GCTAGAAGGGTTATCTGC
* * * *
857943 CAACAAAGACTTTCGAGTTTGATTACACTCAGCTCAAAAGCACATCATTTGCAGCATAACTCAAG
1 CAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAAG
* *
858008 GCGAGAAGGGCTATCTGC
66 GCTAGAAGGGTTATCTGC
* * * *
858026 CAACAAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATATCAAATTTATAGAATAACTC
1 CAAC-AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATC--ATTTACAGCATAACTC
** *
858091 AAGGAAAGAAGGGTTATCTGT
63 AAGGCTAGAAGGGTTATCTGC
* * * * * * *
858112 CATCAAAGACCTTCGAGTTCGGTTACATTCAACTCAGAGGCAAATCAAATTTACAG-AAAAGCTC
1 CAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATC--ATTTACAGCATAA-CTC
* * *
858176 AAGGCAAGAAGGGTTATATGT
63 AAGGCTAGAAGGGTTATCTGC
858197 CAACAAA
1 CAACAAA
858204 ATTATCAAGT
Statistics
Matches: 1016, Mismatches: 147, Indels: 29
0.85 0.12 0.02
Matches are distributed among these distances:
82 3 0.00
83 569 0.56
84 335 0.33
85 76 0.07
86 33 0.03
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.24
Consensus pattern (83 bp):
CAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAAG
GCTAGAAGGGTTATCTGC
Found at i:857404 original size:250 final size:250
Alignment explanation
Indices: 856953--858219 Score: 1593
Period size: 250 Copynumber: 5.1 Consensus size: 250
856943 AACAAAAGTC
* * * **
856953 CTTT-GAGTTCGATTACACTCAGCTCAAAGACGCATCATTTGCAGCACAGCTCAAGGTGAGAAGG
1 CTTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAGG
* * * * *
857017 GATATCTGCCAACAAAATACCTTCGAGTTCAATTACACTCAGCTCAAA-AGTACATCATTTACAG
66 GCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGA-CACATCATTTGCAG
* * * * * * *
857081 CATAACTCAAGGCTAGAAGGGTTATATGTCAACAAAGACCTTCGATTTCGATTACACTCAGCACA
130 CATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGATTACACTTAGCTCA
*
857146 AAGGCACATCATTTACAGTATAACTCAAGGCTAGAAGGGTTATCTATCAACAAAGAA
195 AAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTATCAACAAAG-A
*
857203 C-TTCGAGTTTGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAGG
1 CTTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAGG
*
857267 GCTATCTGCCAACAAAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGACACATCATTTGCAGC
66 GCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGACACATCATTTGCAGC
* * *
857332 ATAGCTCAAGGAAAGAAGGGTTATCTGCCAACAAAGACCATCAAGTTCGATTACACTTAGCTCAA
131 ATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGATTACACTTAGCTCAA
* *
857397 AGGCACATCATTTACAGCATGACTCAAGGCTAGAAGGGTTATCTGTCAACAAAGA
196 AGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTATCAACAAAGA
* *
857452 CCTTCGAGTTCGATTATACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAGG
1 CTTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAGG
* * ** * *
857517 GCTATCTGCCAACAAAAGACCTTCGGGTTTGATTACACTCAGCTCCGAGACACATCATTTGAAGA
66 GCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGACACATCATTTGCAGC
* * * *
857582 ATAGCTCAAGGCGAGAAGGGCTATCTGCCAACAAAATACCTTCGAGTTTGATTACACTTAGCTCA
131 ATAGCTCAAGGCAAGAAGGGTTATCTGCCAAC-AAAGACCTTCGAGTTCGATTACACTTAGCTCA
* * * * * *
857647 ACGGCACTTCATTTACAGCATAACTCAAGG-TAAGAAGGGCTATATACCAATAAAGA
195 AAGGCACATCATTTACAGCATAACTCAAGGCT-AGAAGGGTTATCTATCAACAAAGA
* * * * *
857703 CTTTCTG-GTTCGATTACACTCAACTCAAATGG-ACATCATTTGTAGTATAACTCAAGGCTAGAA
1 CTTTC-GAGTTCGATTACACTCAGCTCAAA-GGCACATCATTTGCAGCATAGCTCAAGGCAAGAA
* ** * * *
857766 GGGTTATCTATCAAC-AAAGACCTTCGAGTTCGATTACACTCTGCTCAAAGGCACATCATTTGTA
64 GGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGACACATCATTTGCA
* * * * *
857830 GCATAGCTCAAGGCAAGAAGGGTTATCTACCAATAAAGAGCATCGAGTTCGATTACACTCAGCTC
129 GCATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGATTACACTTAGCTC
*
857895 AAAGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTATCAACAAAGA
194 AAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTATCAACAAAGA
* * * *
857952 CTTTCGAGTTTGATTACACTCAGCTCAAAAGCACATCATTTGCAGCATAACTCAAGGCGAGAAGG
1 CTTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAGG
* * * **
858017 GCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATATCAAATTTATA
66 GCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGACACATC--ATTTGCA
* * * * * * *
858082 GAATAACTCAAGGAAAGAAGGGTTATCTGTCATCAAAGACCTTCGAGTTCGGTTACA-TTCAACT
129 GCATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGATTACACTT-AGCT
* * * * * *
858146 CAGAGGCAAATCAAATTTACAG-AAAAGCTCAAGGCAAGAAGGGTTATATGTCAACAAA-A
193 CAAAGGCACATC--ATTTACAGCATAA-CTCAAGGCTAGAAGGGTTATCTATCAACAAAGA
*
858205 -TTATCAAGTTCGATT
1 CTT-TCGAGTTCGATT
858220 CTATTCATCT
Statistics
Matches: 884, Mismatches: 115, Indels: 33
0.86 0.11 0.03
Matches are distributed among these distances:
248 2 0.00
249 143 0.16
250 480 0.54
251 139 0.16
252 71 0.08
253 14 0.02
254 35 0.04
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.24
Consensus pattern (250 bp):
CTTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAGG
GCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGACACATCATTTGCAGC
ATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGATTACACTTAGCTCAA
AGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTATCAACAAAGA
Found at i:858787 original size:21 final size:22
Alignment explanation
Indices: 858762--858809 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
858752 TTACGTAGCA
* *
858762 TATATATATATATT-ATATTAT
1 TATATATACACATTAATATTAT
858783 TATATATACACATTACATATTAT
1 TATATATACACATTA-ATATTAT
858806 TATA
