Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007731.1 Hibiscus syriacus cultivar Beakdansim tig00109983_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: 835416
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:646350 original size:107 final size:106
Alignment explanation
Indices: 646164--646490 Score: 411
Period size: 107 Copynumber: 3.0 Consensus size: 106
646154 CTAAACAATA
* * * * *
646164 TGATGTTTTCAAATGAATTTTGAAAGAAGCTAAGCATGATTTTCAGGGCTTTCTTGATGTATTCA
1 TGATGTTTTCAAATGAATTTTGAAAGGAGCTAAGCCTGATTTTCAGGGGTTTCTTGATGTTTTTA
*
646229 AATGAATTTTGAAAGAAACTAAGCCTGATTTTTAGGGTTTCT
66 AATGAATTTTGAAAGAAACTAAGCCT-AATTTTAGGGTTTCT
* * * * * *
646271 TGATGTCTTCAAATAAATTTTGAAAGGAGTTAAACCTAATTTTCAGGGGTTTCTTAATGTTTTTA
1 TGATGTTTTCAAATGAATTTTGAAAGGAGCTAAGCCTGATTTTCAGGGGTTTCTTGATGTTTTTA
* * *
646336 AATGAATTTAGAAAGGAGCTAAGCCTAACTTTTAGGAGTTTCT
66 AATGAATTTTGAAAGAAACTAAGCCTAA-TTTTAGG-GTTTCT
* * * *
646379 TGATGTTTTTAAATGAATTTTGAAAGGAGCTAAGCCTGATTTTAAGGAGTTACTTGATGTTTTTA
1 TGATGTTTTCAAATGAATTTTGAAAGGAGCTAAGCCTGATTTTCAGGGGTTTCTTGATGTTTTTA
* * *
646444 AATGGATTTTTGAAAGAATCTAAGCCTTATTTTAGGGGTTTCT
66 AAT-GAATTTTGAAAGAAACTAAGCCTAATTTTA-GGGTTTCT
646487 TGAT
1 TGAT
646491 AACTGTAAAT
Statistics
Matches: 186, Mismatches: 30, Indels: 7
0.83 0.13 0.03
Matches are distributed among these distances:
106 1 0.01
107 84 0.45
108 79 0.42
109 22 0.12
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (106 bp):
TGATGTTTTCAAATGAATTTTGAAAGGAGCTAAGCCTGATTTTCAGGGGTTTCTTGATGTTTTTA
AATGAATTTTGAAAGAAACTAAGCCTAATTTTAGGGTTTCT
Found at i:646501 original size:54 final size:54
Alignment explanation
Indices: 646164--646490 Score: 381
Period size: 54 Copynumber: 6.1 Consensus size: 54
646154 CTAAACAATA
* * *
646164 TGATGTTTTCAAATGAATTTTGAAAGAAGCTAAGCATGATTTTCAGGGCTTTCT
1 TGATGTTTTTAAATGAATTTTGAAAGAAGCTAAGCCTGATTTTCAGGGGTTTCT
* * * *
646218 TGATGTATTCAAATGAATTTTGAAAGAAACTAAGCCTGATTTTTA-GGGTTTCT
1 TGATGTTTTTAAATGAATTTTGAAAGAAGCTAAGCCTGATTTTCAGGGGTTTCT
* * * * * * *
646271 TGATGTCTTCAAATAAATTTTGAAAGGAGTTAAACCTAATTTTCAGGGGTTTCT
1 TGATGTTTTTAAATGAATTTTGAAAGAAGCTAAGCCTGATTTTCAGGGGTTTCT
* * * * *
646325 TAATGTTTTTAAATGAATTTAGAAAGGAGCTAAGCCTAACTTTT-AGGAGTTTCT
1 TGATGTTTTTAAATGAATTTTGAAAGAAGCTAAGCCTGA-TTTTCAGGGGTTTCT
* * * *
646379 TGATGTTTTTAAATGAATTTTGAAAGGAGCTAAGCCTGATTTTAAGGAGTTACT
1 TGATGTTTTTAAATGAATTTTGAAAGAAGCTAAGCCTGATTTTCAGGGGTTTCT
* * *
646433 TGATGTTTTTAAATGGATTTTTGAAAGAATCTAAGCCTTATTTT-AGGGGTTTCT
1 TGATGTTTTTAAAT-GAATTTTGAAAGAAGCTAAGCCTGATTTTCAGGGGTTTCT
646487 TGAT
1 TGAT
646491 AACTGTAAAT
Statistics
Matches: 238, Mismatches: 31, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
53 48 0.20
54 161 0.68
55 29 0.12
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (54 bp):
TGATGTTTTTAAATGAATTTTGAAAGAAGCTAAGCCTGATTTTCAGGGGTTTCT
Found at i:647404 original size:91 final size:91
Alignment explanation
Indices: 647242--647594 Score: 562
Period size: 91 Copynumber: 3.9 Consensus size: 91
647232 CCAACCAAAA
*
647242 TTTCCAGTGGATAGTTCATAATGAGAAGAACTCATCCAATGAGGGAGAAGAAGTTCATAATGAGA
1 TTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGGAGAAGAAGTTCATAATGAGA
*
647307 ATAACTTGTTCAACCTTTGCTCAACG
66 AGAACTTGTTCAACCTTTGCTCAACG
* * ** * *
647333 TTTCTAGTGGAGAGTTAATAATGAGAAGAACTCATCCAACAATGGAGAAGAAGTTCATAATTAGA
1 TTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGGAGAAGAAGTTCATAATGAGA
* *
647398 AGAACTTGTTCAACCCTTGTTCAACG
66 AGAACTTGTTCAACCTTTGCTCAACG
* *
647424 TTTCCAGTGGAGAGTTCATAATGAGGAGAACTCATCTAATGAGGGAGAAGAAGTTCATAATGAGA
1 TTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGGAGAAGAAGTTCATAATGAGA
* * *
647489 AAAACTTGTTCAACCTTGGCTCAACA
66 AGAACTTGTTCAACCTTTGCTCAACG
*
647515 TTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGA
1 TTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGGAGAAGAAGTTCATAATGAGA
647580 AGAACTTGTTCAACC
66 AGAACTTGTTCAACC
647595 ATAGCTCGAT
Statistics
Matches: 235, Mismatches: 27, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
91 235 1.00
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (91 bp):
TTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGGAGAAGAAGTTCATAATGAGA
AGAACTTGTTCAACCTTTGCTCAACG
Found at i:647782 original size:117 final size:116
Alignment explanation
Indices: 647646--647993 Score: 482
Period size: 117 Copynumber: 3.0 Consensus size: 116
647636 TCACTCGAGG
* * *
647646 GATCAACATTTCCAATGGAGAATTAATAATGAGAAGAACTCATCCAATGAGGGAGAAGAAGTTCA
1 GATCAACATTTCCAGTGGAGAATTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCA
* * * *
