Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007864.1 Hibiscus syriacus cultivar Beakdansim tig00110236_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: 1537186
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 8
Found at i:867532 original size:20 final size:20
Alignment explanation
Indices: 867502--867567 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
867492 ATTTGACTAC
867502 CGCAACGCGAAAATGGCTAT
1 CGCAACGCGAAAATGGCTAT
** ***
867522 CGCAATTCG-AAATGAAAAAT
1 CGCAACGCGAAAATG-GCTAT
867542 CGCAACGCGAAAATGGCTAT
1 CGCAACGCGAAAATGGCTAT
867562 CGCAAC
1 CGCAAC
867568 TAGAAAATCG
Statistics
Matches: 34, Mismatches: 10, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
19 5 0.15
20 24 0.71
21 5 0.15
ACGTcount: A:0.39, C:0.24, G:0.21, T:0.15
Consensus pattern (20 bp):
CGCAACGCGAAAATGGCTAT
Found at i:867635 original size:19 final size:19
Alignment explanation
Indices: 867613--867680 Score: 111
Period size: 19 Copynumber: 3.6 Consensus size: 19
867603 GATTTTCTCG
867613 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
867632 TTGCAATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
867651 TTGCCG-TTTTCATTTCGCA
1 TTG-CGATTTTCATTTCGCA
867670 TTGCGATTTTC
1 TTGCGATTTTC
867681 TCGTTGCGAT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
18 2 0.04
19 42 0.93
20 1 0.02
ACGTcount: A:0.15, C:0.22, G:0.15, T:0.49
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:869313 original size:43 final size:42
Alignment explanation
Indices: 869266--869359 Score: 125
Period size: 42 Copynumber: 2.2 Consensus size: 42
869256 CCTCTTCAAC
* * *
869266 GATGACAGTGGCCTCTTGAACGGTGGGGGGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGGGGACTCTTGAGG
* *
869309 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGGGGACTCTTGAGG
*
869351 AATGACAGG
1 GATGACAGG
869360 TGAGTCGGGC
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
42 23 0.52
43 21 0.48
ACGTcount: A:0.21, C:0.15, G:0.43, T:0.21
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGGGGACTCTTGAGG
Found at i:869720 original size:20 final size:20
Alignment explanation
Indices: 869695--869767 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
869685 GAAGAATAGT
*
869695 TTACTTTCGCAACACGAAAC
1 TTACTTTCGCAACACGAAAA
*
869715 TTACTTTCGCAACGCGAAAA
1 TTACTTTCGCAACACGAAAA
* * * *
869735 TGACTATCGCAACGCGGAAA
1 TTACTTTCGCAACACGAAAA
* *
869755 TGACTATCGCAAC
1 TTACTTTCGCAAC
869768 GCGGAAATGG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.22
Consensus pattern (20 bp):
TTACTTTCGCAACACGAAAA
Found at i:869745 original size:40 final size:40
Alignment explanation
Indices: 869701--869786 Score: 111
Period size: 40 Copynumber: 2.1 Consensus size: 40
869691 TAGTTTACTT
* *
869701 TCGCAACAC-GAAACTTACTTTCGCAACGCGAAAATGACTA
1 TCGCAACACGGAAA-TGACTATCGCAACGCGAAAATGACTA
* * *
869741 TCGCAACGCGGAAATGACTATCGCAACGCGGAAATGGCTA
1 TCGCAACACGGAAATGACTATCGCAACGCGAAAATGACTA
869781 TCGCAA
1 TCGCAA
869787 TGCGAAATGA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
40 36 0.90
41 4 0.10
ACGTcount: A:0.35, C:0.27, G:0.21, T:0.17
Consensus pattern (40 bp):
TCGCAACACGGAAATGACTATCGCAACGCGAAAATGACTA
Found at i:869768 original size:20 final size:20
Alignment explanation
Indices: 869721--869796 Score: 118
Period size: 20 Copynumber: 3.9 Consensus size: 20
869711 AAACTTACTT
*
869721 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
869741 TCGCAACGCGGAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
869761 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
*
869781 TCGCAATGC-GAAATGA
1 TCGCAACGCGGAAATGA
869797 AAATCACAAC
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 6 0.12
20 46 0.88
ACGTcount: A:0.36, C:0.24, G:0.25, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:869807 original size:39 final size:40
Alignment explanation
Indices: 869724--869807 Score: 107
Period size: 40 Copynumber: 2.1 Consensus size: 40
869714 CTTACTTTCG
** *
869724 CAACGCGAAAATGACTATCGCAACGCGGAAATGACTATCG
1 CAACGCGAAAATGACTATCGCAACGCGGAAATGAAAATCA
* * *
869764 CAACGCGGAAATGGCTATCGCAATGC-GAAATGAAAATCA
1 CAACGCGAAAATGACTATCGCAACGCGGAAATGAAAATCA
869803 CAACG
1 CAACG
869808 ACAAAATCGC
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
39 15 0.39
40 23 0.61
ACGTcount: A:0.39, C:0.24, G:0.23, T:0.14
Consensus pattern (40 bp):
CAACGCGAAAATGACTATCGCAACGCGGAAATGAAAATCA
Found at i:869855 original size:19 final size:19
Alignment explanation
Indices: 869833--869929 Score: 88
Period size: 19 Copynumber: 5.6 Consensus size: 19
869823 GAAACACAAA
869833 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
869852 TCGCGTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
869868 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
869885 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
869901 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
869918 TCGTATTGCGAT
1 TCGCATTGCGAT
869930 AGCCATTTCC
Statistics
Matches: 63, Mismatches: 5, Indels: 20
0.72 0.06 0.23
Matches are distributed among these distances:
14 12 0.19
15 6 0.10
16 8 0.13
17 8 0.13
18 6 0.10
19 23 0.37
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:869874 original size:14 final size:14
Alignment explanation
Indices: 869855--869913 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
869845 TTTCATTTCG
869855 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
869869 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
869886 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
869902 CGTTGCGATTTT
1 CGTTGCGATTTT
869914 CATTTCGTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 18 0.47
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.16
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:869880 original size:33 final size:33
Alignment explanation
Indices: 869838--869929 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
869828 ACAAATCGCA
*
869838 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
869871 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
869904 TTGCGATTTTCATTTCGTATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
869930 AGCCATTTCC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.49
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:869948 original size:20 final size:20
Alignment explanation
Indices: 869923--869968 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
869913 TCATTTCGTA
869923 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
* * *
869943 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGCCATTTCCGCG
869963 TTGCGA
1 TTGCGA
869969 AAGTAAACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.37
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:870532 original size:18 final size:18
Alignment explanation
Indices: 870509--870556 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
870499 CGGGTCGATC
870509 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
870527 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
870545 AGGTGATGGCTC
1 AGGTGATGGCTC
870557 CCGAAGTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.12, G:0.46, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:871901 original size:20 final size:20
Alignment explanation
Indices: 871876--871918 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
871866 AATAGTTTCT
871876 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
*
871896 GAAAATGAAAATCGCAACGC
1 GAAAATGAAAATCGCAACAC
871916 GAA
1 GAA
871919 TTTGACTATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.53, C:0.19, G:0.19, T:0.09
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:872527 original size:41 final size:41
Alignment explanation
Indices: 872408--872545 Score: 161
Period size: 41 Copynumber: 3.4 Consensus size: 41
872398 CGCTTTGAAA
* * *
872408 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
* * ** * * *
872449 ATTGAGTTGCGAAATT-AAGTATCGAGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
*
872489 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
*
872530 ACCGCGTTGCGATTTT
1 ATCGCGTTGCGATTTT
872546 CCAAATTCGC
Statistics
Matches: 77, Mismatches: 19, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
40 32 0.42
41 45 0.58
ACGTcount: A:0.23, C:0.16, G:0.25, T:0.36
Consensus pattern (41 bp):
ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
Found at i:872542 original size:20 final size:20
Alignment explanation
Indices: 872428--872541 Score: 104
Period size: 20 Copynumber: 5.7 Consensus size: 20
872418 GATTATGTAT
*
872428 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* * * *
872448 TATTGAGTTGCGAAATTAAG
1 TATCGCGTTGCGAAAGTCAG
*
872468 TATCGAGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
** *
872488 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
872509 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
872529 TACCGCGTTGCGA
1 TATCGCGTTGCGA
872542 TTTTCCAAAT
Statistics
Matches: 76, Mismatches: 15, Indels: 6
0.78 0.15 0.06
Matches are distributed among these distances:
19 3 0.04
20 57 0.75
21 14 0.18
22 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:872561 original size:41 final size:41
Alignment explanation
Indices: 872475--872563 Score: 108
Period size: 41 Copynumber: 2.2 Consensus size: 41
872465 AAGTATCGAG
* * ** * *
872475 TTGCGAAAGTCAGTATCGCGTTGCGATTTTGTATTATCGCG
1 TTGCGATAGTCAGTACCGCGTTGCGATTTTCAAATATCGCA
872516 TTGCGATAGTCAGTACCGCGTTGCGATTTTCCAAAT-TCGCA
1 TTGCGATAGTCAGTACCGCGTTGCGATTTT-CAAATATCGCA
872557 TTGCGAT
1 TTGCGAT
872564 TTTCCAAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 39 0.95
42 2 0.05
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (41 bp):
TTGCGATAGTCAGTACCGCGTTGCGATTTTCAAATATCGCA
Found at i:872562 original size:21 final size:21
Alignment explanation
Indices: 872536--872603 Score: 102
Period size: 21 Copynumber: 3.3 Consensus size: 21
872526 CAGTACCGCG
872536 TTGCGATTTTCCAAATTCGCA
1 TTGCGATTTTCCAAATTCGCA
872557 TTGCGATTTTCCAAATTCGCA
1 TTGCGATTTTCCAAATTCGCA
* **
872578 TTGCGA-TTTACTTATTCGCA
1 TTGCGATTTTCCAAATTCGCA
872598 TTGCGA
1 TTGCGA
872604 ATTGGGAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
20 17 0.39
21 27 0.61