1 TATA
858810 CATTAGCATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 12 0.52
23 11 0.48
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (22 bp):
TATATATACACATTAATATTAT
Found at i:858836 original size:36 final size:35
Alignment explanation
Indices: 858792--858863 Score: 81
Period size: 36 Copynumber: 2.0 Consensus size: 35
858782 TTATATATAC
** *
858792 ACATTACATATTATTATACATTAGCATGTTTTATT
1 ACATTACATATTACAATACATTAACATGTTTTATT
* * *
858827 ACATATACATGTTACAATATATTAACTTGTTTTATT
1 ACAT-TACATATTACAATACATTAACATGTTTTATT
858863 A
1 A
858864 TTTGGATACA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
35 4 0.13
36 26 0.87
ACGTcount: A:0.36, C:0.11, G:0.06, T:0.47
Consensus pattern (35 bp):
ACATTACATATTACAATACATTAACATGTTTTATT
Found at i:859900 original size:10 final size:9
Alignment explanation
Indices: 859885--859993 Score: 67
Period size: 10 Copynumber: 11.2 Consensus size: 9
859875 ATCCTCGTAT
859885 TTTTATTTAA
1 TTTTATTT-A
*
859895 TTTTATTTT
1 TTTTATTTA
859904 TCTTTATTTA
1 T-TTTATTTA
*
859914 TTTAATTTA
1 TTTTATTTA
* *
859923 ATTAATTTTA
1 TTTTA-TTTA
859933 TTTTTATTTTTA
1 -TTTTA--TTTA
859945 TTTTTATTTA
1 -TTTTATTTA
*
859955 TTATATATTA
1 TTTTAT-TTA
* *
859965 TATTATTTT
1 TTTTATTTA
859974 TTTTATTT-
1 TTTTATTTA
859982 TTATTATTTA
1 TT-TTATTTA
859992 TT
1 TT
859994 ATTAATGTAT
Statistics
Matches: 81, Mismatches: 11, Indels: 14
0.76 0.10 0.13
Matches are distributed among these distances:
8 2 0.02
9 32 0.40
10 33 0.41
11 3 0.04
12 11 0.14
ACGTcount: A:0.25, C:0.01, G:0.00, T:0.74
Consensus pattern (9 bp):
TTTTATTTA
Found at i:859902 original size:5 final size:5
Alignment explanation
Indices: 859885--859982 Score: 62
Period size: 5 Copynumber: 19.8 Consensus size: 5
859875 ATCCTCGTAT
* * * *
859885 TTTTA TTTAA TTTTA TTTT- TCTTTA -TTTA -TTTA ATTTA ATTAA TTTTA
1 TTTTA TTTTA TTTTA TTTTA T-TTTA TTTTA TTTTA TTTTA TTTTA TTTTA
* * *
859933 TTTTTA TTTTTA TTTT- TATTTA TTATA TATTA TATTA TTTT- TTTTA
1 -TTTTA -TTTTA TTTTA T-TTTA TTTTA TTTTA TTTTA TTTTA TTTTA
859979 TTTT
1 TTTT
859983 TATTATTTAT
Statistics
Matches: 77, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
4 14 0.18
5 51 0.66
6 12 0.16
ACGTcount: A:0.24, C:0.01, G:0.00, T:0.74
Consensus pattern (5 bp):
TTTTA
Found at i:859971 original size:37 final size:34
Alignment explanation
Indices: 859887--860027 Score: 97
Period size: 37 Copynumber: 3.8 Consensus size: 34
859877 CCTCGTATTT
*
859887 TTATTTAATTTTATTTTTCTTTATTTATTTAATT-TAA
1 TTATTTATTTTTA-TTTT-TTT-TTTATTT-ATTATAA
859924 TTAATTTTATTTTTATTTTTATTTTTATTTATTATATA
1 TT-A-TTTATTTTTATTTTT-TTTTTATTTATTATA-A
859962 TTATATTATTTTT-TTTATTTTTATTATTTATTATTAA
1 TTAT-TTATTTTTATTT-TTTTT-TTATTTATTA-TAA
* * *
859999 TGTATATATGTATTCTTTTTGTTTTTATT
1 T-TATTTAT-TTTTATTTTT-TTTTTATT
860028 GTTTTTCTCT
Statistics
Matches: 88, Mismatches: 3, Indels: 25
0.76 0.03 0.22
Matches are distributed among these distances:
36 10 0.11
37 38 0.43
38 25 0.28
39 15 0.17
ACGTcount: A:0.25, C:0.01, G:0.02, T:0.72
Consensus pattern (34 bp):
TTATTTATTTTTATTTTTTTTTTATTTATTATAA
Found at i:859982 original size:34 final size:32
Alignment explanation
Indices: 859886--859986 Score: 100
Period size: 34 Copynumber: 3.1 Consensus size: 32
859876 TCCTCGTATT
* * *
859886 TTTATTTAATTTTATTTTTCTTTATTTA-TTTAA
1 TTTAATTAATTTTATTATT-TTT-TTTATTTTTA
859919 TTTAATTAATTTTATT-TTTATTTTTATTTTTA
1 TTTAATTAATTTTATTATTT-TTTTTATTTTTA
859951 TTT-ATTATATATTATATTATTTTTTTTATTTTTA
1 TTTAATTA-AT-TT-TATTATTTTTTTTATTTTTA
859985 TT
1 TT
859987 ATTTATTATT
Statistics
Matches: 60, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
31 9 0.15
32 13 0.22
33 17 0.28
34 18 0.30
35 3 0.05
ACGTcount: A:0.25, C:0.01, G:0.00, T:0.74
Consensus pattern (32 bp):
TTTAATTAATTTTATTATTTTTTTTATTTTTA
Found at i:859996 original size:40 final size:42
Alignment explanation
Indices: 859895--860136 Score: 131
Period size: 40 Copynumber: 5.9 Consensus size: 42
859885 TTTTATTTAA
* *
859895 TTTTATTTTTCTTTATTTATTTAATT--TA-ATTA-ATT-TTAT
1 TTTTATTTTT-ATTATTTATTT-ATTAGTATATTATATTATTTT
859934 TTTTATTTTTATT-TTTATTTATTA-TATATTATATTATTTT
1 TTTTATTTTTATTATTTATTTATTAGTATATTATATTATTTT
* *
859974 TTTTATTTTTATTATTTA-TTATTAATGTATATATGTATTCTTTTTGT
1 TTTTATTTTTATTATTTATTTATT-A-GTATAT-TATA-T-TATTT-T
* * * *
860021 TTTTATTGTTTTTCTCTTTA-TTATTAGTATCATTATACCTACTCTT
1 TTTTATT-TTTAT-TATTTATTTATTAGTAT-ATTATA-TTA-TTTT
** *
860067 TTTTA----T-TTATTTATTTATTTCTAT-TTAT-TTATTTA
1 TTTTATTTTTATTATTTATTTATTAGTATATTATATTATTTT
* *
860102 TTTTATTTTTATTA-TTATTTAATACTATATTATAT
1 TTTTATTTTTATTATTTATTTATTAGTATATTATAT
860137 ACCTACACAC
Statistics
Matches: 160, Mismatches: 19, Indels: 46
0.71 0.08 0.20
Matches are distributed among these distances:
35 7 0.04
36 5 0.03
37 9 0.06
38 10 0.06
39 31 0.19
40 37 0.23
41 7 0.04
43 5 0.03
44 3 0.02
45 1 0.01
46 11 0.07
47 17 0.11
48 7 0.04
49 10 0.06
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.69
Consensus pattern (42 bp):
TTTTATTTTTATTATTTATTTATTAGTATATTATATTATTTT
Found at i:860077 original size:4 final size:4
Alignment explanation
Indices: 860068--860122 Score: 58
Period size: 4 Copynumber: 13.0 Consensus size: 4
860058 CCTACTCTTT
*
860068 TTTA TTTA TTTA TTTA TTTCTA TTTA TTTA TTTA TTTTA TTTT TATTA
1 TTTA TTTA TTTA TTTA -TT-TA TTTA TTTA TTTA -TTTA TTTA T-TTA
860116 -TTA TTTA
1 TTTA TTTA
860123 ATACTATATT