647711 TAATGAGAAGAAATTGTTCAACATTGGTTAAATTCCATCACAGAAGAAGGTA
66 TAATGAGAAGAACTTGTTCAACCTTGGTT-GATTCCATCACAGAAGGAGGTA
* * * * *
647763 GATCAACATTTCTAGTGGAGATTTCATAATGAGAGGAACTCATCCAACGACGAAGAAGAAGTTCA
1 GATCAACATTTCCAGTGGAGAATTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCA
* * *
647828 TAATGAGAATAACTTGTTCAACCTTGGTTCGATTCTATCACAGAAGGAGGTG
66 TAATGAGAAGAACTTGTTCAACCTTGGTT-GATTCCATCACAGAAGGAGGTA
* ** * **
647880 GATCAACATTTCCAGTAGAGAGCTCATAATGAGAAAAACTCATCTGACGAGGGAGAAGAAGTTCA
1 GATCAACATTTCCAGTGGAGAATTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCA
647945 TAATGAGAAGAACTTGTTCAACCTTGG-TGATTCCATCACAGAAGGAGGT
66 TAATGAGAAGAACTTGTTCAACCTTGGTTGATTCCATCACAGAAGGAGGT
647994 GGATTGACAT
Statistics
Matches: 203, Mismatches: 28, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
115 20 0.10
116 1 0.00
117 182 0.90
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.24
Consensus pattern (116 bp):
GATCAACATTTCCAGTGGAGAATTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCA
TAATGAGAAGAACTTGTTCAACCTTGGTTGATTCCATCACAGAAGGAGGTA
Found at i:651133 original size:137 final size:137
Alignment explanation
Indices: 650886--651137 Score: 350
Period size: 137 Copynumber: 1.8 Consensus size: 137
650876 TGAAATCTTG
* *
650886 GGCTCTAATATTAACTTAAATTAATTTTAATCAATATCGCAATTCGAATAATTGAAGTGGAACCT
1 GGCTCTAATATTAACCTAAATTAATTTTAATCAATATCG-AATTCAAATAATTGAAGTGGAACCT
* *** * *
650951 CGATCAAAAGGGAGGACCAAATTAAGAATTCTCCTAATTTAAGGACTAAATACGAAATTAGGCCT
65 CGAGCAAAAACAAGGACCAAATAAAGAATTCACCTAATTTAAGGACTAAATACGAAATTAGGCCT
651016 AAGATGGA
130 AAGATGGA
*
651024 GGCTCTAATATTAATCCT-AATTAATTTTAATCAATTATACG-A-TCAAATAATT-AATTTGGAA
1 GGCTCTAATATTAA-CCTAAATTAATTTTAATCAA-TAT-CGAATTCAAATAATTGAA-GTGGAA
651085 CCTCGAGCAAAAACAAGGACCAAATAAAGAATTCACCTAATTTAAGGACTAAA
62 CCTCGAGCAAAAACAAGGACCAAATAAAGAATTCACCTAATTTAAGGACTAAA
651138 CCTAAAATAA
Statistics
Matches: 101, Mismatches: 9, Indels: 9
0.85 0.08 0.08
Matches are distributed among these distances:
136 2 0.02
137 61 0.60
138 31 0.31
139 5 0.05
140 2 0.02
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (137 bp):
GGCTCTAATATTAACCTAAATTAATTTTAATCAATATCGAATTCAAATAATTGAAGTGGAACCTC
GAGCAAAAACAAGGACCAAATAAAGAATTCACCTAATTTAAGGACTAAATACGAAATTAGGCCTA
AGATGGA
Found at i:656538 original size:3 final size:3
Alignment explanation
Indices: 656519--656606 Score: 60
Period size: 3 Copynumber: 29.3 Consensus size: 3
656509 TTGTCCGGAA
* *
656519 TAT TAT TAA TAT CTAT TAT TAT TAT TAT T-T ATAT TAC TAT TAT TAT
1 TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT
* *
656565 TAT CT-T TAT TA- TAT GTA- TAT GTA- TAT TTT TAT TTT TAT TAT T
1 TAT -TAT TAT TAT TAT -TAT TAT -TAT TAT TAT TAT TAT TAT TAT T
656607 TTGCAAGCTT
Statistics
Matches: 67, Mismatches: 8, Indels: 20
0.71 0.08 0.21
Matches are distributed among these distances:
2 8 0.12
3 50 0.75
4 9 0.13
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:656692 original size:31 final size:31
Alignment explanation
Indices: 656654--656723 Score: 140
Period size: 31 Copynumber: 2.3 Consensus size: 31
656644 ACAACCCAAG
656654 TTGGGCCCCAATTACATTCCAACCCAACAAA
1 TTGGGCCCCAATTACATTCCAACCCAACAAA
656685 TTGGGCCCCAATTACATTCCAACCCAACAAA
1 TTGGGCCCCAATTACATTCCAACCCAACAAA
656716 TTGGGCCC
1 TTGGGCCC
656724 AACAACAAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.31, C:0.36, G:0.13, T:0.20
Consensus pattern (31 bp):
TTGGGCCCCAATTACATTCCAACCCAACAAA
Found at i:656738 original size:31 final size:31
Alignment explanation
Indices: 656654--656738 Score: 82
Period size: 31 Copynumber: 2.7 Consensus size: 31
656644 ACAACCCAAG
** **
656654 TTGGGCCCCAATTACATTCCAACCCAACAAA
1 TTGGGCCCCAACAACAACCCAACCCAACAAA
** **
656685 TTGGGCCCCAATTACATTCCAACCCAACAAA
1 TTGGGCCCCAACAACAACCCAACCCAACAAA
656716 TTGGG-CCCAACAACAAACCCAAC
1 TTGGGCCCCAACAAC-AACCCAAC
656739 AGAACTAGGC
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
30 7 0.14
31 42 0.86
ACGTcount: A:0.36, C:0.36, G:0.11, T:0.16
Consensus pattern (31 bp):
TTGGGCCCCAACAACAACCCAACCCAACAAA
Found at i:656884 original size:23 final size:23
Alignment explanation
Indices: 656833--656940 Score: 99
Period size: 26 Copynumber: 4.4 Consensus size: 23
656823 TTCCAGCCAT
*
656833 CGCCGCCGTCGTTGAGAGTCTCCTAC
1 CGCCGCCGCCGTTGAGAGTCT-C--C
*
656859 CGCCGCCGCCGTTCAGAGTCTCC
1 CGCCGCCGCCGTTGAGAGTCTCC
* *
656882 CGCCATCGCCGCCATTGAGAGTCTCA
1 CG-C--CGCCGCCGTTGAGAGTCTCC
* * *
656908 TGCCGTCGCTGTTGAGAGTCTCC
1 CGCCGCCGCCGTTGAGAGTCTCC
656931 CGCCGCCGCC
1 CGCCGCCGCC
656941 ACTATTCTGG
Statistics
Matches: 66, Mismatches: 13, Indels: 9
0.75 0.15 0.10