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.40
Consensus pattern (21 bp):
TTGCGATTTTCCAAATTCGCA
Found at i:872623 original size:21 final size:20
Alignment explanation
Indices: 872593--872645 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 20
872583 ATTTACTTAT
872593 TCGCATTGCGAATTGGGAAAA
1 TCGCATTGCGAATT-GGAAAA
*
872614 TCGCAATGCGAAATTGGAAAA
1 TCGCATTGCG-AATTGGAAAA
872635 TCGCATTGCGA
1 TCGCATTGCGA
872646 TAGTCATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 1 0.03
21 24 0.83
22 4 0.14
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.23
Consensus pattern (20 bp):
TCGCATTGCGAATTGGAAAA
Found at i:879902 original size:102 final size:102
Alignment explanation
Indices: 879775--880077 Score: 341
Period size: 102 Copynumber: 3.0 Consensus size: 102
879765 GTTATATAAG
* * *
879775 GTGAGATGAAATTTTGTTTCAAGTGAAACAATTTTAAAATTTACTTTTCAAGGGAAAACTATCTC
1 GTGAGAT-CAATTTTGTTTCAAGTGAAACAATTTCAAAATTTACTTTTCAAGGGAAAACTGTCTC
879840 AAGCGAGACGAAATTTGTTTTTAGGAAAACAATCTCAA
65 AAGCGAGACGAAATTTGTTTTTAGGAAAACAATCTCAA
** * * *
879878 GTGAGATCAATTTTGTTTCAAGTGAAACAATTTCAAAATTT-CTATTTTGAGAGAAAATTGTCTT
1 GTGAGATCAATTTTGTTTCAAGTGAAACAATTTCAAAATTTACT-TTTCAAGGGAAAACTGTCTC
*
879942 AAGCGATACG-AA-TT-TTTTTAGGAAAACAATCTCAA
65 AAGCGAGACGAAATTTGTTTTTAGGAAAACAATCTCAA
* * * ***
879977 CTGAGATCAATTTT-TTTCAAGTGAAACAACTTCAAAATCTAGGCTTCAAGGG-AAACTGTCTCA
1 GTGAGATCAATTTTGTTTCAAGTGAAACAATTTCAAAATTTACTTTTCAAGGGAAAACTGTCTCA
* * * * *
880040 AACAAGATGAAACTTTG-TTTCAAGAGAAACAATCTCAA
66 AGCGAGACGAAA-TTTGTTTTTAGGA-AAACAATCTCAA
880078 AGGTTTATGT
Statistics
Matches: 167, Mismatches: 26, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
97 14 0.08
98 31 0.19
99 34 0.20
100 10 0.06
101 16 0.10
102 55 0.33
103 7 0.04
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (102 bp):
GTGAGATCAATTTTGTTTCAAGTGAAACAATTTCAAAATTTACTTTTCAAGGGAAAACTGTCTCA
AGCGAGACGAAATTTGTTTTTAGGAAAACAATCTCAA
Found at i:880205 original size:65 final size:64
Alignment explanation
Indices: 880021--880209 Score: 234
Period size: 66 Copynumber: 2.9 Consensus size: 64
880011 AAATCTAGGC
* * * *
880021 TTCAAGGGAAACTGTCTCAAACAAGATGAAACTTTGTTTCAAGAGAAACAATCTCAAAGGTTTAT
1 TTCAAGAGAAACTGTCTCAAGCGAGAT-AAAATTTGTTTCAAGAGAAACAATCTC-AAGGTTTAT
880086 G
64 G
* * * * * *
880087 TTCAAGAGAATCTATCTCAAGCGAGACAAAACTTTTTTTCGAGAGAAATAATCTCAAGGTTTATG
1 TTCAAGAGAAACTGTCTCAAGCGAGATAAAA-TTTGTTTCAAGAGAAACAATCTCAAGGTTTATG
* *
880152 TTTTAAGAGAAACTGTCTCAAGTGAGATAAAATTTGTTTCAAGAGAAACAATCTCAAG
1 -TTCAAGAGAAACTGTCTCAAGCGAGATAAAATTTGTTTCAAGAGAAACAATCTCAAG
880210 AGAGACTGAC
Statistics
Matches: 103, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
65 36 0.35
66 67 0.65
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.29
Consensus pattern (64 bp):
TTCAAGAGAAACTGTCTCAAGCGAGATAAAATTTGTTTCAAGAGAAACAATCTCAAGGTTTATG
Found at i:883182 original size:19 final size:18
Alignment explanation
Indices: 883131--883182 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
883121 AAAAAGTAAT
883131 AAAAATAAATAAGA-TAAA
1 AAAAATAAATAA-ATTAAA
883149 AAACAATTAAA-AAATTAAA
1 AAA-AA-TAAATAAATTAAA
883168 AAAAATGAAATAAAT
1 AAAAAT-AAATAAAT
883183 AAGATAAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
17 1 0.03
18 9 0.31
19 15 0.52
20 4 0.14
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.19
Consensus pattern (18 bp):
AAAAATAAATAAATTAAA
Found at i:883189 original size:9 final size:10
Alignment explanation
Indices: 883177--883232 Score: 55
Period size: 9 Copynumber: 5.7 Consensus size: 10
883167 AAAAAATGAA
883177 ATAAAT-AAG
1 ATAAATAAAG
883186 ATAAGATAAAG
1 ATAA-ATAAAG
*
883197 A-AAATAAAA
1 ATAAATAAAG
883206 ATAAAATAAAG
1 AT-AAATAAAG
*
883217 ATAAAT-AGG
1 ATAAATAAAG
883226 ATAAATA
1 ATAAATA
883233 TAATAAAGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
9 18 0.46
10 8 0.21
11 13 0.33
ACGTcount: A:0.70, C:0.00, G:0.11, T:0.20
Consensus pattern (10 bp):
ATAAATAAAG
Found at i:883246 original size:40 final size:38
Alignment explanation
Indices: 883159--883256 Score: 101
Period size: 40 Copynumber: 2.5 Consensus size: 38
883149 AAACAATTAA
* *
883159 AAAATTAAAAAAAATGAAATAAATAAGATAAGATAAAG
1 AAAATAAAAAAAAATAAAATAAATAAGATAAGATAAAG
* *
883197 AAAATAAAAATAAAATAAAGATAAATAGGATAA-ATATAAT
1 AAAATAAAAA-AAAATAAA-ATAAATAAGATAAGATA-AAG
883237 AAAGA-AAAAAAATAATAAAA
1 AAA-ATAAAAAAA-AATAAAA
883257 AATATAAAGA
Statistics
Matches: 51, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
38 9 0.18
39 13 0.25
40 28 0.55
41 1 0.02
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.18
Consensus pattern (38 bp):
AAAATAAAAAAAAATAAAATAAATAAGATAAGATAAAG
Found at i:883365 original size:9 final size:9
Alignment explanation
Indices: 883351--883377 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
883341 ATAAAAAAAT
883351 TTAAATAAA
1 TTAAATAAA
883360 TTAAATAAA
1 TTAAATAAA
883369 TTAAATAAA
1 TTAAATAAA
883378 AAAAGTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
TTAAATAAA
Found at i:883446 original size:3 final size:3
Alignment explanation
Indices: 883438--883675 Score: 145
Period size: 3 Copynumber: 77.7 Consensus size: 3
883428 ATATATATTT
883438 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * **
883486 TAA -AGG GAA -AA CATA TATA TGT TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TA-A TAA TAA TA-A TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * **
883532 TAA TAA TAG TTA TAA T-A TATA TATA TATA TATA TAC GCA TAA -ACA
1 TAA TAA TAA TAA TAA TAA TA-A TA-A TA-A TA-A TAA TAA TAA TA-A
* *
883577 -AA GTAG TAGA -AA AAA TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA
1 TAA -TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
883621 TAA TAA TAA -AA GAA TTAA -AA TAA -AA TAA AAA TAA TATA TATA TATA
1 TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TA-A TA-A TA-A
883667 TATA TAA TA
1 TA-A TAA TA
883676 TCGTATAAAT
Statistics
Matches: 195, Mismatches: 23, Indels: 34
0.77 0.09 0.13
Matches are distributed among these distances:
2 16 0.08
3 140 0.72
4 39 0.20
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:883547 original size:70 final size:70
Alignment explanation
Indices: 883388--883629 Score: 292
Period size: 70 Copynumber: 3.4 Consensus size: 70
883378 AAAAGTATAT
* * *
883388 ATAATGATAATAACAATAATAATAATAATAAAGGGAAAACATATATATTTTAATAATAATAATAA
1 ATAATAATAATAATAATAATAATAATAATAAAGGGAAAACATATATATGTTAATAATAATAATAA
883453 TAATA
66 TAATA
883458 ATAATAATAATAATAATAATAATAATAATAAAGGGAAAACATATATATGTTAATAATAATAATAA
1 ATAATAATAATAATAATAATAATAATAATAAAGGGAAAACATATATATGTTAATAATAATAATAA
883523 TAATA
66 TAATA
* * * * * *
883528 ATAATAATAATAGTTATAATATATATATATATATATATACGCATAAACAAAGTAGTA-G-AAAAA
1 ATAATAATAATA---ATAATA-ATA-ATA-ATA-ATAAAGGGA-AAACATA-TA-TATGTTAATA
883591 ATAATAATAA-AATA
56 ATAATAATAATAATA
883605 ATAATAATAATAATAATAATAATAA
1 ATAATAATAATAATAATAATAATAA
883630 AAGAATTAAA
Statistics
Matches: 153, Mismatches: 9, Indels: 19
0.85 0.05 0.10
Matches are distributed among these distances:
70 79 0.52
71 1 0.01
72 3 0.02
73 9 0.06
74 9 0.06
75 3 0.02
76 3 0.02
77 22 0.14
78 19 0.12
79 3 0.02
80 2 0.01
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.31
Consensus pattern (70 bp):
ATAATAATAATAATAATAATAATAATAATAAAGGGAAAACATATATATGTTAATAATAATAATAA
TAATA
Found at i:883692 original size:7 final size:7
Alignment explanation
Indices: 883682--883728 Score: 51
Period size: 7 Copynumber: 6.4 Consensus size: 7
883672 AATATCGTAT
883682 AAATAAA
1 AAATAAA
*
883689 AAATAAG
1 AAATAAA
883696 AAATAAA
1 AAATAAA
883703 GTAAA-AATA
1 --AAATAA-A
883712 AAATAAA
1 AAATAAA
883719 AAATAAA
1 AAATAAA
883726 AAA
1 AAA
883729 AGATAAAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
7 26 0.76
8 4 0.12
9 4 0.12
ACGTcount: A:0.81, C:0.00, G:0.04, T:0.15
Consensus pattern (7 bp):
AAATAAA
Found at i:883701 original size:18 final size:19
Alignment explanation
Indices: 883680--883728 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
883670 ATAATATCGT
*
883680 ATAAATAAAAAATAAGA-A
1 ATAAATAAAAAATAAAATA
883698 ATAAAGT-AAAAATAAAATA
1 ATAAA-TAAAAAATAAAATA
*
883717 AAAAATAAAAAA
1 ATAAATAAAAAA
883729 AGATAAAAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 15 0.58
19 11 0.42
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (19 bp):
ATAAATAAAAAATAAAATA
Found at i:883722 original size:12 final size:12
Alignment explanation
Indices: 883688--883726 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
883678 GTATAAATAA
*
883688 AAAATAAGAAAT
1 AAAATAAAAAAT
*
883700 AAAGT-AAAAAT
1 AAAATAAAAAAT
883711 AAAATAAAAAAT
1 AAAATAAAAAAT
883723 AAAA
1 AAAA
883727 AAAGATAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
11 9 0.39
12 14 0.61
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.15
Consensus pattern (12 bp):
AAAATAAAAAAT
Found at i:886217 original size:21 final size:21
Alignment explanation
Indices: 886193--886232 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
886183 AAGACTTTAT
886193 TTTCAAAATAT-AAAAATGATA
1 TTTCAAAAT-TGAAAAATGATA
886214 TTTCAAAATTGAAAAATGA
1 TTTCAAAATTGAAAAATGA
886233 AAATAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.33
Consensus pattern (21 bp):
TTTCAAAATTGAAAAATGATA
Found at i:889265 original size:31 final size:31
Alignment explanation
Indices: 889227--889335 Score: 164
Period size: 31 Copynumber: 3.5 Consensus size: 31
889217 AGGGTCGAGG
* *
889227 GTTTACCTATGTTCTTTGGGACATATGAACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
889258 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
889289 ATTTACCTATGTTCTTCGGGATATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
889320 GATTACCTACGTTCTT
1 GTTTACCTATGTTCTT
889336 TAGAATCTAT
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 71 1.00
ACGTcount: A:0.21, C:0.18, G:0.19, T:0.41
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:889347 original size:31 final size:32
Alignment explanation
Indices: 889249--889351 Score: 95
Period size: 31 Copynumber: 3.3 Consensus size: 32
889239 TCTTTGGGAC
* * * * *
889249 ATATGAACTG-TTTACCTATGTTCTTCGGGAC
1 ATATGGACTGATTTACCTACGTTCTTCAGAAT
* * *
889280 ATATGGACT-ATTTACCTATGTTCTTCGGGAT
1 ATATGGACTGATTTACCTACGTTCTTCAGAAT
*