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
3 3 0.07
4 29 0.66
5 10 0.23
6 2 0.05
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:860093 original size:14 final size:14
Alignment explanation
Indices: 860074--860109 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
860064 CTTTTTTATT
*
860074 TATTTATTTATTTC
1 TATTTATTTATTTA
860088 TATTTATTTATTTA
1 TATTTATTTATTTA
860102 T-TTTATTT
1 TATTTATTT
860110 TTATTATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 7 0.33
14 14 0.67
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (14 bp):
TATTTATTTATTTA
Found at i:860093 original size:22 final size:23
Alignment explanation
Indices: 860068--860122 Score: 80
Period size: 22 Copynumber: 2.5 Consensus size: 23
860058 CCTACTCTTT
860068 TTTATTTATTTA-TTTATTTCTA
1 TTTATTTATTTATTTTATTTCTA
*
860090 TTTATTTATTTATTTTATTTTTA
1 TTTATTTATTTATTTTATTTCTA
860113 -TTA-TTATTTA
1 TTTATTTATTTA
860123 ATACTATATT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
21 7 0.23
22 15 0.48
23 9 0.29
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.75
Consensus pattern (23 bp):
TTTATTTATTTATTTTATTTCTA
Found at i:860117 original size:18 final size:17
Alignment explanation
Indices: 860067--860109 Score: 77
Period size: 18 Copynumber: 2.5 Consensus size: 17
860057 ACCTACTCTT
860067 TTTTATTTATTTATTTA
1 TTTTATTTATTTATTTA
860084 TTTCTATTTATTTATTTA
1 TTT-TATTTATTTATTTA
860102 TTTTATTT
1 TTTTATTT
860110 TTATTATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTATTTATTTATTTA
Found at i:860386 original size:4 final size:4
Alignment explanation
Indices: 860354--860466 Score: 63
Period size: 4 Copynumber: 26.5 Consensus size: 4
860344 TTCTTTACTA
* *
860354 TTAT TT-T TTCT TTAT CTTAC TTAT CTTAT TTAT TTAT TT-T TCT-T CTT-T
1 TTAT TTAT TTAT TTAT -TTAT TTAT -TTAT TTAT TTAT TTAT T-TAT -TTAT
* *
860402 TTAT TTAT TTATT TTATT TTCT TTAT CTTCGT TCTAT TTAT TCATAT TTAT
1 TTAT TTAT TTA-T TTA-T TTAT TTAT -TT-AT T-TAT TTAT T--TAT TTAT
860453 TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TT
860467 TTGTCTTTAT
Statistics
Matches: 90, Mismatches: 7, Indels: 24
0.74 0.06 0.20
Matches are distributed among these distances:
3 7 0.08
4 56 0.62
5 21 0.23
6 6 0.07
ACGTcount: A:0.18, C:0.10, G:0.01, T:0.72
Consensus pattern (4 bp):
TTAT
Found at i:860397 original size:32 final size:29
Alignment explanation
Indices: 860352--860431 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 29
860342 ATTTCTTTAC
860352 TATTATTTTTTCTTTATCTTACTTATCTTATT
1 TATT-TTTTTTCTTTATCTT-CTTAT-TTATT
*
860384 TATTTATTTTTC--T-TCTTTTTATTTATT
1 TATTT-TTTTTCTTTATCTTCTTATTTATT
860411 TATTTTATTTTCTTTATCTTC
1 TATTTT-TTTTCTTTATCTTC
860432 GTTCTATTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
26 1 0.02
27 15 0.37
28 4 0.10
29 5 0.12
30 5 0.12
31 1 0.02
32 10 0.24
ACGTcount: A:0.16, C:0.11, G:0.00, T:0.72
Consensus pattern (29 bp):
TATTTTTTTTCTTTATCTTCTTATTTATT
Found at i:860407 original size:23 final size:24
Alignment explanation
Indices: 860364--860425 Score: 81
Period size: 23 Copynumber: 2.5 Consensus size: 24
860354 TTATTTTTTC
860364 TTTATCTTACTTATCTTATTTATTTAT
1 TTTATCTT-CTT-T-TTATTTATTTAT
860391 TTT-TCTTCTTTTTATTTATTTAT
1 TTTATCTTCTTTTTATTTATTTAT
*
860414 TTTATTTTCTTT
1 TTTATCTTCTTT
860426 ATCTTCGTTC
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
23 15 0.45
24 8 0.24
25 3 0.09
26 4 0.12
27 3 0.09
ACGTcount: A:0.16, C:0.10, G:0.00, T:0.74
Consensus pattern (24 bp):
TTTATCTTCTTTTTATTTATTTAT
Found at i:860421 original size:19 final size:19
Alignment explanation
Indices: 860382--860421 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
860372 ACTTATCTTA
*
860382 TTTATTTATTTTTCTTCTT
1 TTTATTTATTTTTCTTATT
860401 TTTATTTATTTATT-TTATT
1 TTTATTTATTT-TTCTTATT
860420 TT
1 TT
860422 CTTTATCTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 17 0.89
20 2 0.11
ACGTcount: A:0.15, C:0.05, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTATTTATTTTTCTTATT
Found at i:860460 original size:33 final size:33
Alignment explanation
Indices: 860380--860460 Score: 101
Period size: 33 Copynumber: 2.5 Consensus size: 33
860370 TTACTTATCT
* * * *
860380 TATTTATTTATTTTTCTTCTTTTTATTTATTTA
1 TATTTATTTATTTATCTTCGTTCTATTTATTCA
*
860413 T-TTTATTTTCTTTATCTTCGTTCTATTTATTCA
1 TATTTA-TTTATTTATCTTCGTTCTATTTATTCA
860446 TATTTATTTATTTAT
1 TATTTATTTATTTAT
860461 TTATTTTTGT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
32 4 0.10
33 32 0.80
34 4 0.10
ACGTcount: A:0.19, C:0.09, G:0.01, T:0.72
Consensus pattern (33 bp):
TATTTATTTATTTATCTTCGTTCTATTTATTCA
Found at i:860516 original size:28 final size:26
Alignment explanation
Indices: 860472--860549 Score: 79
Period size: 26 Copynumber: 2.9 Consensus size: 26
860462 TATTTTTGTC
860472 TTTATCTATATTTTTACTTTCTTTATAT
1 TTTATCT-T-TTTTTACTTTCTTTATAT
* *
860500 TTATATTTTTTATTTAC-TT-TTTATCT
1 TT-TATCTTTT-TTTACTTTCTTTATAT
*
860526 TTTATCTTTTTTTATTTTCTTTAT
1 TTTATCTTTTTTTACTTTCTTTAT
860550 CTCGTTTTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
24 4 0.10
25 9 0.21
26 13 0.31
27 4 0.10
28 8 0.19
29 4 0.10
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.73
Consensus pattern (26 bp):
TTTATCTTTTTTTACTTTCTTTATAT
Found at i:860545 original size:52 final size:51
Alignment explanation
Indices: 860401--860549 Score: 148
Period size: 52 Copynumber: 3.0 Consensus size: 51