Matches are distributed among these distances:
23 26 0.39
24 1 0.02
25 2 0.03
26 37 0.56
ACGTcount: A:0.11, C:0.42, G:0.27, T:0.20
Consensus pattern (23 bp):
CGCCGCCGCCGTTGAGAGTCTCC
Found at i:657245 original size:11 final size:10
Alignment explanation
Indices: 657198--657255 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
657188 TGGATTCGAG
657198 AGAAAAAATGAA
1 AGAAAAAA-G-A
657210 AGAAAAAA-A
1 AGAAAAAAGA
* *
657219 TGAAAAAACA
1 AGAAAAAAGA
657229 ACGAAAAAAGA
1 A-GAAAAAAGA
657240 GAGAAAAAAGA
1 -AGAAAAAAGA
657251 AGAAA
1 AGAAA
657256 CTTACCTCGG
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
9 8 0.20
10 6 0.15
11 17 0.43
12 9 0.22
ACGTcount: A:0.76, C:0.03, G:0.17, T:0.03
Consensus pattern (10 bp):
AGAAAAAAGA
Found at i:657535 original size:6 final size:6
Alignment explanation
Indices: 657517--657548 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
657507 AAAGAAAAGA
657517 AAAG-G AAAG-G AAAGTG AAAGTG AAAGTG AAAG
1 AAAGTG AAAGTG AAAGTG AAAGTG AAAGTG AAAG
657549 AAAGAAGATG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 9 0.35
6 17 0.65
ACGTcount: A:0.56, C:0.00, G:0.34, T:0.09
Consensus pattern (6 bp):
AAAGTG
Found at i:657543 original size:12 final size:11
Alignment explanation
Indices: 657512--657552 Score: 50
Period size: 10 Copynumber: 3.8 Consensus size: 11
657502 AAAAAAAAGA
*
657512 AAAGAAAAG-G
1 AAAGGAAAGTG
657522 AAAGGAAAGTG
1 AAAGGAAAGTG
657533 AAAGTGAAAGTG
1 AAAG-GAAAGTG
657545 AAA-GAAAG
1 AAAGGAAAG
657553 AAGATGAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 13 0.46
11 5 0.18
12 10 0.36
ACGTcount: A:0.61, C:0.00, G:0.32, T:0.07
Consensus pattern (11 bp):
AAAGGAAAGTG
Found at i:658066 original size:14 final size:14
Alignment explanation
Indices: 658043--658080 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
658033 TCTGTCTATA
*
658043 TGCAGAGATTT-TT
1 TGCAGGGATTTATT
658056 TCGCAGGGATTTATT
1 T-GCAGGGATTTATT
658071 TGCAGGGATT
1 TGCAGGGATT
658081 ACTTCCCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 1 0.05
14 18 0.82
15 3 0.14
ACGTcount: A:0.21, C:0.11, G:0.29, T:0.39
Consensus pattern (14 bp):
TGCAGGGATTTATT
Found at i:660725 original size:22 final size:21
Alignment explanation
Indices: 660700--660743 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
660690 ATCCTATTTG
660700 TAATAATTTTGCC-ATTTTGTTA
1 TAATAATTTT-CCTATTTT-TTA
660722 TAATAATTTTCCTATTTTTTA
1 TAATAATTTTCCTATTTTTTA
660743 T
1 T
660744 CCTCTTGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.27, C:0.09, G:0.05, T:0.59
Consensus pattern (21 bp):
TAATAATTTTCCTATTTTTTA
Found at i:668754 original size:3 final size:3
Alignment explanation
Indices: 668746--668802 Score: 69
Period size: 3 Copynumber: 18.7 Consensus size: 3
668736 TTTGTCTAGG
* * *
668746 TTA TTA TTA ATA TTTA ATA TTA TTA TTA TTA TTA TTA TTA TTA TTT
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
668792 TTA GTA TTA TT
1 TTA TTA TTA TT
668803 TTTTTACAGA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
3 43 0.96
4 2 0.04
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:669527 original size:18 final size:18
Alignment explanation
Indices: 669504--669538 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
669494 GAATGGGTTT
669504 ATGGGGGAGTGTTTGGTG
1 ATGGGGGAGTGTTTGGTG
669522 ATGGGGGAGTGTTTGGT
1 ATGGGGGAGTGTTTGGT
669539 ATATCTTCGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.00, G:0.54, T:0.34
Consensus pattern (18 bp):
ATGGGGGAGTGTTTGGTG
Found at i:680265 original size:21 final size:19
Alignment explanation
Indices: 680227--680272 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
680217 AATTAATCCT
680227 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
680247 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
680268 A-TAAT
1 ACTAAT
680273 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:682950 original size:71 final size:72
Alignment explanation
Indices: 682801--683023 Score: 283
Period size: 71 Copynumber: 3.1 Consensus size: 72
682791 TCCAAATGGT
*
682801 TTTTGAAAATATATATATAATATAT-GATTTTGAAAACATGTTTTAAAACATTTATATATTATAT
1 TTTTGAAAATA-A-ATATAATATATAG-TTTTGAAAACAT-TTTTGAAA-A-TTATATATTATAT
*
682865 AATTTTTAAAACA
60 AGTTTTTAAAACA
* *
682878 TTTTGAAAATAAATATAATATATAGTTTTTAAAACATTTTTGAAAA-TATATATTTTATAGTTTT
1 TTTTGAAAATAAATATAATATATAGTTTTGAAAACATTTTTGAAAATTATATATTATATAGTTTT
682942 TAAAACA
66 TAAAACA
* * *
682949 TTTTG-AAAT-TATATAATATATAGTTTTGAAAATATTTTTGAAAAATTATATAATATATAGTTT
1 TTTTGAAAATAAATATAATATATAGTTTTGAAAACATTTTTG-AAAATTATATATTATATAGTTT
*
683012 TAAAAACA
65 TTAAAACA
683020 TTTT