889311 ATATGGACTGA-TTACCTACGTTCTTTAGAAT
1 ATATGGACTGATTTACCTACGTTCTTCAGAAT
*
889342 CTATGGACTG
1 ATATGGACTG
889352 GTCTTTCGGG
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
31 62 0.98
32 1 0.02
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.39
Consensus pattern (32 bp):
ATATGGACTGATTTACCTACGTTCTTCAGAAT
Found at i:889347 original size:62 final size:62
Alignment explanation
Indices: 889228--889350 Score: 158
Period size: 62 Copynumber: 2.0 Consensus size: 62
889218 GGGTCGAGGG
* * * * *
889228 TTTACCTATGTTCTTTGGGACATATGAACTGTTTACCTATGTTCTTCGGGACATATGGACTA
1 TTTACCTATGTTCTTCGGGACATATGAACTGATTACCTACGTTCTTCAGAACATATGGACTA
* * *
889290 TTTACCTATGTTCTTCGGGATATATGGACTGATTACCTACGTTCTTTAGAATC-TATGGACT
1 TTTACCTATGTTCTTCGGGACATATGAACTGATTACCTACGTTCTTCAGAA-CATATGGACT
889351 GGTCTTTCGG
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
62 51 0.98
63 1 0.02
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.41
Consensus pattern (62 bp):
TTTACCTATGTTCTTCGGGACATATGAACTGATTACCTACGTTCTTCAGAACATATGGACTA
Found at i:890063 original size:21 final size:21
Alignment explanation
Indices: 890033--890072 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
890023 AACGAAAGTT
*
890033 ACTGTTGCAGTGCATCGATGC
1 ACTGTAGCAGTGCATCGATGC
890054 ACTGTAGCAGTGCATCGAT
1 ACTGTAGCAGTGCATCGAT
890073 ACACAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.28
Consensus pattern (21 bp):
ACTGTAGCAGTGCATCGATGC
Found at i:891097 original size:97 final size:97
Alignment explanation
Indices: 890931--891126 Score: 374
Period size: 97 Copynumber: 2.0 Consensus size: 97
890921 AGTAGAGTGT
890931 GGACATTAGTTGAAAGGCCTAGTAATAAATCTACTGTAGGTACTAGATGGGTATTTAGGAATAAG
1 GGACATTAGTTGAAAGGCCTAGTAATAAATCTACTGTAGGTACTAGATGGGTATTTAGGAATAAG
890996 CTTGATGAAAGTGGTAATATAGTAAGAAACAA
66 CTTGATGAAAGTGGTAATATAGTAAGAAACAA
* *
891028 GGACATTAGTTGAAAGGCCTAGTAATAAATCTACTGTATGTACTATATGGGTATTTAGGAATAAG
1 GGACATTAGTTGAAAGGCCTAGTAATAAATCTACTGTAGGTACTAGATGGGTATTTAGGAATAAG
891093 CTTGATGAAAGTGGTAATATAGTAAGAAACAA
66 CTTGATGAAAGTGGTAATATAGTAAGAAACAA
891125 GG
1 GG
891127 CTAGACTTGT
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
97 97 1.00
ACGTcount: A:0.39, C:0.08, G:0.24, T:0.29
Consensus pattern (97 bp):
GGACATTAGTTGAAAGGCCTAGTAATAAATCTACTGTAGGTACTAGATGGGTATTTAGGAATAAG
CTTGATGAAAGTGGTAATATAGTAAGAAACAA
Found at i:892745 original size:22 final size:23
Alignment explanation
Indices: 892717--892774 Score: 82
Period size: 22 Copynumber: 2.6 Consensus size: 23
892707 TGGTGCTCTA
892717 GGTATCGATACCCCCTTGCA-TG
1 GGTATCGATACCCCCTTGCAGTG
* *
892739 GGTATCGATTCCCCCTTTCAGTG
1 GGTATCGATACCCCCTTGCAGTG
*
892762 GGTACCGATACCC
1 GGTATCGATACCC
892775 TCCACGGGGT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 18 0.58
23 13 0.42
ACGTcount: A:0.17, C:0.33, G:0.22, T:0.28
Consensus pattern (23 bp):
GGTATCGATACCCCCTTGCAGTG
Found at i:894280 original size:25 final size:25
Alignment explanation
Indices: 894251--894313 Score: 117
Period size: 25 Copynumber: 2.5 Consensus size: 25
894241 CTCATTTCCT
894251 TAACAAAATCGGGATGAATAAAGGA
1 TAACAAAATCGGGATGAATAAAGGA
894276 TAACAAAATCGGGATGAATAAAGGA
1 TAACAAAATCGGGATGAATAAAGGA
*
894301 TAACTAAATCGGG
1 TAACAAAATCGGG
894314 CAATGGGTTC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.49, C:0.10, G:0.24, T:0.17
Consensus pattern (25 bp):
TAACAAAATCGGGATGAATAAAGGA
Found at i:894860 original size:2 final size:2
Alignment explanation
Indices: 894853--894877 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
894843 TGTTTGAACT
894853 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
894878 GGGTTTGATT
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:900795 original size:51 final size:51
Alignment explanation
Indices: 900734--900835 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
900724 CTCTTTTACT
900734 TTCAAATGTGAAAATGTTTGATGAAAAAGTTTTGAAAAATGATGCCCCTTA
1 TTCAAATGTGAAAATGTTTGATGAAAAAGTTTTGAAAAATGATGCCCCTTA
900785 TTCAAATGTGAAAATGTTTGATGAAAAAGTTTTGAAAAATGATGCCCCTTA
1 TTCAAATGTGAAAATGTTTGATGAAAAAGTTTTGAAAAATGATGCCCCTTA
900836 CTTTGGGTTC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33
Consensus pattern (51 bp):
TTCAAATGTGAAAATGTTTGATGAAAAAGTTTTGAAAAATGATGCCCCTTA
Found at i:901619 original size:20 final size:20
Alignment explanation
Indices: 901594--901634 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
901584 GGTGAATTGA
901594 TTCTAGATCTTTGAACCAGT
1 TTCTAGATCTTTGAACCAGT
901614 TTCTAGATCTTTGAACCAGT
1 TTCTAGATCTTTGAACCAGT
901634 T
1 T
901635 GTACTTGCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41
Consensus pattern (20 bp):
TTCTAGATCTTTGAACCAGT
Found at i:901727 original size:11 final size:10
Alignment explanation
Indices: 901713--901766 Score: 65
Period size: 11 Copynumber: 5.3 Consensus size: 10
901703 TTCTTTTCCC
901713 TTTTTCTTATT
1 TTTTTCTT-TT
901724 TTTTTCTTATT
1 TTTTTCTT-TT
901735 TTTTTC-TTT
1 TTTTTCTTTT
*
901744 TTTTTCTCTT
1 TTTTTCTTTT
*
901754 TTTTCCTTTT
1 TTTTTCTTTT
901764 TTT
1 TTT
901767 GCCTTGATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
9 8 0.21
10 14 0.36
11 17 0.44
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:904718 original size:2 final size:2
Alignment explanation
Indices: 904706--904749 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
904696 AAAAGTTAAA
*
904706 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
904748 AT
1 AT
904750 CATGCACGTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:906261 original size:20 final size:20
Alignment explanation
Indices: 906238--906276 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
906228 TCAACCTTAC
*
906238 AGTATTGATACCCACTCTAT
1 AGTATTAATACCCACTCTAT
906258 AGTATTAATACCCACTCTA
1 AGTATTAATACCCACTCTA
906277 CATTATCGAT
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:0.33, C:0.26, G:0.08, T:0.33
Consensus pattern (20 bp):
AGTATTAATACCCACTCTAT
Found at i:920338 original size:16 final size:17
Alignment explanation
Indices: 920310--920341 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
920300 ATCGTCGACC
920310 AAATTTCACTATTCACT
1 AAATTTCACTATTCACT
920327 AAATTT-ACTATTCAC
1 AAATTTCACTATTCAC
920342 GTGAATAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATTTCACTATTCACT
Found at i:925397 original size:3 final size:3
Alignment explanation
Indices: 925391--925437 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
925381 TAGTGACGAT
925391 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
925438 CAATATGAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:929849 original size:20 final size:21
Alignment explanation
Indices: 929817--929855 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
929807 CAGAGATTTT
929817 ATCCCCAAACGGCTAGAAATC
1 ATCCCCAAACGGCTAGAAATC
929838 ATCCCC-AACGGCTAGAAA
1 ATCCCCAAACGGCTAGAAA
929856 CAGCCATAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.38, C:0.33, G:0.15, T:0.13
Consensus pattern (21 bp):
ATCCCCAAACGGCTAGAAATC
Found at i:931108 original size:12 final size:12
Alignment explanation
Indices: 931073--931115 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
931063 GAGGAAGATG
931073 ATGAAGAAAAGA
1 ATGAAGAAAAGA
*
931085 ATGACA-ATAAGA
1 ATGA-AGAAAAGA
931097 ATGAAGAAAAGA
1 ATGAAGAAAAGA
931109 A-GAAGAA
1 ATGAAGAA
931116 TGTAGGCATT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 7 0.26
12 19 0.70
13 1 0.04
ACGTcount: A:0.65, C:0.02, G:0.23, T:0.09
Consensus pattern (12 bp):
ATGAAGAAAAGA
Found at i:933328 original size:20 final size:21
Alignment explanation
Indices: 933294--933334 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
933284 TACAGAGATT
933294 TCATCCCCAAACAGCTAGAAA
1 TCATCCCCAAACAGCTAGAAA
933315 TCATCCCC-AACAGCTAGAAA
1 TCATCCCCAAACAGCTAGAAA
933335 CGGCCATAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.41, C:0.34, G:0.10, T:0.15
Consensus pattern (21 bp):
TCATCCCCAAACAGCTAGAAA
Found at i:934035 original size:9 final size:9
Alignment explanation
Indices: 934018--934051 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
934008 TTAAACTATA
*
934018 AAATTAATT
1 AAATCAATT
934027 AAATCAATT
1 AAATCAATT
934036 AAATCAATT
1 AAATCAATT
934045 AAATCAA
1 AAATCAA
934052 AGGGCTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.32
Consensus pattern (9 bp):
AAATCAATT
Found at i:934759 original size:16 final size:16
Alignment explanation
Indices: 934704--934764 Score: 68
Period size: 16 Copynumber: 3.8 Consensus size: 16
934694 TTAGGTTAAA
* * *
934704 TTCGGTTTGGTTTGCT
1 TTCGGTTCGGGTTGTT
* *
934720 TTCGGTTTGAGTTGTT
1 TTCGGTTCGGGTTGTT
*
934736 TTCAGTTCGGGTTGTT
1 TTCGGTTCGGGTTGTT
934752 TTCGGTTCGGGTT
1 TTCGGTTCGGGTT
934765 AATTTTGATT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.03, C:0.11, G:0.33, T:0.52
Consensus pattern (16 bp):
TTCGGTTCGGGTTGTT
Found at i:936882 original size:21 final size:21
Alignment explanation
Indices: 936853--936893 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
936843 TAAAAGAGGA
*
936853 TGAAGAAGAAAGAAATGAAGG
1 TGAAGAAGAAAGAAAGGAAGG
* *
936874 TGAATAAGAACGAAAGGAAG
1 TGAAGAAGAAAGAAAGGAAG
936894 CATCGGCACT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.56, C:0.02, G:0.32, T:0.10
Consensus pattern (21 bp):
TGAAGAAGAAAGAAAGGAAGG
Found at i:936927 original size:35 final size:35
Alignment explanation
Indices: 936881--936948 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
936871 AGGTGAATAA
***
936881 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAGT
1 GAACGAAAGGAAGCATAAACACTTTCGATTCAAGT
936916 GAACGAAAGGAAGCATAAACACTTTCGATTCAA
1 GAACGAAAGGAAGCATAAACACTTTCGATTCAA
936949 TTGTTCATCT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.40, C:0.19, G:0.22, T:0.19
Consensus pattern (35 bp):
GAACGAAAGGAAGCATAAACACTTTCGATTCAAGT
Found at i:937534 original size:29 final size:28
Alignment explanation
Indices: 937485--937555 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 28
937475 TTTTTTTTTT
* * *
937485 TTGTAATTTATGAGAAATTTT-TTCTTTA
1 TTGTAATTTAT-AAAAATTTTGATATTTA
937513 CTTGTAATTTATAAAAAGTTTTGATATTTA
1 -TTGTAATTTATAAAAA-TTTTGATATTTA
937543 TTGTAATTTATAA
1 TTGTAATTTATAA
937556 TTATGTACAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 4 0.11