860391 TTTTCTTCTT
* ** * * *
860401 TTTATTTATTTATTT-TATTT-TCTTTATCT-TCGTTCTA-TTTATTCATA
1 TTTATTTATTTATTTATTTTTATCTTTATCTATATTTTTACTTTCTTTATA
*
860448 TTTATTTATTTATTTATTTTTGTCTTTATCTATATTTTTACTTTCTTTATA
1 TTTATTTATTTATTTATTTTTATCTTTATCTATATTTTTACTTTCTTTATA
* *
860499 TTTATATTTTTTATTTACTTTTTATCTTTTATCT-T-TTTTTATTTTCTTTAT
1 TTTAT-TTATTTATTTA-TTTTTATC-TTTATCTATATTTTTACTTTCTTTAT
860550 CTCGTTTTAT
Statistics
Matches: 86, Mismatches: 9, Indels: 9
0.83 0.09 0.09
Matches are distributed among these distances:
47 15 0.17
48 4 0.05
49 9 0.10
50 5 0.06
51 13 0.15
52 25 0.29
53 8 0.09
54 7 0.08
ACGTcount: A:0.18, C:0.09, G:0.01, T:0.72
Consensus pattern (51 bp):
TTTATTTATTTATTTATTTTTATCTTTATCTATATTTTTACTTTCTTTATA
Found at i:860557 original size:29 final size:28
Alignment explanation
Indices: 860505--860559 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
860495 TATATTTATA
*
860505 TTTTTTATTTACTTTTTATCTTTTATCT
1 TTTTTTATTTACTTTATATCTTTTATCT
* *
860533 TTTTTTATTTTCTTTATCTCGTTTTAT
1 TTTTTTATTTACTTTATATC-TTTTAT
860560 TTACATCATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 17 0.74
29 6 0.26
ACGTcount: A:0.13, C:0.11, G:0.02, T:0.75
Consensus pattern (28 bp):
TTTTTTATTTACTTTATATCTTTTATCT
Found at i:862248 original size:46 final size:46
Alignment explanation
Indices: 862161--862255 Score: 122
Period size: 46 Copynumber: 2.1 Consensus size: 46
862151 ACTAGAATAG
* *
862161 TTTGTTCCTAAACTACTTTGAATTTATAAGAAGGGTAAATTAGTAT
1 TTTGTTCCTAAACTACTTTGAATTTATAAGAAAGCTAAATTAGTAT
* *
862207 TTTGTTCCTAAACTACCTTT-AATTTATAA-AAATCTCTAATTAGTAT
1 TTTGTTCCTAAACTA-CTTTGAATTTATAAGAAAGCT-AAATTAGTAT
862253 TTT
1 TTT
862256 ATCTAAATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
45 3 0.07
46 36 0.84
47 4 0.09
ACGTcount: A:0.34, C:0.12, G:0.09, T:0.45
Consensus pattern (46 bp):
TTTGTTCCTAAACTACTTTGAATTTATAAGAAAGCTAAATTAGTAT
Found at i:873819 original size:2 final size:2
Alignment explanation
Indices: 873812--873836 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
873802 ATGAAATGAA
873812 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
873837 CACGCACATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:875102 original size:29 final size:31
Alignment explanation
Indices: 875070--875133 Score: 96
Period size: 29 Copynumber: 2.1 Consensus size: 31
875060 AAATGGATTT
*
875070 AGTTTAGTGACC-AAATTATAAA-TTTGAAA
1 AGTTTAGTGACCAAAAGTATAAACTTTGAAA
*
875099 AGTTTTGTGACCAAAAGTATAAACTTTGAAA
1 AGTTTAGTGACCAAAAGTATAAACTTTGAAA
875130 AGTT
1 AGTT
875134 CAGGGATCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 11 0.35
30 9 0.29
31 11 0.35
ACGTcount: A:0.42, C:0.08, G:0.16, T:0.34
Consensus pattern (31 bp):
AGTTTAGTGACCAAAAGTATAAACTTTGAAA
Found at i:875145 original size:31 final size:30
Alignment explanation
Indices: 875078--875145 Score: 75
Period size: 31 Copynumber: 2.3 Consensus size: 30
875068 TTAGTTTAGT
* ** *
875078 GACC-AAATTATAAATTTGAAAAGTTTTGT
1 GACCAAAAGTATAAATTTGAAAAGTTCAGG
875107 GACCAAAAGTATAAACTTTGAAAAGTTCAGG
1 GACCAAAAGTATAAA-TTTGAAAAGTTCAGG
*
875138 GATCAAAA
1 GACCAAAA
875146 TGGTAATTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 4 0.12
30 9 0.28
31 19 0.59
ACGTcount: A:0.46, C:0.10, G:0.16, T:0.28
Consensus pattern (30 bp):
GACCAAAAGTATAAATTTGAAAAGTTCAGG
Found at i:876624 original size:24 final size:20
Alignment explanation
Indices: 876561--876626 Score: 114
Period size: 20 Copynumber: 3.3 Consensus size: 20
876551 TATAAAATTA
876561 TGATTTGTACAGATCGTGAT
1 TGATTTGTACAGATCGTGAT
876581 TGATTTGTACAGATCGTGAT
1 TGATTTGTACAGATCGTGAT
* *
876601 TGATTTGTACATATCGTGGT
1 TGATTTGTACAGATCGTGAT
876621 TGATTT
1 TGATTT
876627 ATGACTAAGA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.23, C:0.09, G:0.24, T:0.44
Consensus pattern (20 bp):
TGATTTGTACAGATCGTGAT
Found at i:877356 original size:33 final size:33
Alignment explanation
Indices: 877314--877378 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
877304 TATGAAAAGG
877314 GATCTATGAGACCATACAAGAATGTTACACAAT
1 GATCTATGAGACCATACAAGAATGTTACACAAT
** *
877347 GATCTATGAGGTCATACAAGAATGTTATACAA
1 GATCTATGAGACCATACAAGAATGTTACACAA
877379 GTTAGATGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.26
Consensus pattern (33 bp):
GATCTATGAGACCATACAAGAATGTTACACAAT
Found at i:877562 original size:21 final size:20
Alignment explanation
Indices: 877538--877606 Score: 54
Period size: 21 Copynumber: 3.5 Consensus size: 20
877528 ATATGATAGG
877538 TCCTTCGGGACACATATGACA
1 TCCTTCGGGACACATATG-CA
* ** *
877559 TCCTTCAGGA-TGATA-G-G
1 TCCTTCGGGACACATATGCA
*
877576 TCATTCGGGACACATATGGCA
1 TCCTTCGGGACACATAT-GCA
877597 TCCTTCGGGA
1 TCCTTCGGGA
877607 TGATAGGTCC
Statistics
Matches: 34, Mismatches: 10, Indels: 8
0.65 0.19 0.15
Matches are distributed among these distances:
17 8 0.24
18 3 0.09
19 1 0.03
20 4 0.12
21 18 0.53
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.26
Consensus pattern (20 bp):
TCCTTCGGGACACATATGCA
Found at i:877619 original size:17 final size:17
Alignment explanation
Indices: 877559--877619 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
877549 ACATATGACA
*
877559 TCCTTCAGGATGATAGG
1 TCCTTCGGGATGATAGG
* **
877576 TCATTCGGGACACATATGG
1 TCCTTCGGGA-TGATA-GG
877595 CATCCTTCGGGATGATAGG
1 --TCCTTCGGGATGATAGG
877614 TCCTTC
1 TCCTTC
877620 AAGACACAGA
Statistics