1 TTTT
683024 TTTAAAACTT
Statistics
Matches: 133, Mismatches: 10, Indels: 12
0.86 0.06 0.08
Matches are distributed among these distances:
69 28 0.21
70 8 0.06
71 54 0.41
73 1 0.01
74 7 0.05
75 22 0.17
76 2 0.02
77 11 0.08
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.47
Consensus pattern (72 bp):
TTTTGAAAATAAATATAATATATAGTTTTGAAAACATTTTTGAAAATTATATATTATATAGTTTT
TAAAACA
Found at i:683004 original size:37 final size:37
Alignment explanation
Indices: 682800--683070 Score: 255
Period size: 37 Copynumber: 7.5 Consensus size: 37
682790 TTCCAAATGG
*
682800 TTTTTGAAAATATATATATAATATAT-GATTTTGAAAACA
1 TTTTTGAAAA-AT-TATATAATATATAG-TTTTTAAAACA
* *
682839 TGTTTT-AAAACATTTATATATTATATAATTTTTAAAACA
1 T-TTTTGAAAA-A-TTATATAATATATAGTTTTTAAAACA
*
682878 -TTTTG-AAAATAAATATAATATATAGTTTTTAAAACA
1 TTTTTGAAAAAT-TATATAATATATAGTTTTTAAAACA
* *
682914 TTTTTG-AAAA-TATATATTTTATAGTTTTTAAAACA
1 TTTTTGAAAAATTATATAATATATAGTTTTTAAAACA
* *
682949 -TTTTG--AAATTATATAATATATAGTTTTGAAAATA
1 TTTTTGAAAAATTATATAATATATAGTTTTTAAAACA
*
682983 TTTTTGAAAAATTATATAATATATAGTTTTAAAAACA
1 TTTTTGAAAAATTATATAATATATAGTTTTTAAAACA
** *
683020 TTTTTTTAAAACT-TAT-ATA-ATA-TTTTTAAAACA
1 TTTTTGAAAAATTATATAATATATAGTTTTTAAAACA
*
683053 -TTTTGAAAACTATATATA
1 TTTTTGAAAAAT-TATATA
683071 TAGTTTTGAA
Statistics
Matches: 195, Mismatches: 24, Indels: 30
0.78 0.10 0.12
Matches are distributed among these distances:
32 7 0.04
33 14 0.07
34 32 0.16
35 31 0.16
36 26 0.13
37 53 0.27
39 27 0.14
40 5 0.03
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.46
Consensus pattern (37 bp):
TTTTTGAAAAATTATATAATATATAGTTTTTAAAACA
Found at i:683060 original size:69 final size:65
Alignment explanation
Indices: 682895--683080 Score: 132
Period size: 69 Copynumber: 2.8 Consensus size: 65
682885 AATAAATATA
* * * *
682895 ATATATAGTTTTTAAAACATTTTTGAAA-ATATATATTTTATAGTTTTTAAAACA-TTTTGAAAT
1 ATATATA-TTTTTAAAACA-TTTTGAAATAAATATAATATATAGTTTTGAAAACATTTTTGAAA-
682958 TATAT
63 -AT-T
* * * *
682963 AATATATAGTTTTGAAAATATTTTTGAAA-AATTATATAATATATAGTTTTAAAAACATTTTTTT
1 -ATATATA-TTTTTAAAACA-TTTTGAAATAA--ATATAATATATAGTTTTGAAAACA-TTTTTG
683027 AAAACTT
60 AAAA-TT
*
683034 ATATAATATTTTTAAAACATTTTG-AA-AACTAT-ATATATAGTTTTGAA
1 ATAT-ATATTTTTAAAACATTTTGAAATAAATATAATATATAGTTTTGAA
683081 TTTTTTTTAA
Statistics
Matches: 100, Mismatches: 11, Indels: 16
0.79 0.09 0.13
Matches are distributed among these distances:
65 14 0.14
66 3 0.03
68 4 0.04
69 32 0.32
70 13 0.13
71 26 0.26
72 1 0.01
73 7 0.07
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (65 bp):
ATATATATTTTTAAAACATTTTGAAATAAATATAATATATAGTTTTGAAAACATTTTTGAAAATT
Found at i:683142 original size:35 final size:33
Alignment explanation
Indices: 682853--683141 Score: 202
Period size: 35 Copynumber: 8.5 Consensus size: 33
682843 TTAAAACATT
* *
682853 TATATATTATATAATTTTTAAAACA-TTTTGAAAA
1 TATATA-TATATAGTTTTTAAAATATTTTTG-AAA
*
682887 TAAATATAATATATAGTTTTTAAAACATTTTTGAAAA
1 T--ATAT-ATATATAGTTTTTAAAATATTTTTG-AAA
* *
682924 TATATATTTTATAGTTTTTAAAACA-TTTTGAAA
1 TATATA-TATATAGTTTTTAAAATATTTTTGAAA
*
682957 TTATATAATATATAGTTTTGAAAATATTTTTGAAAAA
1 -TATAT-ATATATAGTTTTTAAAATATTTTTG--AAA
* * *
682994 TTATATAATATATAGTTTTAAAAACATTTTTTTAAA
1 -TATAT-ATATATAGTTTTTAAAATA-TTTTTGAAA
*
683030 -ACT-TATATAATA-TTTTTAAAACA-TTTTGAAA
1 TA-TATATAT-ATAGTTTTTAAAATATTTTTGAAA
* * *
683061 -ACTATATATATAG-TTTT-GAATTTTTTTTAAA
1 TA-TATATATATAGTTTTTAAAATATTTTTGAAA
**
683092 TATA-ATATATAGTTTAAAAAAATATTTTTGAAA
1 TATATATATATAGTTT-TTAAAATATTTTTGAAA
683125 TATATATTATATAGTTT
1 TATATA-TATATAGTTT
683142 ATATCATATT
Statistics
Matches: 214, Mismatches: 19, Indels: 43
0.78 0.07 0.16
Matches are distributed among these distances:
30 10 0.05
31 28 0.13
32 6 0.03
33 32 0.15
34 33 0.15
35 38 0.18
36 24 0.11
37 38 0.18
38 5 0.02
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.48
Consensus pattern (33 bp):
TATATATATATAGTTTTTAAAATATTTTTGAAA
Found at i:684550 original size:11 final size:9
Alignment explanation
Indices: 684506--684541 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
684496 TCATCTTTCG
*
684506 ATTTTTTTA
1 ATTTTTTTT
684515 ATTTTTCTTT
1 ATTTTT-TTT
684525 ATTTTTTTT
1 ATTTTTTTT
684534 ATTTTTTT
1 ATTTTTTT
684542 GTCATTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 17 0.68
10 8 0.32
ACGTcount: A:0.14, C:0.03, G:0.00, T:0.83
Consensus pattern (9 bp):
ATTTTTTTT
Found at i:685142 original size:19 final size:19
Alignment explanation
Indices: 685118--685155 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
685108 TGGCCGTAAT
* *
685118 GCATCTCGAAGGGATTTTA