29 28 0.76
30 5 0.14
ACGTcount: A:0.34, C:0.03, G:0.10, T:0.54
Consensus pattern (28 bp):
TTGTAATTTATAAAAATTTTGATATTTA
Found at i:942179 original size:16 final size:15
Alignment explanation
Indices: 942142--942182 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
942132 TCGAAAGTTC
942142 CGGGTACCCGAAAAT
1 CGGGTACCCGAAAAT
942157 CGGGTACCCGAAAAT
1 CGGGTACCCGAAAAT
942172 CTGGGTACCCG
1 C-GGGTACCCG
942183 GATTTGCACA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.27, C:0.29, G:0.29, T:0.15
Consensus pattern (15 bp):
CGGGTACCCGAAAAT
Found at i:945746 original size:31 final size:31
Alignment explanation
Indices: 945664--945746 Score: 105
Period size: 31 Copynumber: 2.7 Consensus size: 31
945654 GGGCTTGAGA
* *
945664 GCCTACCCAAGAAAGTTCTCAGGGCCACAGG
1 GCCTACCCAAGAAAGATCTCGGGGCCACAGG
** *
945695 GAATACCCAAGAGAA-ATCTCGGGGCCGCAGG
1 GCCTACCCAAGA-AAGATCTCGGGGCCACAGG
945726 GCCTACCCAAGAAAGATCTCG
1 GCCTACCCAAGAAAGATCTCG
945747 AGGTAGCAGA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
30 2 0.05
31 39 0.91
32 2 0.05
ACGTcount: A:0.31, C:0.30, G:0.27, T:0.12
Consensus pattern (31 bp):
GCCTACCCAAGAAAGATCTCGGGGCCACAGG
Found at i:945761 original size:31 final size:31
Alignment explanation
Indices: 945698--945767 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
945688 CCACAGGGAA
* * *
945698 TACCCAAGAGAAATCTCGGGGCCGCAGGGCC
1 TACCCAAGAGAAATCTCGAGGCAGCAGAGCC
*
945729 TACCCAAGA-AAGATCTCGAGGTAGCAGAGCC
1 TACCCAAGAGAA-ATCTCGAGGCAGCAGAGCC
*
945760 TATCCAAG
1 TACCCAAG
945768 GGTCGCTTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
30 2 0.06
31 31 0.94
ACGTcount: A:0.31, C:0.29, G:0.27, T:0.13
Consensus pattern (31 bp):
TACCCAAGAGAAATCTCGAGGCAGCAGAGCC
Found at i:946626 original size:2 final size:2
Alignment explanation
Indices: 946619--946670 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
946609 GGATGGTAGA
946619 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
946661 AT AT AT AT AT
1 AT AT AT AT AT
946671 TCATTGGTGT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:952203 original size:131 final size:131
Alignment explanation
Indices: 951908--952273 Score: 376
Period size: 131 Copynumber: 2.8 Consensus size: 131
951898 ATGAAGAGTT
* * * ** * * * * *
951908 CTGGTCATCTAAGGGTGACAC-AGCTCCTAC-ATGATGAGGATATCTGGTCGGGGGATAACACGA
1 CTGGTTATCTAGGGGTGACACGA-CTACTACGA-GATGAGGAGGTATGGTCAGTGGATGACACGG
* * *
951971 TTCCTACGCGATGAGGATGACAGACCATCTTTAGGGAGGGTGATAACACGGTTCCTGCGCGATGA
64 TTCATACACGATGAGGATGACAGACCATCTTTAGGGA---TGATAACACGGTTCCTACGCGATGA
952036 GGACCA
126 GGACCA
* * * *
952042 CTGGTTATCTAGGGGTGACACGACTCCTACGAGATGAGGAGGTATGTTCGGTGGATGACATGGTT
1 CTGGTTATCTAGGGGTGACACGACTACTACGAGATGAGGAGGTATGGTCAGTGGATGACACGGTT
* * * * * * * **
952107 CATACATGATGAGGATGATAGACTATATTTAGGGATGATAACACGGTTTCTATGTGATGAGGATG
66 CATACACGATGAGGATGACAGACCATCTTTAGGGATGATAACACGGTTCCTACGCGATGAGGACC
952172 A
131 A
* * * * *
952173 CTTGTTATCTAGGGGTGACACGGCTACTACGTGATGAGGAGGTCTGGTCAGTGGATGACGCGGTT
1 CTGGTTATCTAGGGGTGACACGACTACTACGAGATGAGGAGGTATGGTCAGTGGATGACACGGTT
* *
952238 CCTACGCGATGAGGATGACAGACCATCTTTAGGGAT
66 CATACACGATGAGGATGACAGACCATCTTTAGGGAT
952274 TTGTTTCAAG
Statistics
Matches: 193, Mismatches: 37, Indels: 7
0.81 0.16 0.03
Matches are distributed among these distances:
131 111 0.58
134 80 0.41
135 2 0.01
ACGTcount: A:0.25, C:0.17, G:0.32, T:0.25
Consensus pattern (131 bp):
CTGGTTATCTAGGGGTGACACGACTACTACGAGATGAGGAGGTATGGTCAGTGGATGACACGGTT
CATACACGATGAGGATGACAGACCATCTTTAGGGATGATAACACGGTTCCTACGCGATGAGGACC
A
Found at i:952435 original size:64 final size:65
Alignment explanation
Indices: 952367--952540 Score: 201
Period size: 66 Copynumber: 2.7 Consensus size: 65
952357 TTAAAGATGG
* **
952367 GGTGTTTTAAGAGAAACTGTCTC-AAGAGAGACAAAATTTTGTTTA-TTAAACAAACTAAAAGAT
1 GGTGTTTCAAGAGAAACTGTCTCAAAG-GAGACAAAATTTTGTTTAGGGAAACAAACTAAAAGAT
952430 T
65 T
* * * * * *
952431 GGTGTTTCAAGAGAAACTGTTTTAAAGGAGACAAAACTTGTT-TTAAGGGAAACAGACTCAAAGT
1 GGTGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAA-TT-TTGTTTAGGGAAACAAACTAAAAGA
952495 TT
64 TT
* *
952497 GGTGTTTCAAGAGAAAATATCTCAAAGGAGACAAAATTTTGTTT
1 GGTGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAATTTTGTTT
952541 CAAGTAAAAA
Statistics
Matches: 91, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
64 31 0.34
65 12 0.13
66 48 0.53
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.30
Consensus pattern (65 bp):
GGTGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAATTTTGTTTAGGGAAACAAACTAAAAGATT
Found at i:953941 original size:13 final size:13
Alignment explanation
Indices: 953923--953970 Score: 62
Period size: 13 Copynumber: 3.8 Consensus size: 13
953913 TCTTTTGTTC
*
953923 TTTTTCCTTTGA-
1 TTTTTTCTTTGAT
*
953935 TTTTTTCTTTGCT
1 TTTTTTCTTTGAT
*
953948 TTTTTTCTTTTAT
1 TTTTTTCTTTGAT
953961 TTTTTTCTTT
1 TTTTTTCTTT
953971 ACTTTTATCC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
12 10 0.32
13 21 0.68
ACGTcount: A:0.04, C:0.12, G:0.04, T:0.79
Consensus pattern (13 bp):
TTTTTTCTTTGAT
Found at i:953952 original size:26 final size:26
Alignment explanation
Indices: 953923--953976 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
953913 TCTTTTGTTC
* *
953923 TTTTTCCTTTGA-TTTTTTCTTTGCT
1 TTTTTTCTTTGATTTTTTTCTTTACT
*
953948 TTTTTTCTTTTATTTTTTTCTTTACT
1 TTTTTTCTTTGATTTTTTTCTTTACT
953974 TTT
1 TTT
953977 ATCCTCACCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 10 0.40
26 15 0.60
ACGTcount: A:0.06, C:0.13, G:0.04, T:0.78
Consensus pattern (26 bp):
TTTTTTCTTTGATTTTTTTCTTTACT
Found at i:953976 original size:13 final size:13
Alignment explanation
Indices: 953935--953976 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
953925 TTTCCTTTGA
*
953935 TTTTTTCTTTGCT
1 TTTTTTCTTTACT
953948 TTTTTTCTTTTA-T
1 TTTTTTC-TTTACT
953961 TTTTTTCTTTACT
1 TTTTTTCTTTACT
953974 TTT
1 TTT
953977 ATCCTCACCT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
12 4 0.15
13 19 0.73
14 3 0.12
ACGTcount: A:0.05, C:0.12, G:0.02, T:0.81
Consensus pattern (13 bp):
TTTTTTCTTTACT
Found at i:959579 original size:3 final size:3
Alignment explanation
Indices: 959571--959614 Score: 65
Period size: 3 Copynumber: 15.0 Consensus size: 3
959561 CCTTTTTCTT
959571 TTA TTA TTA TTA TTA TT- TT- TTCA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA
959615 AATAAAAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 4 0.10
3 33 0.85
4 2 0.05
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:959598 original size:20 final size:19
Alignment explanation
Indices: 959569--959607 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
959559 TTCCTTTTTC
959569 TTTTATTATTATTATTATT
1 TTTTATTATTATTATTATT
959588 TTTTCATTATTATTATTATT
1 TTTT-ATTATTATTATTATT
959608 ATTATTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTTATTATTATTATTATT
Found at i:961201 original size:2 final size:2
Alignment explanation
Indices: 961194--961223 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
961184 ATATTCTGCT
961194 TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
961224 TATTTTTTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:961324 original size:155 final size:150
Alignment explanation
Indices: 960941--961380 Score: 424
Period size: 158 Copynumber: 2.8 Consensus size: 150
960931 GTTTAAATAA
* *
960941 TAATATTTATTTATTTTTAATATCAAAGAAAAGGACAGTCTTAAAGCAACTAGATGTTCTATTCT
1 TAATATTTATTTATTTTTAATATTAAAGAAAA-GACAGTCTTAAAGCAACTAGATG-TCTTTTCT
* * * * * * *
961006 GGTATTTTAAAAATAAATAAATA-TCTTACTTATAAAAACCAGAAAATACATATTTTTTTATTTA
64 GATATTTTAAAAATAAATAAATATTC-TACTTAT--AAA-C--TATATATATA-TATATTATATA
*
961070 AATTATTTTCTTAGGAAAATTATTATTTT
122 TATTATTTTCTTAGGAAAATTATTATTTT
* *
961099 TAATATTTATTTATTTTCCAAATATT-AAGAAATGACAGTCTTAAAGCAACTAGATGTCTTATTC
1 TAATATTTATTTATTTT--TAATATTAAAGAAAAGACAGTCTTAAAGCAACTAGATGTCTT-TTC
* * *
961163 TAATATTTTAAAAATAAATAAATATTCTGCTTATATA-TATATATATATATATTATATATATTAT
63 TGATATTTTAAAAATAAATAAATATTCTACTTATAAACTATATATATATATATTATATATATTAT
961227 TTT-TTAGGAAAATTATTATATTCTTAT
128 TTTCTTAGGAAAATTA-T-TA-T-TT-T
** * * *
961254 TAATATTTATTTATTTATTAATATTAAAGAAAAGACAGTCTTAAAATAATTGGATGTCCTTTTAT
1 TAATATTTATTTATTT-TTAATATTAAAGAAAAGACAGTCTTAAAGCAACTAGATGT-CTTTTCT
* * * *
961319 GATATTTGT--AAATAAATAAATGTCCTATTTACAAAACTATATATATATATATATATATATAT
64 GATATTT-TAAAAATAAATAAATATTCTACTTA-TAAACTATATATATATATAT-TATATATAT
961381 ATATATATTA
Statistics
Matches: 237, Mismatches: 29, Indels: 33
0.79 0.10 0.11
Matches are distributed among these distances:
150 12 0.05
151 17 0.07
152 9 0.04
153 1 0.00
154 26 0.11
155 54 0.23
156 22 0.09
157 12 0.05
158 71 0.30
159 8 0.03
160 5 0.02
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44
Consensus pattern (150 bp):
TAATATTTATTTATTTTTAATATTAAAGAAAAGACAGTCTTAAAGCAACTAGATGTCTTTTCTGA
TATTTTAAAAATAAATAAATATTCTACTTATAAACTATATATATATATATTATATATATTATTTT
CTTAGGAAAATTATTATTTT
Found at i:961363 original size:2 final size:2
Alignment explanation
Indices: 961356--961388 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
961346 TTTACAAAAC
961356 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 T
961389 TAATATTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:962819 original size:36 final size:36
Alignment explanation
Indices: 962772--962843 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
962762 GAGCTATGCA
* *
962772 CACAAAGATCCTATTATATTAATACCAAAAGTATTC
1 CACAAAGATCCTATTAGATTAATACCAAAAGCATTC
* *
962808 CACAAAGATCCTGTTAGATTGATACCAAAAGCATTC
1 CACAAAGATCCTATTAGATTAATACCAAAAGCATTC
962844 TATGGTAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.42, C:0.21, G:0.10, T:0.28
Consensus pattern (36 bp):
CACAAAGATCCTATTAGATTAATACCAAAAGCATTC
Found at i:963361 original size:43 final size:44
Alignment explanation
Indices: 963296--963382 Score: 131
Period size: 43 Copynumber: 2.0 Consensus size: 44
963286 TGGCTTTAGA
* * *
963296 GAAGTTAGGAGGGAAAGTTATCCCCTATATGT-AAAGTTTTGTT
1 GAAGTTAGGACGGAAAGCTATCCCCTACATGTAAAAGTTTTGTT
*
963339 GAAGTTAGGACTGAAAGCTATCCCCTACATGTAAAAGTTTTGTT
1 GAAGTTAGGACGGAAAGCTATCCCCTACATGTAAAAGTTTTGTT
963383 TGATGCACCA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