Matches: 33, Mismatches: 7, Indels: 8
0.69 0.15 0.17
Matches are distributed among these distances:
17 14 0.42
18 3 0.09
19 4 0.12
20 3 0.09
21 9 0.27
ACGTcount: A:0.21, C:0.23, G:0.26, T:0.30
Consensus pattern (17 bp):
TCCTTCGGGATGATAGG
Found at i:877627 original size:38 final size:38
Alignment explanation
Indices: 877530--877619 Score: 153
Period size: 38 Copynumber: 2.4 Consensus size: 38
877520 TTCGAGACAT
877530 ATGATAGGTCCTTCGGGACACATATGACATCCTTCAGG
1 ATGATAGGTCCTTCGGGACACATATGACATCCTTCAGG
* * *
877568 ATGATAGGTCATTCGGGACACATATGGCATCCTTCGGG
1 ATGATAGGTCCTTCGGGACACATATGACATCCTTCAGG
877606 ATGATAGGTCCTTC
1 ATGATAGGTCCTTC
877620 AAGACACAGA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 48 1.00
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.28
Consensus pattern (38 bp):
ATGATAGGTCCTTCGGGACACATATGACATCCTTCAGG
Found at i:877766 original size:30 final size:30
Alignment explanation
Indices: 877732--877791 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
877722 AAGTTCTCAG
* * *
877732 TAATGTACATGGGCTTATAAAATATATCAA
1 TAATGTACATGAGCCTATAAAAGATATCAA
*
877762 TAATGTATATGAGCCTATAAAAGATATCAA
1 TAATGTACATGAGCCTATAAAAGATATCAA
877792 AAGTGTTTGC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.32
Consensus pattern (30 bp):
TAATGTACATGAGCCTATAAAAGATATCAA
Found at i:878006 original size:24 final size:24
Alignment explanation
Indices: 877979--878025 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
877969 TGTATTACAT
877979 GATAATGATATTGATGTTGATAAA
1 GATAATGATATTGATGTTGATAAA
*
878003 GATAATGATGTTGATGTTGATAA
1 GATAATGATATTGATGTTGATAA
878026 TTATGGCATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.23, T:0.38
Consensus pattern (24 bp):
GATAATGATATTGATGTTGATAAA
Found at i:878026 original size:18 final size:18
Alignment explanation
Indices: 877978--878017 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
877968 ATGTATTACA
*
877978 TGATAATGATATTGATGT
1 TGATAATGATAATGATGT
*
877996 TGATAAAGATAATGATGT
1 TGATAATGATAATGATGT
878014 TGAT
1 TGAT
878018 GTTGATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.23, T:0.40
Consensus pattern (18 bp):
TGATAATGATAATGATGT
Found at i:880416 original size:21 final size:20
Alignment explanation
Indices: 880390--880449 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 20
880380 ACTAAAAAAC
*
880390 AAAAAAAAATGAAGAAAGAAG
1 AAAAAAAAA-GAAAAAAGAAG
880411 AAAAAAAGAAGAAAAAAGAAG
1 AAAAAAA-AAGAAAAAAGAAG
880432 AAGAAAAAAAAGAAAAAA
1 -A-AAAAAAAAGAAAAAA
880450 TGAGAGATGC
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
21 17 0.49
22 12 0.34
23 6 0.17
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.02
Consensus pattern (20 bp):
AAAAAAAAAGAAAAAAGAAG
Found at i:880427 original size:10 final size:10
Alignment explanation
Indices: 880383--880449 Score: 57
Period size: 10 Copynumber: 6.6 Consensus size: 10
880373 CATAAGAACT
*
880383 AAAAAACAA-
1 AAAAAAGAAG
*
880392 AAAAAA-ATG
1 AAAAAAGAAG
*
880401 AAGAAAGAAG
1 AAAAAAGAAG
880411 AAAAAAAGAAG
1 -AAAAAAGAAG
880422 AAAAAAGAAG
1 AAAAAAGAAG
*
880432 AAGAAAAAAAAG
1 -A-AAAAAGAAG
880444 AAAAAA
1 AAAAAA
880450 TGAGAGATGC
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
8 1 0.02
9 11 0.23
10 17 0.35
11 11 0.23
12 8 0.17
ACGTcount: A:0.82, C:0.01, G:0.15, T:0.01
Consensus pattern (10 bp):
AAAAAAGAAG
Found at i:880432 original size:24 final size:22
Alignment explanation
Indices: 880391--880449 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
880381 CTAAAAAACA
*
880391 AAAAAAAATGAAGAAAGAAGAA-
1 AAAAAAAA-GAAAAAAGAAGAAG
*
880413 AAAAAGAAGAAAAAAGAAGAAG
1 AAAAAAAAGAAAAAAGAAGAAG
880435 AAAAAAAAGAAAAAA
1 AAAAAAAAGAAAAAA
880450 TGAGAGATGC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 12 0.36
22 21 0.64
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (22 bp):
AAAAAAAAGAAAAAAGAAGAAG
Found at i:884238 original size:33 final size:33
Alignment explanation
Indices: 884196--884260 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
884186 TATGAAAAGG
884196 GATCTATGAGATCATACAAGAATGTTACACAAT
1 GATCTATGAGATCATACAAGAATGTTACACAAT
*
884229 GATCTATGAGATCATACAAGAATGTTATACAA
1 GATCTATGAGATCATACAAGAATGTTACACAA
884261 GTTACATGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.28
Consensus pattern (33 bp):
GATCTATGAGATCATACAAGAATGTTACACAAT
Found at i:884441 original size:17 final size:17
Alignment explanation
Indices: 884419--884483 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
884409 ACAGATGACA
884419 TCCTTCGGGATGATAGG
1 TCCTTCGGGATGATAGG
* *
884436 TCCTTCGGGACGCAGATGG
1 TCCTTCGGGATG-ATA-GG
*
884455 CATCCTTTGGGATGATAGG
1 --TCCTTCGGGATGATAGG
*
884474 TCTTTCGGGA
1 TCCTTCGGGA
884484 CAGATTACCT
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
17 19 0.51
18 2 0.05
19 4 0.11
20 2 0.05
21 10 0.27
ACGTcount: A:0.17, C:0.20, G:0.34, T:0.29
Consensus pattern (17 bp):
TCCTTCGGGATGATAGG
Found at i:884452 original size:38 final size:38
Alignment explanation
Indices: 884397--884485 Score: 142
Period size: 38 Copynumber: 2.3 Consensus size: 38
884387 GGTTACATAT
884397 GTCCTTCGGGACACAGATGACATCCTTCGGGATGATAG
1 GTCCTTCGGGACACAGATGACATCCTTCGGGATGATAG
* * *
884435 GTCCTTCGGGACGCAGATGGCATCCTTTGGGATGATAG
1 GTCCTTCGGGACACAGATGACATCCTTCGGGATGATAG
*
884473 GTCTTTCGGGACA
1 GTCCTTCGGGACA
884486 GATTACCTAT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 46 1.00