1 GCATCTCCAAAGGATTTTA
685137 GCATCTCCAAAGGATTTTA
1 GCATCTCCAAAGGATTTTA
685156 AATCCCTGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (19 bp):
GCATCTCCAAAGGATTTTA
Found at i:685592 original size:19 final size:19
Alignment explanation
Indices: 685568--685627 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
685558 CCATGTCCCA
685568 ATAATTGAAA-AAATAGAAT
1 ATAATTGAAATAAATA-AAT
*
685587 ATAATTTAAATAAATAAAT
1 ATAATTGAAATAAATAAAT
**
685606 AT-ATAAAAATAAGATAAAT
1 ATAATTGAAATAA-ATAAAT
685625 ATA
1 ATA
685628 TATGAATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 8 0.23
19 22 0.63
20 5 0.14
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (19 bp):
ATAATTGAAATAAATAAAT
Found at i:685628 original size:19 final size:18
Alignment explanation
Indices: 685594--685629 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
685584 AATATAATTT
685594 AAATAAATAAATATATAA
1 AAATAAATAAATATATAA
685612 AAATAAGATAAATATATA
1 AAATAA-ATAAATATATA
685630 TGAATTATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (18 bp):
AAATAAATAAATATATAA
Found at i:686511 original size:23 final size:22
Alignment explanation
Indices: 686485--686549 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 22
686475 ATATATTCAC
686485 TTTAATAATAAATCTATATAAAA
1 TTTAATAAT-AATCTATATAAAA
* * *
686508 TTTAAAAATAAT-AAAATAAAA
1 TTTAATAATAATCTATATAAAA
686529 TTTAAATTAATAATCTATATA
1 TTT-AA-TAATAATCTATATA
686550 TTGATGTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
21 10 0.30
22 5 0.15
23 14 0.42
24 4 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.38
Consensus pattern (22 bp):
TTTAATAATAATCTATATAAAA
Found at i:687964 original size:87 final size:86
Alignment explanation
Indices: 687864--688026 Score: 256
Period size: 87 Copynumber: 1.9 Consensus size: 86
687854 TAACTCTTAA
*
687864 TTTTTTTTAATAAAATTAACCCAAATGATGGAACATTAATGATGCTTTTAAACTGAACTAACTT-
1 TTTTTTTTAATAAAATTAACACAAATGATGGAACATTAATGATGCTTTTAAACTGAACTAACTTG
687928 TGGTGGTAAAGAGAGTTAAACT
66 T-GTGGTAAAGAGAGTTAAACT
* * * *
687950 TTTTTTATTTATAAAATTGACACAAATGATGGAACATTAATGATGGTTTTAAATTGAACTAACTT
1 TTTTTT-TTAATAAAATTAACACAAATGATGGAACATTAATGATGCTTTTAAACTGAACTAACTT
688015 GTGTGGTAAAGA
65 GTGTGGTAAAGA
688027 AGGTGTTCCT
Statistics
Matches: 70, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
86 6 0.09
87 63 0.90
88 1 0.01
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.37
Consensus pattern (86 bp):
TTTTTTTTAATAAAATTAACACAAATGATGGAACATTAATGATGCTTTTAAACTGAACTAACTTG
TGTGGTAAAGAGAGTTAAACT
Found at i:692679 original size:21 final size:19
Alignment explanation
Indices: 692643--692681 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
692633 CAATTTAAAA
*
692643 CAATTTAAAATTAAGCAAG
1 CAATTTAAAATAAAGCAAG
692662 CAATTTCAGAAATAAAGCAA
1 CAATTT-A-AAATAAAGCAA
692682 TGACCTAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 1 0.06
21 10 0.59
ACGTcount: A:0.54, C:0.13, G:0.10, T:0.23
Consensus pattern (19 bp):
CAATTTAAAATAAAGCAAG
Found at i:694180 original size:3 final size:3
Alignment explanation
Indices: 694167--694248 Score: 57
Period size: 3 Copynumber: 28.0 Consensus size: 3
694157 GTCGAGTTTG
** *
694167 TAA TAAA TAA TAA TAA TAA T-A TTT TATA TAA -AA AAA TAA T-A TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
* *
694211 CAA TGAA -AA TAA TAA TAG TAA TAA TAA T-A TAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
694249 CAATTGAAAA
Statistics
Matches: 63, Mismatches: 8, Indels: 16
0.72 0.09 0.18
Matches are distributed among these distances:
2 10 0.16
3 46 0.73
4 7 0.11
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:694242 original size:20 final size:20
Alignment explanation
Indices: 694196--694247 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
694186 TATTTTATAT
*
694196 AAAAAAATAATATAACAATG
1 AAAATAATAATATAACAATG
*
694216 AAAATAATAATAGTAATAAT-
1 AAAATAATAATA-TAACAATG
*
694236 AATATAATAATA
1 AAAATAATAATA
694248 ACAATTGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 22 0.79
21 6 0.21
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (20 bp):
AAAATAATAATATAACAATG
Found at i:694522 original size:41 final size:40
Alignment explanation
Indices: 694409--694522 Score: 133
Period size: 40 Copynumber: 2.8 Consensus size: 40
694399 CCACCTCCTT
* * *
694409 CTAAGGTGATGGTGATCCGACTCCTTATATGATGGATGAC
1 CTAAGGTGATGTTGATCCAACTCCTTATGTGATGGATGAC
694449 CTAAGGTGATGTTGATCCAACTCCTTATGTGATGGATGAGC
1 CTAAGGTGATGTTGATCCAACTCCTTATGTGATGGATGA-C
* * *
694490 C-AAGGTTA-GTACTGTTCTAACTCCTTATGTGAT
1 CTAAGGTGATGT--TGATCCAACTCCTTATGTGAT
694523 AGAATTAAGC