43 28 0.72
44 11 0.28
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (44 bp):
GAAGTTAGGACGGAAAGCTATCCCCTACATGTAAAAGTTTTGTT
Found at i:969399 original size:54 final size:54
Alignment explanation
Indices: 969280--969433 Score: 150
Period size: 54 Copynumber: 2.9 Consensus size: 54
969270 AAAATCTGTG
* * * * *
969280 CAGAAACAAC-AGAAAAAGATGAATGTGTTATCAAATGCTTTAAGAACATATGGC
1 CAGAAACCACAAG-AAAGGATGAATGTGTTATCAAATGCTTTACGAAAATACGGC
* * *
969334 CAGAAGCCACAAGAAAGGATGAATGTGTTATCAAAAGCTTTACGAAAATCCGTG-
1 CAGAAACCACAAGAAAGGATGAATGTGTTATCAAATGCTTTACGAAAATACG-GC
* * * * * *
969388 TAGAAATCACAAGAAATGATGAATTTGTTGTCAAATGTTTTACGAA
1 CAGAAACCACAAGAAAGGATGAATGTGTTATCAAATGCTTTACGAA
969434 CCAGTGATTA
Statistics
Matches: 82, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
54 79 0.96
55 3 0.04
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.25
Consensus pattern (54 bp):
CAGAAACCACAAGAAAGGATGAATGTGTTATCAAATGCTTTACGAAAATACGGC
Found at i:969823 original size:22 final size:22
Alignment explanation
Indices: 969793--969859 Score: 98
Period size: 22 Copynumber: 3.0 Consensus size: 22
969783 TATCTACATC
*
969793 TACATTCTTCAAAGATGATAGA
1 TACACTCTTCAAAGATGATAGA
969815 TACACTCTTCAAAGATGATAGA
1 TACACTCTTCAAAGATGATAGA
* * *
969837 TTCTCTTTTCAAAGATGATAGA
1 TACACTCTTCAAAGATGATAGA
969859 T
1 T
969860 TCTCTTTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.34
Consensus pattern (22 bp):
TACACTCTTCAAAGATGATAGA
Found at i:969860 original size:22 final size:22
Alignment explanation
Indices: 969800--969876 Score: 118
Period size: 22 Copynumber: 3.5 Consensus size: 22
969790 ATCTACATTC
* * *
969800 TTCAAAGATGATAGATACACTC
1 TTCAAAGATGATAGATTCTCTT
969822 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
969844 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
969866 TTTAAAGATGA
1 TTCAAAGATGA
969877 AAGCCTTATT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.36
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:970612 original size:45 final size:45
Alignment explanation
Indices: 970544--971290 Score: 1170
Period size: 45 Copynumber: 16.6 Consensus size: 45
970534 CTATTTCTCA
970544 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * **
970589 CATTTGTAAGTCCTTCAGTGCATGATGCATTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * *
970634 CATCTGTAATCTCTTCAGTGCATGATGTTTTCAAAACCTTCGGGC
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
970679 CATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
970724 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * * *
970769 CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAACCTTCAGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
970814 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
970859 CATCTGTAAGCCCTTCAATGCATGATGTTTTCAAAACCTTCAGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
970904 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGAGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
970949 CATCTGTATGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGAGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * * *
970994 CATCCGTAAGCCCTTTAGTGCATGATATTTTCAAAACCTTCAGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
971039 CATCTGTAAGTCCTTCAGTGCATGATATTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * *
971084 CATCTGTAAGCCCTTTAGTGCATGGTGTTTTCAAAACCATCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
971129 CATCTGTAAGCCTTTTAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
971174 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGAT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * *
971219 CATTTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTCCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * *
971264 CATCTGTAAGACCTACAGTGCAAGATG
1 CATCTGTAAGCCCTTCAGTGCATGATG
971291 ATAAGACCTT
Statistics
Matches: 643, Mismatches: 59, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 643 1.00
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.34
Consensus pattern (45 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
Found at i:971475 original size:3 final size:3
Alignment explanation
Indices: 971467--971527 Score: 81
Period size: 3 Copynumber: 20.0 Consensus size: 3
971457 CCTTTTTCTT
971467 TTA TTA TTA TTA TTA TTA TTAA TT- TT- TTCA TTA TTA TTA TTAA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TT-A TTA TTA TTA TT-A TTA
971513 TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
971528 AATAAAAAAT
Statistics
Matches: 54, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.07
3 42 0.78
4 8 0.15
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:975747 original size:17 final size:18
Alignment explanation
Indices: 975725--975759 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
975715 TCTAGTTGGC
*
975725 ATGTATATTTAT-ATGTG
1 ATGTATATATATAATGTG
975742 ATGTATATATATAATGTG
1 ATGTATATATATAATGTG
975760 TTAATGATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.49
Consensus pattern (18 bp):
ATGTATATATATAATGTG
Found at i:976092 original size:43 final size:42
Alignment explanation
Indices: 976039--976119 Score: 101
Period size: 42 Copynumber: 1.9 Consensus size: 42
976029 TTTATGGAAA
*
976039 AAAATGCCGCAATC-GGTCTAAATCTATAGCCGCGTTTTTTTAG
1 AAAACGCCGCAA-CAGGTC-AAATCTATAGCCGCGTTTTTTTAG
** *
976082 AAAACGCCGCAACAGGTCAGCTCTATAGCGGCGTTTTT
1 AAAACGCCGCAACAGGTCAAATCTATAGCCGCGTTTTT
976120 CGGAACAAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
42 18 0.55
43 15 0.45
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.28
Consensus pattern (42 bp):
AAAACGCCGCAACAGGTCAAATCTATAGCCGCGTTTTTTTAG
Found at i:976241 original size:111 final size:112
Alignment explanation
Indices: 976039--976247 Score: 264
Period size: 111 Copynumber: 1.9 Consensus size: 112
976029 TTTATGGAAA
* ** ** *
976039 AAAATGCCGCAATCGGTCTAAATCTATAGCCGCGTTTTTTTAGAAAACGCCGCAACAGGTCAGCT
1 AAAACGCCGCAAAAGGTCTAAATCTATAGCCGCGTTTTTGGAGAAAACGCCGCAACAGGTCAGAT
* *
976104 CTATAGCGGCGTTTTTCGGAACAAACGCCGCAATAAGTCGAGCTCCG
66 CTATAACGGCGTTTTTAGGAACAAACGCCGCAATAAGTCGAGCTCCG
* *
976151 AAAACGCCGCAAAAGGTC-AAATCTATAGCGGCGTTTTTGGA-ACAAACGCCGCAATAGGTCGAG
1 AAAACGCCGCAAAAGGTCTAAATCTATAGCCGCGTTTTTGGAGA-AAACGCCGCAACAGGTC-AG
*
976214 ATCTATAACGGCGTTTTCTATG-A-AAACGCCGCAA
64 ATCTATAACGGCGTTTT-TAGGAACAAACGCCGCAA
976248 AATGTCAGAT
Statistics
Matches: 83, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
110 1 0.01
111 47 0.57
112 33 0.40
113 2 0.02
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.22
Consensus pattern (112 bp):
AAAACGCCGCAAAAGGTCTAAATCTATAGCCGCGTTTTTGGAGAAAACGCCGCAACAGGTCAGAT
CTATAACGGCGTTTTTAGGAACAAACGCCGCAATAAGTCGAGCTCCG
Found at i:976271 original size:42 final size:40
Alignment explanation
Indices: 976150--976360 Score: 242
Period size: 42 Copynumber: 5.0 Consensus size: 40
976140 GTCGAGCTCC
*
976150 GAAAACGCCGCAAAAGGTCAAATCTATAGCGGCGTTTTTG
1 GAAAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTG
* * *
976190 GAACAAACGCCGCAATAGGTCGAGATCTATAACGGCGTTTTCTAT
1 G-A-AAACGCCGCAAAAGGTC-AGATCTATAGCGGCGTTTT-T-G
*
976235 GAAAACGCCGCAAAATGTCAGATCTATAGCGGCGTTTTTGG
1 GAAAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTT-G
* *
976276 AGAAAACGCTGCAAAAGGTCAGATTTATAGCGGCGTTTTTG
1 -GAAAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTG
* * **
976317 GAATAAACGTCGTAAAATTTCAGATCTATAGCGGCGTTTTTG
1 G-A-AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTG
976359 GA
1 GA
976361 TGCAAACGCC
Statistics
Matches: 145, Mismatches: 18, Indels: 15
0.81 0.10 0.08
Matches are distributed among these distances:
40 2 0.01
41 5 0.03
42 103 0.71
43 32 0.22
44 2 0.01
45 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (40 bp):
GAAAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTG
Found at i:976348 original size:84 final size:85
Alignment explanation
Indices: 976150--976372 Score: 283
Period size: 85 Copynumber: 2.6 Consensus size: 85
976140 GTCGAGCTCC
* * *
976150 GAAAACGCCGCAAAAGGTCAAATCTATAGCGGCGTTTTTGGA-ACAAACGCCGCAATAGGTCGAG
1 GAAAACGCCGCAAAATGTCAGATCTATAGCGGCGTTTTTGGAGA-AAACGCCGCAAAAGGTCGAG
*
976214 ATCTATAACGGCGTTTTCTAT
65 ATCTATAACGGCGTTTTCTAG
*
976235 GAAAACGCCGCAAAATGTCAGATCTATAGCGGCGTTTTTGGAGAAAACGCTGCAAAAGGTC-AGA
1 GAAAACGCCGCAAAATGTCAGATCTATAGCGGCGTTTTTGGAGAAAACGCCGCAAAAGGTCGAGA
* *
976299 TTTATAGCGGCGTTTT-T-G
66 TCTATAACGGCGTTTTCTAG
* * * *
976317 GAATAAACGTCGTAAAATTTCAGATCTATAGCGGCGTTTTTGGATGCAAACGCCGC
1 G-A-AAACGCCGCAAAATGTCAGATCTATAGCGGCGTTTTTGGA-GAAAACGCCGC
976373 TAATTATCGT
Statistics
Matches: 122, Mismatches: 12, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
82 1 0.01
83 2 0.02
84 54 0.44
85 64 0.52
86 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (85 bp):
GAAAACGCCGCAAAATGTCAGATCTATAGCGGCGTTTTTGGAGAAAACGCCGCAAAAGGTCGAGA
TCTATAACGGCGTTTTCTAG
Found at i:981102 original size:41 final size:41
Alignment explanation
Indices: 981048--981228 Score: 222
Period size: 41 Copynumber: 4.4 Consensus size: 41
981038 TTGTAAACAC
*
981048 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
1 AAACGCCGCTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
* * *
981089 AAATGCCGCTAAAGAACGTA-TCTATAGCGGCGTTTGAATAA
1 AAACGCCGCTAAAGTACG-AGTCTATAGCGGCGTTTGTATAA
* * * *
981130 AAACGCCACTAAAGTATGTGTCTATAGCGGCTTTTGTATAA
1 AAACGCCGCTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
* * * *
981171 AAACGCCGCTAAAGTACTACTCT-TTGCGGTGTTTGTATAAA
1 AAACGCCGCTAAAGTACGAGTCTATAGCGGCGTTTGTAT-AA
981212 AAACGCCGCTAAAGTAC
1 AAACGCCGCTAAAGTAC
981229 TACTCGGCGT
Statistics
Matches: 118, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
40 12 0.10
41 105 0.89
42 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (41 bp):
AAACGCCGCTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
Found at i:981214 original size:82 final size:82
Alignment explanation
Indices: 981048--981228 Score: 249
Period size: 82 Copynumber: 2.2 Consensus size: 82
981038 TTGTAAACAC
*
981048 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAATGCCGCTAAAGAACGTATCTA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCCGCTAAAGAACGTATCTA
981113 TAGCGGCGTTTGAATAA
66 TAGCGGCGTTTGAATAA
* * * *