ACGTcount: A:0.20, C:0.22, G:0.31, T:0.26
Consensus pattern (38 bp):
GTCCTTCGGGACACAGATGACATCCTTCGGGATGATAG
Found at i:884460 original size:21 final size:21
Alignment explanation
Indices: 884398--884466 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 21
884388 GTTACATATG
* *
884398 TCCTTCGGGACACAGATGACA
1 TCCTTCGGGACGCAGATGGCA
* *
884419 TCCTTCGGGATG-ATA-GG--
1 TCCTTCGGGACGCAGATGGCA
884436 TCCTTCGGGACGCAGATGGCA
1 TCCTTCGGGACGCAGATGGCA
*
884457 TCCTTTGGGA
1 TCCTTCGGGA
884467 TGATAGGTCT
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
17 11 0.30
18 2 0.05
19 3 0.08
20 2 0.05
21 19 0.51
ACGTcount: A:0.20, C:0.25, G:0.30, T:0.25
Consensus pattern (21 bp):
TCCTTCGGGACGCAGATGGCA
Found at i:887277 original size:13 final size:13
Alignment explanation
Indices: 887258--887291 Score: 59
Period size: 13 Copynumber: 2.5 Consensus size: 13
887248 CATAAGAGCT
887258 AAAAAAAGAAAAAG
1 AAAAAAA-AAAAAG
887272 AAAAAAAAAAAAG
1 AAAAAAAAAAAAG
887285 AAAAAAA
1 AAAAAAA
887292 TGAGAGATGC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.65
14 7 0.35
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAG
Found at i:888828 original size:29 final size:31
Alignment explanation
Indices: 888796--888858 Score: 78
Period size: 29 Copynumber: 2.1 Consensus size: 31
888786 AAATGGATTT
* * *
888796 AGTTTTG-TTACCAAATTATAAA-TTTGTAA
1 AGTTTTGCTGACCAAAGTATAAACTTTGAAA
888825 AG-TTTGCTGACCAAAGTATAAACTTTGAAA
1 AGTTTTGCTGACCAAAGTATAAACTTTGAAA
888855 AGTT
1 AGTT
888859 CAGGTATCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
28 4 0.14
29 15 0.54
30 8 0.29
31 1 0.04
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (31 bp):
AGTTTTGCTGACCAAAGTATAAACTTTGAAA
Found at i:890916 original size:33 final size:33
Alignment explanation
Indices: 890874--890971 Score: 187
Period size: 33 Copynumber: 3.0 Consensus size: 33
890864 TATGAAAAGG
890874 GATCTATGAGATCATACAAGAATGTTACACAAT
1 GATCTATGAGATCATACAAGAATGTTACACAAT
890907 GATCTATGAGATCATACAAGAATGTTACACAAT
1 GATCTATGAGATCATACAAGAATGTTACACAAT
*
890940 GATCTATGAGATCATACAAGAATGTTATACAA
1 GATCTATGAGATCATACAAGAATGTTACACAA
890972 GTTACATGAT
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 64 1.00
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.28
Consensus pattern (33 bp):
GATCTATGAGATCATACAAGAATGTTACACAAT
Found at i:891179 original size:38 final size:38
Alignment explanation
Indices: 891123--891223 Score: 157
Period size: 38 Copynumber: 2.7 Consensus size: 38
891113 TTCGAGACAT
* *
891123 ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
1 ATGATAGGTCCTTTGGGACACAGATGACATCCTTCAGG
* *
891161 ATGATAAGTCCTTTGGGACACAGATGTCATCCTTCAGG
1 ATGATAGGTCCTTTGGGACACAGATGACATCCTTCAGG
*
891199 ATGATAGGTCCTTTGGGACATAGAT
1 ATGATAGGTCCTTTGGGACACAGAT
891224 TACCTATGTT
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 57 1.00
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.28
Consensus pattern (38 bp):
ATGATAGGTCCTTTGGGACACAGATGACATCCTTCAGG
Found at i:891357 original size:30 final size:30
Alignment explanation
Indices: 891321--891383 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
891311 CCTTAAGTTC
*
891321 TCAGTAATATACATGGGCTTATAAAAGAAA
1 TCAGTAATATACATGGGCCTATAAAAGAAA
* * * *
891351 TCAGTAATGTATATGGGCCTCTAAAAGATA
1 TCAGTAATATACATGGGCCTATAAAAGAAA
891381 TCA
1 TCA
891384 AAAGTGTTTG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (30 bp):
TCAGTAATATACATGGGCCTATAAAAGAAA
Found at i:892361 original size:3 final size:3
Alignment explanation
Indices: 892353--892386 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
892343 GCATATTTTT
*
892353 ATA ATA ATA GTA AT- ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
892387 TATTAAAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:892371 original size:14 final size:14
Alignment explanation
Indices: 892352--892386 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
892342 AGCATATTTT
*
892352 TATAATAATAGTAA
1 TATAATAATAATAA
892366 TATAATAATAATAA
1 TATAATAATAATAA
892380 TAATAAT
1 T-ATAAT
892387 TATTAAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.74
15 5 0.26
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (14 bp):
TATAATAATAATAA
Found at i:893560 original size:23 final size:22
Alignment explanation
Indices: 893483--893612 Score: 155
Period size: 21 Copynumber: 6.0 Consensus size: 22
893473 ACACAAATTG
893483 CCATAGTACACAAAGTACTACTA
1 CCATAGTACACAAAGTACT-CTA
893506 -CA-AGTACACAAAGTA--CTA
1 CCATAGTACACAAAGTACTCTA
*
893524 CTATAGGTACACAAAGTACTCTTA
1 CCATA-GTACACAAAGTACTC-TA
*
893548 CCATAGTACACAAAGTACTCTTG
1 CCATAGTACACAAAGTACTC-TA
893571 CCATAGTACACAAAGTACTACT-
1 CCATAGTACACAAAGTACT-CTA
893593 CCA-AGTACACAAAGTACTCT
1 CCATAGTACACAAAGTACTCT
893613 TAAGAAAATG
Statistics
Matches: 97, Mismatches: 3, Indels: 17
0.83 0.03 0.15
Matches are distributed among these distances:
18 3 0.03
19 1 0.01
20 3 0.03
21 40 0.41
22 5 0.05
23 38 0.39
24 7 0.07
ACGTcount: A:0.41, C:0.25, G:0.11, T:0.23
Consensus pattern (22 bp):
CCATAGTACACAAAGTACTCTA
Found at i:896097 original size:138 final size:138
Alignment explanation
Indices: 895849--896122 Score: 381
Period size: 138 Copynumber: 2.0 Consensus size: 138
895839 TTGGTTATAT
* * * ***
895849 GGATGACACTGCTCCTTCACGTTGAGGAGATCTAGTCAGTGGGTGACATTTTCCTTCGTGTTGAG
1 GGATGACACTACTCATTCACGTTGACGAGATCTAGTCAGTGAACGACATTTTCCTTCGTGTTGAG