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
39 2 0.03
40 42 0.65
41 21 0.32
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.33
Consensus pattern (40 bp):
CTAAGGTGATGTTGATCCAACTCCTTATGTGATGGATGAC
Found at i:695654 original size:12 final size:12
Alignment explanation
Indices: 695617--695676 Score: 54
Period size: 12 Copynumber: 5.1 Consensus size: 12
695607 ACTTTTTCAT
*
695617 TTTCACTTTTTC
1 TTTCATTTTTTC
*
695629 ATTC-TTTTTCTC
1 TTTCATTTTT-TC
695641 TTTCATTTTTTC
1 TTTCATTTTTTC
695653 -TTCATTTTTGTC
1 TTTCATTTTT-TC
*
695665 TTT-TTTTTTTC
1 TTTCATTTTTTC
695676 T
1 T
695677 AAGTGTAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
11 16 0.40
12 17 0.43
13 7 0.17
ACGTcount: A:0.07, C:0.18, G:0.02, T:0.73
Consensus pattern (12 bp):
TTTCATTTTTTC
Found at i:695673 original size:24 final size:24
Alignment explanation
Indices: 695608--695675 Score: 70
Period size: 24 Copynumber: 2.9 Consensus size: 24
695598 ATTGAACCCA
*
695608 CTTTTTCAT-TTTCACTTTTTCATT
1 CTTTTTC-TCTTTCATTTTTTCATT
695632 CTTTTTCTCTTTCATTTTTTC-TT
1 CTTTTTCTCTTTCATTTTTTCATT
* *
695655 CATTTTTGTCTTT-TTTTTTTC
1 C-TTTTTCTCTTTCATTTTTTC
695676 TAAGTGTAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
23 11 0.28
24 28 0.72
ACGTcount: A:0.07, C:0.19, G:0.01, T:0.72
Consensus pattern (24 bp):
CTTTTTCTCTTTCATTTTTTCATT
Found at i:705372 original size:20 final size:20
Alignment explanation
Indices: 705347--705384 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
705337 CCAAACAGAA
705347 CCCAAAACCCGACCCGAAGG
1 CCCAAAACCCGACCCGAAGG
*
705367 CCCAAAACCTGACCCGAA
1 CCCAAAACCCGACCCGAA
705385 TCTAAACCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.45, G:0.16, T:0.03
Consensus pattern (20 bp):
CCCAAAACCCGACCCGAAGG
Found at i:716931 original size:2 final size:2
Alignment explanation
Indices: 716924--716954 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
716914 TATATTTCCT
*
716924 TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
716955 TATTTGCTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:717478 original size:13 final size:15
Alignment explanation
Indices: 717461--717498 Score: 62
Period size: 13 Copynumber: 2.7 Consensus size: 15
717451 AAAATAAATA
717461 AATAATAATATT-TT
1 AATAATAATATTATT
717475 -ATAATAATATTATT
1 AATAATAATATTATT
717489 AATAATAATA
1 AATAATAATA
717499 GTTGAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 11 0.50
14 2 0.09
15 9 0.41
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AATAATAATATTATT
Found at i:721497 original size:5 final size:5
Alignment explanation
Indices: 721487--721520 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
721477 ACACAGTGCC
*
721487 GAGTG GAGTG GAGTG GAGTG GAGTG GAGTA GAGT
1 GAGTG GAGTG GAGTG GAGTG GAGTG GAGTG GAGT
721521 TTGAGTATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.24, C:0.00, G:0.56, T:0.21
Consensus pattern (5 bp):
GAGTG
Found at i:721751 original size:14 final size:14
Alignment explanation
Indices: 721732--721758 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
721722 TATTTTAAAA
721732 AAATATTAATATAT
1 AAATATTAATATAT
721746 AAATATTAATATA
1 AAATATTAATATA
721759 ATTAATAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AAATATTAATATAT
Found at i:722095 original size:13 final size:13
Alignment explanation
Indices: 722077--722101 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
722067 TGATTTATTT
722077 ATTTAATAAAATA
1 ATTTAATAAAATA
722090 ATTTAATAAAAT
1 ATTTAATAAAAT
722102 GAAAATTCCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
ATTTAATAAAATA
Found at i:722385 original size:39 final size:39
Alignment explanation
Indices: 722342--722440 Score: 135
Period size: 39 Copynumber: 2.5 Consensus size: 39
722332 ACGTATAGAT
*
722342 TCTAGGAGTGCACGACGTCTTCAGGCGAATGGTTAAAAC
1 TCTAGGAGTGCACGACGTCTTCAGGCGAATGGATAAAAC
* * * *
722381 TCTAGGAGTGCACGACATCTTCATGCTAATGGATAAGAC
1 TCTAGGAGTGCACGACGTCTTCAGGCGAATGGATAAAAC
* *
722420 TCCAAGAGTGCACGACGTCTT
1 TCTAGGAGTGCACGACGTCTT
722441 TAGGTCATGC
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 52 1.00
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.24
Consensus pattern (39 bp):
TCTAGGAGTGCACGACGTCTTCAGGCGAATGGATAAAAC
Found at i:722794 original size:28 final size:28
Alignment explanation
Indices: 722719--722794 Score: 125
Period size: 28 Copynumber: 2.7 Consensus size: 28
722709 TTTAATATGT
* * *
722719 AAGTATTATTCGAATAAGACTTTATTTT
1 AAGTATTATTCGAATAAAATTTTATTTG
722747 AAGTATTATTCGAATAAAATTTTATTTG
1 AAGTATTATTCGAATAAAATTTTATTTG
722775 AAGTATTATTCGAATAAAAT
1 AAGTATTATTCGAATAAAAT