981130 AAACGCCACTAAAGTATGTGTCTATAGCGGCTTTTGTATAAAAACGCCGCTAAAGTAC-TACTCT
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCCGCTAAAGAACGTA-TCT
* * *
981194 -TTGCGGTGTTTGTATAAA
65 ATAGCGGCGTTTGAAT-AA
*
981212 AAACGCCGCTAAAGTAC
1 AAACGCCACTAAAGTAC
981229 TACTCGGCGT
Statistics
Matches: 87, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
81 14 0.16
82 73 0.84
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (82 bp):
AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCCGCTAAAGAACGTATCTA
TAGCGGCGTTTGAATAA
Found at i:981289 original size:59 final size:68
Alignment explanation
Indices: 981194--981355 Score: 198
Period size: 59 Copynumber: 2.5 Consensus size: 68
981184 GTACTACTCT
* * *
981194 TTGCGGTGTTTGTATAAAAAACGCCGCTAAAGTACTAC-T-CGGCG-TT-T-T-AAAATGCCA-T
1 TTGCGGCGTTTGTAT-AAAAACGCCACTAAAGTACTACTTGCGGCGTTTGTATAAAAACGCCACT
*
981252 CCTA
65 ACTA
981256 TTGCGGCGTTT-TAT-AAAACGCCACTAAAGTACTACTATTGCGGCGTTTGTATAAAAACGCCAC
1 TTGCGGCGTTTGTATAAAAACGCCACTAAAGTACTAC--TTGCGGCGTTTGTATAAAAACGCCAC
981319 TACTA
64 TACTA
981324 TTGCGGCGTTTGTATAAAAACGCCACTAAAGT
1 TTGCGGCGTTTGTATAAAAACGCCACTAAAGT
981356 TGTGGTGTTT
Statistics
Matches: 85, Mismatches: 4, Indels: 14
0.83 0.04 0.14
Matches are distributed among these distances:
59 20 0.24
61 3 0.04
62 11 0.13
63 5 0.06
64 2 0.02
65 1 0.01
66 1 0.01
67 8 0.09
68 15 0.18
69 3 0.04
70 16 0.19
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (68 bp):
TTGCGGCGTTTGTATAAAAACGCCACTAAAGTACTACTTGCGGCGTTTGTATAAAAACGCCACTA
CTA
Found at i:981321 original size:31 final size:31
Alignment explanation
Indices: 981286--981351 Score: 132
Period size: 31 Copynumber: 2.1 Consensus size: 31
981276 CCACTAAAGT
981286 ACTACTATTGCGGCGTTTGTATAAAAACGCC
1 ACTACTATTGCGGCGTTTGTATAAAAACGCC
981317 ACTACTATTGCGGCGTTTGTATAAAAACGCC
1 ACTACTATTGCGGCGTTTGTATAAAAACGCC
981348 ACTA
1 ACTA
981352 AAGTTGTGGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (31 bp):
ACTACTATTGCGGCGTTTGTATAAAAACGCC
Found at i:983775 original size:54 final size:54
Alignment explanation
Indices: 983711--983877 Score: 282
Period size: 54 Copynumber: 3.1 Consensus size: 54
983701 TCTGTAACAC
*
983711 GTGCAACCCACGGAATTCATCATATGTTGATGAACGACCGTATAGACACTAAGT
1 GTGCAACCCACGGAATTCATCATATGTTGATGAACGACCGTATAGGCACTAAGT
*
983765 GTGCAACCCACGGAATTCATCATATGTTGATGAACGACTGTATAGGCACTAAGT
1 GTGCAACCCACGGAATTCATCATATGTTGATGAACGACCGTATAGGCACTAAGT
**
983819 GTGCAACCCACATAATTCATCATATGTTGATGAACGACCGTATAGGCACTACA-T
1 GTGCAACCCACGGAATTCATCATATGTTGATGAACGACCGTATAGGCACTA-AGT
983873 GTGCA
1 GTGCA
983878 TCTCAAAGAA
Statistics
Matches: 107, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
54 106 0.99
55 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.25
Consensus pattern (54 bp):
GTGCAACCCACGGAATTCATCATATGTTGATGAACGACCGTATAGGCACTAAGT
Found at i:985760 original size:29 final size:29
Alignment explanation
Indices: 985672--985776 Score: 140
Period size: 29 Copynumber: 3.6 Consensus size: 29
985662 GTTTTTCATT
*
985672 TAAGTACCTAAAGTA-TTTTTGGTCAAAA
1 TAAGTACTTAAAGTATTTTTTGGTCAAAA
* *
985700 TAAGAATTTAAAGTTATCTTTTTGGTCAAAA
1 TAAGTACTTAAAG-TAT-TTTTTGGTCAAAA
*
985731 TAAGTACTTAAAGTATTTTTTGATCAAAA
1 TAAGTACTTAAAGTATTTTTTGGTCAAAA
*
985760 TAGGTACTTAAAGTATT
1 TAAGTACTTAAAGTATT
985777 CAGTTGTTTT
Statistics
Matches: 67, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
28 10 0.15
29 30 0.45
30 3 0.04
31 24 0.36
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.40
Consensus pattern (29 bp):
TAAGTACTTAAAGTATTTTTTGGTCAAAA
Found at i:989637 original size:3 final size:3
Alignment explanation
Indices: 989629--989655 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
989619 CCTTTGATAG
989629 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
989656 TTGAAAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:992954 original size:159 final size:159
Alignment explanation
Indices: 992846--993150 Score: 522
Period size: 159 Copynumber: 1.9 Consensus size: 159
992836 GTATATAGTA
992846 ACACACTTGCTCAAAAGAAAGAAAAAAAAGATAACATACATGACACAATATATATATGGACAG-A
1 ACACACTTGCTCAAAAGAAAGAAAAAAAAGATAACATACATGACACAATATATATATGGACAGAA
*
992910 AAAAAAGATAACATATATAACACTTGGTCAAAAGAAAGAAAAAAAGATAACATACATGACACAAT
66 AAAAAAGATAACATATATAACACTTAGTCAAAAGAAAGAAAAAAAGATAACATACATGACACAAT
*
992975 ATATATATGTACAGAAAAAAAGATAACAT
131 ATATATATGAACAGAAAAAAAGATAACAT
* * * *
993004 ATACACTTGGTCAAAAGAAAGAAAAAAAAGATAACCTATATGACACAATATATATATGGACAGAA
1 ACACACTTGCTCAAAAGAAAGAAAAAAAAGATAACATACATGACACAATATATATATGGACAGAA
* *
993069 AAAAAAGATAACATATATAACACTTAGTCAAAAGAAAGAAAAAAAGATAACCTATATGACACAAT
66 AAAAAAGATAACATATATAACACTTAGTCAAAAGAAAGAAAAAAAGATAACATACATGACACAAT
*
993134 ATATATATGGACAGAAA
131 ATATATATGAACAGAAA
993151 TATGCATAAT
Statistics
Matches: 138, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
158 59 0.43
159 79 0.57
ACGTcount: A:0.57, C:0.12, G:0.12, T:0.19
Consensus pattern (159 bp):
ACACACTTGCTCAAAAGAAAGAAAAAAAAGATAACATACATGACACAATATATATATGGACAGAA
AAAAAAGATAACATATATAACACTTAGTCAAAAGAAAGAAAAAAAGATAACATACATGACACAAT
ATATATATGAACAGAAAAAAAGATAACAT
Found at i:992972 original size:80 final size:81
Alignment explanation
Indices: 992848--993150 Score: 499
Period size: 81 Copynumber: 3.8 Consensus size: 81
992838 ATATAGTAAC
*
992848 ACACTTGCTCAAAAGAAAGAAAAAAAAGATAACATACATGACACAATATATATATGGACAGAAAA
1 ACACTTGGTCAAAAGAAAGAAAAAAAAGATAACATACATGACACAATATATATATGGACAGAAAA
992913 AAAGATAACATATATA
66 AAAGATAACATATATA
*
992929 ACACTTGGTCAAAAGAAAG-AAAAAAAGATAACATACATGACACAATATATATATGTACAGAAAA
1 ACACTTGGTCAAAAGAAAGAAAAAAAAGATAACATACATGACACAATATATATATGGACAGAAAA
992993 AAAGATAAC--ATAT-
66 AAAGATAACATATATA
* *
993006 ACACTTGGTCAAAAGAAAGAAAAAAAAGATAACCTATATGACACAATATATATATGGACAGAAAA
1 ACACTTGGTCAAAAGAAAGAAAAAAAAGATAACATACATGACACAATATATATATGGACAG-AAA
993071 AAAAGATAACATATATA
65 AAAAGATAACATATATA
* * *
993088 ACACTTAGTCAAAAGAAAG-AAAAAAAGATAACCTATATGACACAATATATATATGGACAGAAA
1 ACACTTGGTCAAAAGAAAGAAAAAAAAGATAACATACATGACACAATATATATATGGACAGAAA
993151 TATGCATAAT
Statistics
Matches: 211, Mismatches: 6, Indels: 11
0.93 0.03 0.05
Matches are distributed among these distances:
77 19 0.09
78 42 0.20
79 13 0.06
80 56 0.27
81 63 0.30
82 18 0.09
ACGTcount: A:0.57, C:0.12, G:0.12, T:0.19
Consensus pattern (81 bp):
ACACTTGGTCAAAAGAAAGAAAAAAAAGATAACATACATGACACAATATATATATGGACAGAAAA
AAAGATAACATATATA
Found at i:994705 original size:20 final size:20
Alignment explanation
Indices: 994677--994731 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 20
994667 TCACGTACGA
* **
994677 AGTACCGATACTGTTTTTAC
1 AGTATCGATACTGTTTGAAC
* *
994697 AGTATCGATACTATATGAAC
1 AGTATCGATACTGTTTGAAC
*
994717 AATATCGATACTGTT
1 AGTATCGATACTGTT
994732 CATGTGGTAC
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (20 bp):
AGTATCGATACTGTTTGAAC
Found at i:996203 original size:87 final size:87
Alignment explanation
Indices: 996047--996205 Score: 196
Period size: 87 Copynumber: 1.8 Consensus size: 87
996037 GTCATATTAG
** * **
996047 GAAAATTTGACTCACTTCATTGCATCTTTAGGGTGTGTTGAATATGGGTCAATTTGCTTCACTGT
1 GAAAATTTGACTCACAACATTGCATCTTCAGGGTGTGTTGAATATGGGTCAATTTGCTTCACTAC
996112 AACTTCAAGATGGTCAGATTGA
66 AACTTCAAGATGGTCAGATTGA
* * ** *
996134 GAAAATTTGATTCACAACATTGCATCTTCATGGTAG-GTTGAATA-GGGATTGATTTGCTTCATT
1 GAAAATTTGACTCACAACATTGCATCTTCAGGGT-GTGTTGAATATGGG-TCAATTTGCTTCACT
996197 ACAACTTCA
64 ACAACTTCA
996206 GGAAGGTTAA
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
86 3 0.05
87 56 0.93
88 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.36
Consensus pattern (87 bp):
GAAAATTTGACTCACAACATTGCATCTTCAGGGTGTGTTGAATATGGGTCAATTTGCTTCACTAC
AACTTCAAGATGGTCAGATTGA
Found at i:1003900 original size:25 final size:24
Alignment explanation
Indices: 1003838--1003911 Score: 91
Period size: 24 Copynumber: 3.1 Consensus size: 24
1003828 AATAATGAAA
1003838 TAATTATTTTTTAACTTAAAATTA-
1 TAATTA-TTTTTAACTTAAAATTAT
*
1003862 T-ATTATTGTT-ACTTACAAATTAT
1 TAATTATTTTTAACTTA-AAATTAT
1003885 TAATTATTTTTAACTTAAAATTTAT
1 TAATTATTTTTAACTTAAAA-TTAT
1003910 TA
1 TA
1003912 TTGCTACATC
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
21 5 0.12
22 10 0.23
23 5 0.12
24 12 0.28
25 11 0.26
ACGTcount: A:0.39, C:0.05, G:0.01, T:0.54
Consensus pattern (24 bp):
TAATTATTTTTAACTTAAAATTAT
Found at i:1005891 original size:32 final size:32
Alignment explanation
Indices: 1005855--1005920 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
1005845 TTAATACTAG
1005855 TATTGATATTAGTATCAATACTACAAGAACAA
1 TATTGATATTAGTATCAATACTACAAGAACAA
* * *
1005887 TATTGATATTGGTATCGATACTACAAGAATAA
1 TATTGATATTAGTATCAATACTACAAGAACAA
1005919 TA
1 TA
1005921 GCGATAGTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (32 bp):
TATTGATATTAGTATCAATACTACAAGAACAA
Found at i:1012923 original size:18 final size:18
Alignment explanation
Indices: 1012902--1012957 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 18
1012892 TAATTTTGGC
1012902 ATCGATACTCAGACAAGT
1 ATCGATACTCAGACAAGT
**
1012920 ATCGATACCTCACCCTGAAGT
1 ATCGATA-CTCAGAC--AAGT
*
1012941 ATCGCTACTCAGACAAG
1 ATCGATACTCAGACAAG
1012958 AGTATTGATA
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
18 10 0.33
19 5 0.17
20 5 0.17
21 10 0.33
ACGTcount: A:0.34, C:0.29, G:0.16, T:0.21
Consensus pattern (18 bp):
ATCGATACTCAGACAAGT
Found at i:1013044 original size:20 final size:20
Alignment explanation
Indices: 1013021--1013070 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1013011 CAACATGTGG
1013021 GTATCGATACTAAA-GGTCTA
1 GTATCGATACTAAAGGGTC-A
*
1013041 GTATCGATAATAAAGGGTCA
1 GTATCGATACTAAAGGGTCA
*
1013061 ATATCGATAC
1 GTATCGATAC
1013071 CCCTGACAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 22 0.85
21 4 0.15
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (20 bp):
GTATCGATACTAAAGGGTCA
Found at i:1018131 original size:20 final size:19
Alignment explanation
Indices: 1018093--1018134 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
1018083 ATTCCACTAC
*
1018093 ATGCAACTAATGCTCCTAA
1 ATGCAACTAATGATCCTAA
*
1018112 ATGCATCTATATGATCCTAA
1 ATGCAACTA-ATGATCCTAA
1018132 ATG
1 ATG
1018135 GACTTTTAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.31
Consensus pattern (19 bp):