*
895914 GATGTCTAGACGTATTGGGAGATAATTTGGAGACAACATGGTTCCTTCGCGTTGAGGAAGTCTGA
66 GATGTCTAGACGTATTGGGAGATAATTTGGAGACAACATGGTTCCTTCGCATTGAGGAAGTCTGA
895979 TTGTCTGA
131 TTGTCTGA
* * * *
895987 GGATGACACTACTCATTCGCGTTGACGAGATCTGGTCGGTGAACGACATTGTTCCTTCTTGTTGA
1 GGATGACACTACTCATTCACGTTGACGAGATCTAGTCAGTGAACGACATT-TTCCTTCGTGTTGA
* * *
896052 GGATGTCTAGCCGTAATT-GGAGAT-ATTTGGAGACAACATTGTTCCTTCGCATTGAGGAATTCT
65 GGATGTCTAGACGT-ATTGGGAGATAATTTGGAGACAACATGGTTCCTTCGCATTGAGGAAGTCT
*
896115 TATTGTCT
129 GATTGTCT
896123 AAAGATAGTT
Statistics
Matches: 119, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
138 84 0.71
139 32 0.27
140 3 0.03
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (138 bp):
GGATGACACTACTCATTCACGTTGACGAGATCTAGTCAGTGAACGACATTTTCCTTCGTGTTGAG
GATGTCTAGACGTATTGGGAGATAATTTGGAGACAACATGGTTCCTTCGCATTGAGGAAGTCTGA
TTGTCTGA
Found at i:896555 original size:95 final size:95
Alignment explanation
Indices: 896316--896623 Score: 284
Period size: 95 Copynumber: 3.1 Consensus size: 95
896306 GTTTCCAGAG
* * * * ** * *
896316 AAACTATCTCAGGTGAGATAAATTGTTTCGAGGGAAACAATTTCAAAATTTACGTTTCAAGGAAA
1 AAACAATCTCAAGTGAGATAAATT-TTTCAAGTGAAACAATTTCAAAATTTGTGTTTGAGGGAAA
*
896381 ATTATCTCAAGAGAGACGAAGTTTGTTTTAAGAA
65 ATTATCTCAAG-GAGACGAAATTTGTTTT-A-AA
* *
896415 AAACAATCTCAAAG-GAGATCAATTTTTTTTTTCAAGTGAAACAATTTCAAACTTTGTGTTCTGA
1 AAACAATCTC-AAGTGAGAT-AA----ATTTTTCAAGTGAAACAATTTCAAAATTTGTGTT-TGA
*
896479 GGGAAAATTGTCTCAAGCGAGACGAAATTTGTTTT-AA
59 GGGAAAATTATCTCAAG-GAGACGAAATTTGTTTTAAA
* *
896516 AAA-AATCTCAAGTGAGATAAATTTTACAAGTGAAACAATTTAAAAATTTGTGTTTCGAGGGAAA
1 AAACAATCTCAAGTGAGATAAATTTTTCAAGTGAAACAATTTCAAAATTTGTGTTT-GAGGGAAA
* * *
896580 ACTATCTCAA-GAGAC-AACATTTGTTTGGAGAG
65 ATTATCTCAAGGAGACGAA-ATTTGTTT-TA-AA
896612 AAACAATCTCAA
1 AAACAATCTCAA
896624 AGGTGACCGA
Statistics
Matches: 174, Mismatches: 21, Indels: 30
0.77 0.09 0.13
Matches are distributed among these distances:
92 2 0.01
93 13 0.07
94 1 0.01
95 46 0.26
96 4 0.02
97 8 0.05
99 19 0.11
100 15 0.09
101 5 0.03
103 26 0.15
104 35 0.20
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.31
Consensus pattern (95 bp):
AAACAATCTCAAGTGAGATAAATTTTTCAAGTGAAACAATTTCAAAATTTGTGTTTGAGGGAAAA
TTATCTCAAGGAGACGAAATTTGTTTTAAA
Found at i:897638 original size:40 final size:40
Alignment explanation
Indices: 897583--897663 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
897573 GTGGGTACTT
*
897583 ATGGAGTTGTTGAACATCATTATCAAAACTTCTTATTTTC
1 ATGGAGTTCTTGAACATCATTATCAAAACTTCTTATTTTC
*
897623 ATGGAGTTCTTGAACATCATTGTCAAAACTTCTTATTTTC
1 ATGGAGTTCTTGAACATCATTATCAAAACTTCTTATTTTC
897663 A
1 A
897664 AACTTGCTCA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.42
Consensus pattern (40 bp):
ATGGAGTTCTTGAACATCATTATCAAAACTTCTTATTTTC
Found at i:898809 original size:18 final size:19
Alignment explanation
Indices: 898773--898810 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
898763 CACGGAATGT
898773 AAGATTACCAGTAGGAATAA
1 AAGATTACCAG-AGGAATAA
898793 AAGATTACCAG-GGAATAA
1 AAGATTACCAGAGGAATAA
898811 GATTAATGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
20 11 0.61
ACGTcount: A:0.50, C:0.11, G:0.21, T:0.18
Consensus pattern (19 bp):
AAGATTACCAGAGGAATAA
Found at i:900378 original size:19 final size:19
Alignment explanation
Indices: 900354--900397 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
900344 AATAACAAGC
* * *
900354 AAAGAAAAAACCGAACAAT
1 AAAGAAAAAAACGAAAAAG
900373 AAAGAAAAAAACGAAAAAG
1 AAAGAAAAAAACGAAAAAG
900392 AAAGAA
1 AAAGAA
900398 TGAGAGGGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.75, C:0.09, G:0.14, T:0.02
Consensus pattern (19 bp):
AAAGAAAAAAACGAAAAAG
Found at i:901564 original size:325 final size:324
Alignment explanation
Indices: 901122--901770 Score: 1175
Period size: 325 Copynumber: 2.0 Consensus size: 324
901112 CTATGTTTTA
901122 TTATATGATTAATTTAGTGAATTTATTTTATAAATTTTTTATTTTCATTTTTATATTAATTTAGG
1 TTATATGATTAATTTAGTGAATTTATTTTATAAATTTTTTATTTTCATTTTTATATTAATTTAGG
901187 AATTGTTAATTTTATCATATTCTTATTTACTAACTTTTCAATTTCATTTCTTTTCA-GGTCGTTC
66 AATTGTTAATTTTATCATATTCTTATTTACTAACTTTTCAATTTCATTTCTTTTCAGGGTCGTTC
*
901251 GAATC-AAAC-TCTGACTTTATA-TTATTTATTTTAATTTATTTATCTTATTATTTTTTTCTTCT
131 GAATCAAAACTTCTGACTTTATATTTATTTATTTTAA-TTA-TTATATTA-TATTTTTTTCTTCT
901313 TTTCTTTTCTTAGCTATTCTTTCCTTTTAGAATTATTTTAATTACTTGTTTTAATTTTAAT-TTT
193 TTT-TTTTCTTAGCTATT-TTTCCTTTTAGAATTATTTTAATTACTTGTTTTAATTTTAATATTT
901377 TTTCATTCCTTTTCAGATATGTTCATTAAGATAAATTATTATGTTACTTTAAATTTATTTATTTT
256 TTTCATTCCTTTTCAGATATGTTCATTAAGATAAATTATTATGTTACTTTAAATTTATTTATTTT
901442 ATTC
321 ATTC
901446 TTATATGATTAATTTAGTTGAATTTATTTTATAAATTTTTTATTTTCATTTTTATATTAATTTAG
1 TTATATGATTAATTTAG-TGAATTTATTTTATAAATTTTTTATTTTCATTTTTATATTAATTTAG
901511 GAATTGTTAATTTTATCATATTCTTATTTACTAACTTTTC-ATTTCATTTTCTTTTCAGGGTCGT
65 GAATTGTTAATTTTATCATATTCTTATTTACTAACTTTTCAATTTCA-TTTCTTTTCAGGGTCGT
901575 TCGAATCAAAACTTCTGACTTTATATTTATTTATTTTAATTATTATATTATATTTTTTTCTTCTT
129 TCGAATCAAAACTTCTGACTTTATATTTATTTATTTTAATTATTATATTATATTTTTTTCTTCTT
*
901640 TTTTTTCTTAGCTATTTTTCCTTTTAGAATTATTTTAATTACTTGTTTTAATTTTATTATTTTTT
194 TTTTTTCTTAGCTATTTTTCCTTTTAGAATTATTTTAATTACTTGTTTTAATTTTAATATTTTTT
901705 CATTCCTTTTCAGATATGTTCATTAAGATAAATTATTATGTTACTTTAAATTTATTTATTTTATT
259 CATTCCTTTTCAGATATGTTCATTAAGATAAATTATTATGTTACTTTAAATTTATTTATTTTATT