722795 ATATCTATTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (28 bp):
AAGTATTATTCGAATAAAATTTTATTTG
Found at i:723439 original size:16 final size:16
Alignment explanation
Indices: 723415--723448 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
723405 AATAATAATA
723415 ATAACTTTAATCCAAT
1 ATAACTTTAATCCAAT
* *
723431 ATAATTTTAATCTAAT
1 ATAACTTTAATCCAAT
723447 AT
1 AT
723449 GTCACAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (16 bp):
ATAACTTTAATCCAAT
Found at i:726273 original size:27 final size:27
Alignment explanation
Indices: 726235--726307 Score: 128
Period size: 27 Copynumber: 2.7 Consensus size: 27
726225 TATTGATGTT
*
726235 ATATTTGAATGAATGTGATTAATATCA
1 ATATTTAAATGAATGTGATTAATATCA
726262 ATATTTAAATGAATGTGATTAATATCA
1 ATATTTAAATGAATGTGATTAATATCA
*
726289 ATATTTAAATTAATGTGAT
1 ATATTTAAATGAATGTGAT
726308 GGGTATTTCT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.42, C:0.03, G:0.12, T:0.42
Consensus pattern (27 bp):
ATATTTAAATGAATGTGATTAATATCA
Found at i:728620 original size:97 final size:97
Alignment explanation
Indices: 728477--728728 Score: 239
Period size: 102 Copynumber: 2.6 Consensus size: 97
728467 TTAAACAAAA
* * * *
728477 AATATGTTAAAT-CAAATAAATAGTCTGATTAATTTATATTTACAAT-AAAAT-AGTAAAATTTA
1 AATATGTAAAATAAAAATAAATAGTCT-AATAATTTATATTTACAATAAAAATAAATAAAATTTA
* ** *
728539 AACTAAACCTACCGAAC-CACTCAAATATGATTT
65 AACTAAACCTACCAAACTC-CTCAAATACAACTT
* * *
728572 AATCTGTAAAATAAAAAATAATTAGTCTAATAATTTATA-TTACTCAATAAAAAATAAAAATATA
1 AATATGTAAAAT-AAAAATAAATAGTCTAATAATTTATATTTA--CAAT-AAAAAT--AAATAAA
*
728636 ATTTAAACTAAACTTACCAAACTCCTCAAATACAACTT
60 ATTTAAACTAAACCTACCAAACTCCTCAAATACAACTT
* *
728674 AATATGTAAAATCAAAATAAATAGTATAATAA-TTATAATTTA-AATTAAAAATAAA
1 AATATGTAAAATAAAAATAAATAGTCTAATAATTTAT-ATTTACAA-TAAAAATAAA
728729 AACTACACTA
Statistics
Matches: 128, Mismatches: 16, Indels: 24
0.76 0.10 0.14
Matches are distributed among these distances:
95 13 0.10
96 10 0.08
97 19 0.15
99 13 0.10
100 5 0.04
101 18 0.14
102 49 0.38
103 1 0.01
ACGTcount: A:0.53, C:0.11, G:0.04, T:0.33
Consensus pattern (97 bp):
AATATGTAAAATAAAAATAAATAGTCTAATAATTTATATTTACAATAAAAATAAATAAAATTTAA
ACTAAACCTACCAAACTCCTCAAATACAACTT
Found at i:728756 original size:117 final size:119
Alignment explanation
Indices: 728635--728849 Score: 278
Period size: 117 Copynumber: 1.8 Consensus size: 119
728625 ATAAAAATAT
*
728635 AATTTAAACTAAACTTACCAAACTC-CTCAAATACAACTTAATATGTAAAATCAAAATAAATAGT
1 AATTTAAACTAAACTTACCAAAC-CACTCAAATACAACTTAATATGTAAAATCAAAATAAATAAT
728699 ATAA-TAAT-TATAATTT-AAATTAAAAA-TAAAAACTACACTAAAAATCACACGAA
65 ATAATTAATGTAT-ATTTCAAA-TAAAAATTAAAAACTACACTAAAAATCACACGAA
* * ** * ** * *
728752 AATTTAAATTAAGCTTACCAAACCACTTGAATATAGTTTAATCTGTAAAATCAAAATAAATAATT
1 AATTTAAACTAAACTTACCAAACCACTCAAATACAACTTAATATGTAAAATCAAAATAAATAATA
728817 TAATTAATGTATATTTCAAATAAAAATTAAAAA
66 TAATTAATGTATATTTCAAATAAAAATTAAAAA
728850 TGAAACAATA
Statistics
Matches: 83, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
116 1 0.01
117 56 0.67
118 14 0.17
119 12 0.14
ACGTcount: A:0.53, C:0.12, G:0.04, T:0.31
Consensus pattern (119 bp):
AATTTAAACTAAACTTACCAAACCACTCAAATACAACTTAATATGTAAAATCAAAATAAATAATA
TAATTAATGTATATTTCAAATAAAAATTAAAAACTACACTAAAAATCACACGAA
Found at i:729150 original size:25 final size:25
Alignment explanation
Indices: 729101--729152 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
729091 TTACTAACGT
*
729101 TTCCCACGCCATGCAACTTTGTTGC
1 TTCCCACGCCATGCAACGTTGTTGC
729126 TTCCCACGCCATGCAACAGTT-TTGC
1 TTCCCACGCCATGCAAC-GTTGTTGC
729151 TT
1 TT
729153 TAGAGTCAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 23 0.92
26 2 0.08
ACGTcount: A:0.17, C:0.35, G:0.15, T:0.33
Consensus pattern (25 bp):
TTCCCACGCCATGCAACGTTGTTGC
Found at i:733421 original size:10 final size:11
Alignment explanation
Indices: 733401--733425 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
733391 AAATTGGGCT
733401 AAAAAGAAAAA
1 AAAAAGAAAAA
733412 AAAAAGAAAAA
1 AAAAAGAAAAA
733423 AAA
1 AAA
733426 TGGTCTCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:735806 original size:26 final size:25
Alignment explanation
Indices: 735777--735825 Score: 89
Period size: 26 Copynumber: 1.9 Consensus size: 25
735767 TATGTTACTA
735777 TGAATTTATAAAATTTTAAGAAAGAG
1 TGAATTTATAAAATTTTAA-AAAGAG
735803 TGAATTTATAAAATTTTAAAAAG
1 TGAATTTATAAAATTTTAAAAAG
735826 TAAAAATAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 4 0.17
26 19 0.83
ACGTcount: A:0.51, C:0.00, G:0.12, T:0.37
Consensus pattern (25 bp):
TGAATTTATAAAATTTTAAAAAGAG