ATGCAACTAATGATCCTAA
Found at i:1023814 original size:20 final size:20
Alignment explanation
Indices: 1023777--1023819 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1023767 ATTCCACCAC
*
1023777 ATGCAACTACATGCTCCTAA
1 ATGCAACTACATGATCCTAA
* *
1023797 ATGCATCTATATGATCCTAA
1 ATGCAACTACATGATCCTAA
1023817 ATG
1 ATG
1023820 GGATCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.23, G:0.12, T:0.30
Consensus pattern (20 bp):
ATGCAACTACATGATCCTAA
Found at i:1027269 original size:18 final size:19
Alignment explanation
Indices: 1027246--1027288 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
1027236 TTGGTAACGG
1027246 TACTCAAGG-GAGTATCAA
1 TACTCAAGGAGAGTATCAA
*
1027264 TACTCAGGGTAGAGTATCAA
1 TACTCAAGG-AGAGTATCAA
1027284 TACTC
1 TACTC
1027289 TTGGTAGGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.36
20 14 0.64
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.26
Consensus pattern (19 bp):
TACTCAAGGAGAGTATCAA
Found at i:1027301 original size:21 final size:21
Alignment explanation
Indices: 1027254--1027302 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
1027244 GGTACTCAAG
1027254 GGAGTATCAATACTCAGGGTA
1 GGAGTATCAATACTCAGGGTA
**
1027275 -GAGTATCAATACTCTTGGTA
1 GGAGTATCAATACTCAGGGTA
1027295 GGAGTATC
1 GGAGTATC
1027303 GATATTGGGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 18 0.72
21 7 0.28
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.29
Consensus pattern (21 bp):
GGAGTATCAATACTCAGGGTA
Found at i:1030500 original size:22 final size:22
Alignment explanation
Indices: 1030475--1030577 Score: 98
Period size: 22 Copynumber: 4.5 Consensus size: 22
1030465 TTTTAAAATA
*
1030475 ATTTATTATAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
** *
1030497 ATTTATTTTAAAATAATTTATTTT
1 ATTTATTTTAAAAT-ATGGA-TTG
** * * *
1030521 AAATAATTTATTAGTATGGATTG
1 ATTTATTTTA-AAATATGGATTG
1030544 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
1030566 ATTTATTTTAAA
1 ATTTATTTTAAA
1030578 TAATTTATTA
Statistics
Matches: 61, Mismatches: 17, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
22 35 0.57
23 12 0.20
24 12 0.20
25 2 0.03
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.51
Consensus pattern (22 bp):
ATTTATTTTAAAATATGGATTG
Found at i:1030526 original size:14 final size:15
Alignment explanation
Indices: 1030430--1030532 Score: 109
Period size: 15 Copynumber: 6.5 Consensus size: 15
1030420 TAATAAGATT
1030430 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
**
1030445 ATTTATTACAAAATA
1 ATTTATTTTAAAATA
1030460 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
1030475 ATTTATTATAAAATATGGA
1 ATTTATT-TTAAA-AT--A
1030494 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
1030512 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
1030526 ATTTATT
1 ATTTATT
1030533 AGTATGGATT
Statistics
Matches: 75, Mismatches: 6, Indels: 15
0.78 0.06 0.16
Matches are distributed among these distances:
14 12 0.16
15 42 0.56
16 4 0.05
17 2 0.03
18 1 0.01
19 1 0.01
20 2 0.03
21 4 0.05
22 7 0.09
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:1030578 original size:54 final size:54
Alignment explanation
Indices: 1030512--1030728 Score: 358
Period size: 54 Copynumber: 4.1 Consensus size: 54
1030502 TTTTAAAATA
1030512 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1030566 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1030620 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* *
1030674 ATTTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTTTAAAATATGTATTG
1 ATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAAAATATGGATTG
1030722 ATTTATT
1 ATTTATT
1030729 ATTGTAGTTG
Statistics
Matches: 158, Mismatches: 2, Indels: 10
0.93 0.01 0.06
Matches are distributed among these distances:
48 39 0.25
49 2 0.01
50 2 0.01
52 2 0.01
54 113 0.72
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
Found at i:1030614 original size:22 final size:22
Alignment explanation
Indices: 1030589--1030728 Score: 91
Period size: 22 Copynumber: 5.7 Consensus size: 22
1030579 AATTTATTAG
1030589 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
1030611 TATGGATTGATTTATTTTAAATAA
1 TATGGATTGATTTATTTT-AA-AA
* * *
1030635 TTTATTAGTATGGATTGATTTATTTTAAAA
1 --TA-T-GGATTGATTTA-TT---TTAAAA
***
1030665 TATGGATTGATTTATTATTGTAGTTG
1 TATGGATTGATTTA-T-TT-TA-AAA
1030691 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
*
1030713 TATGTATTGATTTATT
1 TATGGATTGATTTATT
1030729 ATTGTAGTTG
Statistics
Matches: 92, Mismatches: 13, Indels: 26
0.70 0.10 0.20
Matches are distributed among these distances:
22 33 0.36
23 4 0.04
24 5 0.05
25 3 0.03
26 26 0.28
27 3 0.03
28 10 0.11
29 2 0.02
30 2 0.02
31 2 0.02
32 2 0.02
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:1030647 original size:108 final size:108
Alignment explanation
Indices: 1030460--1030728 Score: 359
Period size: 108 Copynumber: 2.6 Consensus size: 108
1030450 TTACAAAATA
* *
1030460 ATTTATTTTAAAATAATTTATTATAAAATATGGATTGATTTATTTT-AAA-AT-A---ATTTATT
1 ATTTATTTT-AAATAATTTAGT-T--AGTATGGATTGATTTATTTTAAAATATGATTGATTTATT
1030519 TTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
62 TTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1030566 ATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTA
1 ATTTATTTTAAATAATTTAGTTAGTATGGATTGATTTATTTTAAAATAT-GATTGATTTATTTTA
1030630 AATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
65 AATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
1030674 ATTTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTTTAAAATATGTATTGATTTATT
1 ATTTATTTTAAATAATTTAGTTAGTATGGATTGATTTATTTTAAAATATG-ATTGATTTATT
1030729 ATTGTAGTTG
Statistics
Matches: 152, Mismatches: 2, Indels: 22
0.86 0.01 0.12
Matches are distributed among these distances:
101 20 0.13
102 43 0.28
103 5 0.03
104 3 0.02
105 11 0.07
106 11 0.07
108 59 0.39
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (108 bp):
ATTTATTTTAAATAATTTAGTTAGTATGGATTGATTTATTTTAAAATATGATTGATTTATTTTAA
ATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
Found at i:1030702 original size:48 final size:48
Alignment explanation
Indices: 1030488--1030759 Score: 304
Period size: 54 Copynumber: 5.4 Consensus size: 48
1030478 TATTATAAAA
* *
1030488 TATGGATTGATTTATTTTAAAATA---ATTTATTTTAAATAATT-TATTAG
1 TATGGATTGATTTATTTTAAAATATGGATTGA-TTT--ATTATTGTATTAG
*
1030535 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTA--TT--AT--TGTATTAG
*
1030589 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTA--TT--AT--TGTATTAG
1030643 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTT-G
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTA-TTAG
*
1030691 TATGGATTGATTTATTTTAAAATATGTATTGATTTATTATTGTAGTT-G
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTA-TTAG
1030739 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
1030760 TAATTTATTA
Statistics
Matches: 210, Mismatches: 4, Indels: 21
0.89 0.02 0.09
Matches are distributed among these distances:
47 25 0.12
48 72 0.34
49 6 0.03
50 6 0.03
51 2 0.01
52 2 0.01
53 1 0.00
54 96 0.46
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (48 bp):
TATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTATTAG
Found at i:1030711 original size:80 final size:78
Alignment explanation
Indices: 1030611--1030979 Score: 310
Period size: 80 Copynumber: 4.7 Consensus size: 78
1030601 TATTTTAAAA
1030611 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATT-GTATGGATTGATTTATTTTAAAATATGGATTGAT
1030676 TTATTATTGTAGTTG
65 TTATTATTGTA-TTG
* * * ***
1030691 TATGGATTGATTTATTTT-AA-AA--TA-TGTATTGATTTA-TTATTGTAGTTGTATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTGTATGGATTGATTTATTTTA-AAATATGGATTGAT
*
1030750 TTATTTTAAATAATTTATTAG
65 TTA--TT--AT--TGTATT-G
* ** * * * ** * * *
1030771 TATAGATTGATTTATTTTAAA-ATATGGATTGAAT-TATTTTAAATAATTTATTAGTATGGATTG
1 TATGGATTGATTTATTTTAAATA-ATTTATTGTATGGA-TTGATTTATTTTA-AAATATGGATTG
***
1030834 ATTTA-T-TT-TAAAA
63 ATTTATTATTGTATTG
* *
1030847 TATGGATTGATTTATTTTAAATAATTTATTTGTATTGATTGATTTATTTTAAAATATGGATTAAT
1 TATGGATTGATTTATTTTAAATAATTTA-TTGTATGGATTGATTTATTTTAAAATATGGATTGAT
1030912 TTATTATTGTAGTTG
65 TTATTATTGTA-TTG
1030927 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAATAATTTATT-GTATGGATTGATTTATTTTAAA
1030980 TAATTTATTA
Statistics
Matches: 231, Mismatches: 35, Indels: 46
0.74 0.11 0.15
Matches are distributed among these distances:
73 7 0.03
74 23 0.10
75 1 0.00
76 41 0.18
77 18 0.08
78 8 0.03
79 8 0.03
80 89 0.39
81 3 0.01
82 1 0.00
83 1 0.00
84 2 0.01
85 8 0.03
86 21 0.09
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (78 bp):
TATGGATTGATTTATTTTAAATAATTTATTGTATGGATTGATTTATTTTAAAATATGGATTGATT
TATTATTGTATTG
Found at i:1030740 original size:22 final size:22
Alignment explanation
Indices: 1030673--1030746 Score: 76
Period size: 22 Copynumber: 3.2 Consensus size: 22
1030663 AATATGGATT
1030673 GATTTATTATTGTAGTTGTATG
1 GATTTATTATTGTAGTTGTATG
* * * *
1030695 GATTGATTTATTTTAAAATATGTATT
1 GATTTA-TTATTGT--AGT-TGTATG
1030721 GATTTATTATTGTAGTTGTATG
1 GATTTATTATTGTAGTTGTATG
1030743 GATT
1 GATT
1030747 GATTTATTTT
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
22 14 0.35
23 8 0.20
25 8 0.20
26 10 0.25
ACGTcount: A:0.27, C:0.00, G:0.19, T:0.54
Consensus pattern (22 bp):
GATTTATTATTGTAGTTGTATG
Found at i:1030808 original size:54 final size:54
Alignment explanation
Indices: 1030739--1030912 Score: 296
Period size: 54 Copynumber: 3.2 Consensus size: 54
1030729 ATTGTAGTTG
*
1030739 TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAA
1 TATGGATTGAATTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAA
*
1030793 TATGGATTGAATTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGAATTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAA
* * *
1030847 TATGGATTGATTTATTTTAAATAATTTATTTGTATTGATTGATTTATTTTAAAA
1 TATGGATTGAATTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAA
1030901 TATGGATT-AATT
1 TATGGATTGAATT
1030913 TATTATTGTA
Statistics
Matches: 114, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
53 3 0.03
54 111 0.97
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (54 bp):
TATGGATTGAATTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAA
Found at i:1030811 original size:236 final size:236
Alignment explanation
Indices: 1030512--1030947 Score: 827
Period size: 236 Copynumber: 1.8 Consensus size: 236
1030502 TTTTAAAATA
* *
1030512 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGAATTATTTTAA
1030577 ATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTA
66 ATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTA
*
1030642 GTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATT
131 GTATGGATTGATTTATTTTAAAATATGGATTAATTTATTATTGTAGTTGTATGGATTGATTTATT
1030707 TTAAAATATGTATTGATTTATTATTGTAGTTGTATGGATTG
196 TTAAAATATGTATTGATTTATTATTGTAGTTGTATGGATTG
1030748 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGAATTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGAATTATTTTAA
*
1030813 ATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTT
66 ATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTA
*
1030878 GTATTGATTGATTTATTTTAAAATATGGATTAATTTATTATTGTAGTTGTATGGATTGATTTATT
131 GTATGGATTGATTTATTTTAAAATATGGATTAATTTATTATTGTAGTTGTATGGATTGATTTATT
1030943 TTAAA
196 TTAAA
1030948 TAATTTATTA
Statistics
Matches: 195, Mismatches: 5, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
236 195 1.00
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.53
Consensus pattern (236 bp):
ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGAATTATTTTAA
ATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTA
GTATGGATTGATTTATTTTAAAATATGGATTAATTTATTATTGTAGTTGTATGGATTGATTTATT
TTAAAATATGTATTGATTTATTATTGTAGTTGTATGGATTG
Found at i:1030850 original size:22 final size:22
Alignment explanation
Indices: 1030825--1030867 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1030815 AATTTATTAG
1030825 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
1030847 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
1030868 TAATTTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:1030866 original size:108 final size:102
Alignment explanation
Indices: 1030739--1030947 Score: 312
Period size: 108 Copynumber: 2.0 Consensus size: 102
1030729 ATTGTAGTTG
1030739 TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATT-AA
* *
1030804 TTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAAAA
65 TT-TATT--AT--TGTAGTT-GTATGGATTGATTTATTTTAAAA
* *
1030847 TATGGATTGATTTATTTTAAATAATTTATTTGTATTGATTGATTTATTTTAAAATATGGATTAAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTAAT
1030912 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAA
66 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAA
1030948 TAATTTATTA
Statistics
Matches: 96, Mismatches: 4, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
102 25 0.26
103 2 0.02
104 2 0.02
106 3 0.03
107 4 0.04
108 60 0.62
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (102 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTAAT
TTATTATTGTAGTTGTATGGATTGATTTATTTTAAAA
Found at i:1030967 original size:32 final size:32
Alignment explanation
Indices: 1030926--1030989 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
1030916 TATTGTAGTT
1030926 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
1030958 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
1030990 TTGTAGTCGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.53
Consensus pattern (32 bp):
GTATGGATTGATTTATTTTAAATAATTTATTA
Found at i:1046788 original size:16 final size:16
Alignment explanation
Indices: 1046767--1046802 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
1046757 GAATCTAAAA
1046767 TGAATATAATATGATC
1 TGAATATAATATGATC
1046783 TGAATATAATATGATC
1 TGAATATAATATGATC
1046799 TGAA
1 TGAA
1046803 AGCCCATTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.44, C:0.06, G:0.14, T:0.36
Consensus pattern (16 bp):
TGAATATAATATGATC
Found at i:1058126 original size:19 final size:21
Alignment explanation
Indices: 1058089--1058136 Score: 64
Period size: 19 Copynumber: 2.4 Consensus size: 21
1058079 TAAAAGCTAT
1058089 ATATTTTTTACTCGTAAATGA
1 ATATTTTTTACTCGTAAATGA
*
1058110 ATATTTTTTA-TCG-AAATTA
1 ATATTTTTTACTCGTAAATGA
*
1058129 ATGTTTTT
1 ATATTTTT
1058137 ATGGGAAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 12 0.48
20 3 0.12
21 10 0.40
ACGTcount: A:0.31, C:0.06, G:0.08, T:0.54
Consensus pattern (21 bp):
ATATTTTTTACTCGTAAATGA
Found at i:1060075 original size:13 final size:14
Alignment explanation
Indices: 1060057--1060092 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1060047 AGTCAACATT
1060057 GTATGATTT-TAAA
1 GTATGATTTCTAAA
*
1060070 GTATGATTTCTAAC
1 GTATGATTTCTAAA
1060084 GTATGATTT
1 GTATGATTT
1060093 AATTTTGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.31, C:0.06, G:0.17, T:0.47
Consensus pattern (14 bp):
GTATGATTTCTAAA
Found at i:1063571 original size:19 final size:19
Alignment explanation
Indices: 1063559--1063602 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1063549 TAAAATCATT
*
1063559 TATTAACCCTAAATTAAAA
1 TATTAACCCTAAAATAAAA
* *
1063578 TATTAACCCTAAACTAAGA
1 TATTAACCCTAAAATAAAA
1063597 TATTAA
1 TATTAA
1063603 TATTAAAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.50, C:0.16, G:0.02, T:0.32
Consensus pattern (19 bp):
TATTAACCCTAAAATAAAA
Found at i:1063663 original size:60 final size:60
Alignment explanation
Indices: 1063553--1063671 Score: 141
Period size: 60 Copynumber: 2.0 Consensus size: 60
1063543 TAACTTTAAA
* ** *
1063553 ATCATTTATTAACCCTAAATTAAAATATTAACCCTAAACTAAGATATTAATATTAAAATC
1 ATCATTTAGTAACCCTAAACCAAAATATTAACCCTAAACTAAGATATTAATAGTAAAATC
* * * * *
1063613 ATCATTTAGTAACCCTAAACCAAAATGTTAATCTTAAA-TCGAGATTTTAATAGTAAAAT
1 ATCATTTAGTAACCCTAAACCAAAATATTAACCCTAAACT-AAGATATTAATAGTAAAAT
1063672 TGTTTGTTAA
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
59 1 0.02
60 48 0.98
ACGTcount: A:0.46, C:0.14, G:0.05, T:0.34
Consensus pattern (60 bp):
ATCATTTAGTAACCCTAAACCAAAATATTAACCCTAAACTAAGATATTAATAGTAAAATC
Found at i:1063741 original size:19 final size:19
Alignment explanation
Indices: 1063691--1063741 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
1063681 ATCCAAACCT
* * *
1063691 TAAATATTAATCATAATCC
1 TAAATATTAACCCTAATAC
*
1063710 CAAATATTAACCCTAATAC
1 TAAATATTAACCCTAATAC
1063729 TAAATATTAACCC
1 TAAATATTAACCC
1063742 CAAATCATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (19 bp):
TAAATATTAACCCTAATAC
Found at i:1064573 original size:456 final size:456
Alignment explanation
Indices: 1063953--1064867 Score: 1776
Period size: 456 Copynumber: 2.0 Consensus size: 456
1063943 ATGATAAAAT
1063953 AACTTTTAATGTACACATGGAACCACCTTTAGCCAATAACAATCATATCAGTTTCGTCGTTTGGC
1 AACTTTTAATGTACACATGGAACCACCTTTAGCCAATAACAATCATATCAGTTTCGTCGTTTGGC
1064018 CTTTAACGACAAGTAGTTATATTGAACCCAATTAATTAGTTAAGTGATTATATTGATAAAAATTT
66 CTTTAACGACAAGTAGTTATATTGAACCCAATTAATTAGTTAAGTGATTATATTGATAAAAATTT
1064083 GAAAACGGTAGTCATTTCCAAATCAACTCCATAATAGGGTGTTCATTCAAGTAGTTAACCCCTTT
131 GAAAACGGTAGTCATTTCCAAATCAACTCCATAATAGGGTGTTCATTCAAGTAGTTAACCCCTTT
1064148 TAAATAGTGGTGTTTAATCAAAATTTTGCCCTAATTGCAATAGTGATCTGAAAATTTTAAGGGTA
196 TAAATAGTGGTGTTTAATCAAAATTTTGCCCTAATTGCAATAGTGATCTGAAAATTTTAAGGGTA
1064213 AAATACACTATGGTCCTCTAATTATAGGGTATTATTTTGTTGAGTCCCTTGACAATTAAAAGTTA
261 AAATACACTATGGTCCTCTAATTATAGGGTATTATTTTGTTGAGTCCCTTGACAATTAAAAGTTA
*
1064278 CAAAATAATTATATGATTATAGGATGTTTTGTTGAGTCCTCCTAACTATTAAAAATTATAAAATG
326 CAAAATAATTATATGATTATAGGATGTTTTGTTGAGTCCTCCTAACTATTAAAAATTATAAAATA
* *
1064343 GTTATTTGACTATTCATATGTTCAAAACTTGTCATTTTGTTAAAAAGTAGATGGGTATATGAACT
391 GTTATTTGACTATTCATATGTTCAAAACTTGTCATTTTGTTAAAAAGTAGACGAGTATATGAACT
1064408 A
456 A
*
1064409 AACTTTTAATGTACACATGGAACCACCTTTAGCCAATAACAATCATATCATTTTCGTCGTTTGGC
1 AACTTTTAATGTACACATGGAACCACCTTTAGCCAATAACAATCATATCAGTTTCGTCGTTTGGC
1064474 CTTTAACGACAAGTAGTTATATTGAACCCAATTAATTAGTTAAGTGATTATATTGATAAAAATTT
66 CTTTAACGACAAGTAGTTATATTGAACCCAATTAATTAGTTAAGTGATTATATTGATAAAAATTT
1064539 GAAAACGGTAGTCATTTCCAAATCAACTCCATAATAGGGTGTTCATTCAAGTAGTTAACCCCTTT
131 GAAAACGGTAGTCATTTCCAAATCAACTCCATAATAGGGTGTTCATTCAAGTAGTTAACCCCTTT
1064604 TAAATAGTGGTGTTTAATCAAAATTTTGCCCTAATTGCAATAGTGATCTGAAAATTTTAAGGGTA
196 TAAATAGTGGTGTTTAATCAAAATTTTGCCCTAATTGCAATAGTGATCTGAAAATTTTAAGGGTA
1064669 AAATACACTATGGTCCTCTAATTATAGGGTATTATTTTGTTGAGTCCCTTGACAATTAAAAGTTA
261 AAATACACTATGGTCCTCTAATTATAGGGTATTATTTTGTTGAGTCCCTTGACAATTAAAAGTTA
1064734 CAAAATAATTATATGATTATAGGATGTTTTGTTGAGTCCTCCTAACTATTAAAAATTATAAAATA
326 CAAAATAATTATATGATTATAGGATGTTTTGTTGAGTCCTCCTAACTATTAAAAATTATAAAATA
* *
1064799 GTTATTTGACTATTTATATGTTCAAAACTTGTCATTTTGTTAAAAAGTATACGAGTATATGAACT
391 GTTATTTGACTATTCATATGTTCAAAACTTGTCATTTTGTTAAAAAGTAGACGAGTATATGAACT
1064864 A
456 A
1064865 AAC
1 AAC
1064868 ATTAGCTTGT
Statistics
Matches: 453, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
456 453 1.00
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (456 bp):
AACTTTTAATGTACACATGGAACCACCTTTAGCCAATAACAATCATATCAGTTTCGTCGTTTGGC
CTTTAACGACAAGTAGTTATATTGAACCCAATTAATTAGTTAAGTGATTATATTGATAAAAATTT
GAAAACGGTAGTCATTTCCAAATCAACTCCATAATAGGGTGTTCATTCAAGTAGTTAACCCCTTT
TAAATAGTGGTGTTTAATCAAAATTTTGCCCTAATTGCAATAGTGATCTGAAAATTTTAAGGGTA
AAATACACTATGGTCCTCTAATTATAGGGTATTATTTTGTTGAGTCCCTTGACAATTAAAAGTTA
CAAAATAATTATATGATTATAGGATGTTTTGTTGAGTCCTCCTAACTATTAAAAATTATAAAATA
GTTATTTGACTATTCATATGTTCAAAACTTGTCATTTTGTTAAAAAGTAGACGAGTATATGAACT
A
Found at i:1090085 original size:13 final size:13
Alignment explanation
Indices: 1090067--1090093 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1090057 GACCTGTTAT
1090067 ATAAAATTATTTA
1 ATAAAATTATTTA
1090080 ATAAAATTATTTA
1 ATAAAATTATTTA
1090093 A
1 A
1090094 ATGTAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATAAAATTATTTA
Found at i:1090103 original size:15 final size:14
Alignment explanation
Indices: 1090067--1090109 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
1090057 GACCTGTTAT
1090067 ATAAAATTATTT-A
1 ATAAAATTATTTAA
1090080 ATAAAATTATTTAA
1 ATAAAATTATTTAA
* *
1090094 ATGTAAATTATATAA
1 AT-AAAATTATTTAA
1090109 A
1 A
1090110 ACATGATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 12 0.46
14 3 0.12
15 11 0.42
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (14 bp):
ATAAAATTATTTAA
Done.