901770 C
324 C
901771 AAATTTTAGC
Statistics
Matches: 316, Mismatches: 2, Indels: 13
0.95 0.01 0.04
Matches are distributed among these distances:
324 64 0.20
325 183 0.58
326 30 0.09
327 11 0.03
328 15 0.05
329 13 0.04
ACGTcount: A:0.26, C:0.09, G:0.06, T:0.59
Consensus pattern (324 bp):
TTATATGATTAATTTAGTGAATTTATTTTATAAATTTTTTATTTTCATTTTTATATTAATTTAGG
AATTGTTAATTTTATCATATTCTTATTTACTAACTTTTCAATTTCATTTCTTTTCAGGGTCGTTC
GAATCAAAACTTCTGACTTTATATTTATTTATTTTAATTATTATATTATATTTTTTTCTTCTTTT
TTTTCTTAGCTATTTTTCCTTTTAGAATTATTTTAATTACTTGTTTTAATTTTAATATTTTTTCA
TTCCTTTTCAGATATGTTCATTAAGATAAATTATTATGTTACTTTAAATTTATTTATTTTATTC
Found at i:901974 original size:31 final size:31
Alignment explanation
Indices: 901939--902007 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 31
901929 ATAATTAGAT
901939 CCTTAAACTTTAGACTTTAT-ACATTTCAGTC
1 CCTTAAACTTTAGA-TTTATCACATTTCAGTC
* * *
901970 CCTT-AACTTTAGATTTCTCATATTTTAGTC
1 CCTTAAACTTTAGATTTATCACATTTCAGTC
902000 CC-TAAACT
1 CCTTAAACT
902008 ATTAATTAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
29 5 0.15
30 24 0.73
31 4 0.12
ACGTcount: A:0.28, C:0.23, G:0.06, T:0.43
Consensus pattern (31 bp):
CCTTAAACTTTAGATTTATCACATTTCAGTC
Found at i:903169 original size:29 final size:29
Alignment explanation
Indices: 903015--903169 Score: 158
Period size: 29 Copynumber: 5.4 Consensus size: 29
903005 ATCGGGTGAC
* * *
903015 ATTTTGGGAA-TTAATTTGAAATGGGTGCT
1 ATTTTAGGAATTTAATTCGAAA-AGGTGCT
*
903044 ATTTT-GAGAATTTAATTCGAAAAGGTGCA
1 ATTTTAG-GAATTTAATTCGAAAAGGTGCT
* *
903073 ATTTTAGGAATTTAATTCGAAAAAGTACT
1 ATTTTAGGAATTTAATTCGAAAAGGTGCT
*
903102 A-TATAGGGAATTTAATTC-AAAA-GTGCT
1 ATTTTA-GGAATTTAATTCGAAAAGGTGCT
* *
903129 ATTTTGGGAATTTAATTCGAAAAGGTTCT
1 ATTTTAGGAATTTAATTCGAAAAGGTGCT
*
903158 ATTTTAGTAATT
1 ATTTTAGGAATT
903170 ATTTTAAAAA
Statistics
Matches: 106, Mismatches: 13, Indels: 14
0.80 0.10 0.11
Matches are distributed among these distances:
27 17 0.16
28 14 0.13
29 64 0.60
30 11 0.10
ACGTcount: A:0.35, C:0.06, G:0.19, T:0.39
Consensus pattern (29 bp):
ATTTTAGGAATTTAATTCGAAAAGGTGCT
Found at i:903180 original size:56 final size:55
Alignment explanation
Indices: 903015--903180 Score: 122
Period size: 56 Copynumber: 2.9 Consensus size: 55
903005 ATCGGGTGAC
* * * ** *
903015 ATTTTGGGAA-TTAATTTGAAATGGGTGCTATTTTGAGAATTTAATTCGAAAAGGTGCA
1 ATTTTGGGAATTTAATTCGAAA-AGGTACTATTTT-AGAA-TT-ATTTTAAAAAGTGCA
* * * * * *
903073 ATTTTAGGAATTTAATTCGAAAAAGTACTA-TATAGGGAATT-TAATTCAAAAGTGCT
1 ATTTTGGGAATTTAATTCGAAAAGGTACTATTTTA--GAATTAT-TTTAAAAAGTGCA
*
903129 ATTTTGGGAATTTAATTCGAAAAGGTTCTATTTTAGTAATTATTTTAAAAAG
1 ATTTTGGGAATTTAATTCGAAAAGGTACTATTTTAG-AATTATTTTAAAAAG
903181 GATGTTATTT
Statistics
Matches: 83, Mismatches: 18, Indels: 16
0.71 0.15 0.14
Matches are distributed among these distances:
55 2 0.02
56 46 0.55
57 8 0.10
58 17 0.20
59 10 0.12
ACGTcount: A:0.37, C:0.05, G:0.19, T:0.39
Consensus pattern (55 bp):
ATTTTGGGAATTTAATTCGAAAAGGTACTATTTTAGAATTATTTTAAAAAGTGCA
Found at i:909330 original size:2 final size:2
Alignment explanation
Indices: 909323--909347 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
909313 GGTCCTACGT
909323 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 T
909348 TGAAAATATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:909821 original size:3 final size:3
Alignment explanation
Indices: 909813--909870 Score: 73
Period size: 3 Copynumber: 19.0 Consensus size: 3
909803 TGTCCCGGTT
*
909813 TTA TTA TTA TTA TTA TTA -TA TTA TTTA TTA TATA TTT TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA T-TA TTA TTA TTA TTA
*
909859 ATA TTA TTA TTA
1 TTA TTA TTA TTA
909871 CAACCAGGCC
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
2 2 0.04
3 40 0.83
4 6 0.12
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:910658 original size:48 final size:50
Alignment explanation
Indices: 910603--910700 Score: 182
Period size: 48 Copynumber: 2.0 Consensus size: 50
910593 GCGGCGAGGT
910603 CAACACCGGCGAACGGCTTCCGGCC-G-GTGCTTCTCTCTATTTTAGAGA
1 CAACACCGGCGAACGGCTTCCGGCCGGTGTGCTTCTCTCTATTTTAGAGA
910651 CAACACCGGCGAACGGCTTCCGGCCGGTGTGCTTCTCTCTATTTTAGAGA
1 CAACACCGGCGAACGGCTTCCGGCCGGTGTGCTTCTCTCTATTTTAGAGA
910701 GAAGCGAGAG
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
48 25 0.52
49 1 0.02
50 22 0.46
ACGTcount: A:0.18, C:0.31, G:0.26, T:0.26
Consensus pattern (50 bp):
CAACACCGGCGAACGGCTTCCGGCCGGTGTGCTTCTCTCTATTTTAGAGA
Found at i:915289 original size:15 final size:15
Alignment explanation
Indices: 915269--915300 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
915259 ATCAATACCT
915269 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
915284 TTTTGCATACATTCA
1 TTTTGCATACATGCA
915299 TT
1 TT
915301 CATTTCATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:922423 original size:19 final size:19
Alignment explanation
Indices: 922399--922459 Score: 81
Period size: 19 Copynumber: 3.2 Consensus size: 19
922389 ATTATGCTTA
922399 AAAAAAAGAAGAAAAAGAG
1 AAAAAAAGAAGAAAAAGAG
922418 AAAAAAAAGAA-AAAAAGAG
1 -AAAAAAAGAAGAAAAAGAG
*
922437 AAAAGAAAAAAGAAAAAGA-
1 AAAA-AAAGAAGAAAAAGAG
922456 AAAA
1 AAAA
922460 GGGGGGTCAA
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
18 4 0.11
19 17 0.45
20 17 0.45
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (19 bp):
AAAAAAAGAAGAAAAAGAG
Done.