Found at i:736036 original size:23 final size:21
Alignment explanation
Indices: 735994--736037 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
735984 CTATGAGCAC
*
735994 TCTCATTTCTTCCTTTAAAGT
1 TCTCATTTCTTCATTTAAAGT
*
736015 TCTCTTTTCTTCTATTTCAAAGT
1 TCTCATTTCTTC-ATTT-AAAGT
736038 AAAATTAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 11 0.58
22 3 0.16
23 5 0.26
ACGTcount: A:0.18, C:0.23, G:0.05, T:0.55
Consensus pattern (21 bp):
TCTCATTTCTTCATTTAAAGT
Found at i:736585 original size:2 final size:2
Alignment explanation
Indices: 736578--736603 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
736568 AATAAAAATA
736578 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
736604 TAGTAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:737460 original size:64 final size:64
Alignment explanation
Indices: 737359--737507 Score: 271
Period size: 64 Copynumber: 2.3 Consensus size: 64
737349 ACTCTCTTTT
*
737359 GTGGTTTTCACCTCCGTATGGGATAGTGGATCGCTCATTGTATTCACGTCTTATGGTCCTCGTG
1 GTGGTTTTCACCTCCGTATGGGATAGTAGATCGCTCATTGTATTCACGTCTTATGGTCCTCGTG
737423 GTGGTTTTCACCTCCGTATGGGATAGTAGATCGCTCATTGTATTCACGTCTTATGGTCCTCGTG
1 GTGGTTTTCACCTCCGTATGGGATAGTAGATCGCTCATTGTATTCACGTCTTATGGTCCTCGTG
* *
737487 ATGGTTTTCACCTCTGTATGG
1 GTGGTTTTCACCTCCGTATGG
737508 ACATAAAGAG
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
64 82 1.00
ACGTcount: A:0.15, C:0.21, G:0.26, T:0.38
Consensus pattern (64 bp):
GTGGTTTTCACCTCCGTATGGGATAGTAGATCGCTCATTGTATTCACGTCTTATGGTCCTCGTG
Found at i:738276 original size:11 final size:12
Alignment explanation
Indices: 738246--738299 Score: 65
Period size: 12 Copynumber: 4.6 Consensus size: 12
738236 GTTATTTAAA
738246 CGGGTATTGGGC
1 CGGGTATTGGGC
*
738258 CGGGTATTGGGT
1 CGGGTATTGGGC
738270 C-GGTATTGGGC
1 CGGGTATTGGGC
* *
738281 CGGGAATCGGGC
1 CGGGTATTGGGC
*
738293 CGTGTAT
1 CGGGTAT
738300 ATATATATAT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
11 10 0.29
12 25 0.71
ACGTcount: A:0.11, C:0.17, G:0.46, T:0.26
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:738357 original size:24 final size:25
Alignment explanation
Indices: 738297--738381 Score: 72
Period size: 24 Copynumber: 3.5 Consensus size: 25
738287 TCGGGCCGTG
738297 TATATA-TATA-TATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
*
738320 TATATATT-TTTTATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
* * *
738344 T-T-TATTAATATTATATATATATATA
1 TATATATT-ATATTATTTAAAT-TAAA
738369 TATATATATATAT
1 TATATAT-TATAT
738382 ATATATATAT
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
22 4 0.08
23 8 0.16
24 24 0.49
25 4 0.08
26 1 0.02
27 7 0.14
28 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
TATATATTATATTATTTAAATTAAA
Found at i:738362 original size:2 final size:2
Alignment explanation
Indices: 738351--738391 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
738341 AAATTTATTA
738351 AT AT -T 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
738392 TATTTTTAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:738436 original size:13 final size:12
Alignment explanation
Indices: 738405--738441 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
738395 TTTTAATATT
*
738405 TATCGGGTCGGG
1 TATCGGGGCGGG
738417 TATCGGGGCGGG
1 TATCGGGGCGGG
738429 TAATCGGGGCGGG
1 T-ATCGGGGCGGG
738442 GATTACCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.11, C:0.16, G:0.54, T:0.19
Consensus pattern (12 bp):
TATCGGGGCGGG
Found at i:748033 original size:33 final size:33
Alignment explanation
Indices: 747991--748101 Score: 109
Period size: 33 Copynumber: 3.4 Consensus size: 33
747981 TCTTGCTTAC
747991 ACAGAAACATTGCGAGAAGAACCACCTTGATTG
1 ACAGAAACATTGCGAGAAGAACCACCTTGATTG
* ** * *
748024 ACAGAAACATTGAGAGGTGAAGCTCCTTGATTG
1 ACAGAAACATTGCGAGAAGAACCACCTTGATTG
* * * *
748057 GCAGTAACATTGCGAGAAGACCCTA-CTTGAATGG
1 ACAGAAACATTGCGAGAAGAACC-ACCTTG-ATTG
748091 A-AGAAACATTG
1 ACAGAAACATTG
748102 GGAGGAGGAA
Statistics
Matches: 60, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
33 57 0.95
34 3 0.05
ACGTcount: A:0.37, C:0.18, G:0.24, T:0.21
Consensus pattern (33 bp):
ACAGAAACATTGCGAGAAGAACCACCTTGATTG
Found at i:758754 original size:23 final size:21
Alignment explanation
Indices: 758728--758772 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 21
758718 AATACAAAAG
758728 ATAAACATAAACATACCATTAAA
1 ATAAACATAAACAT-CCA-TAAA
**
758751 ATAAAGTTAAACATCCATAAA
1 ATAAACATAAACATCCATAAA
758772 A
1 A
758773 CAACCCCAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 3 0.15
23 12 0.60
ACGTcount: A:0.60, C:0.16, G:0.02, T:0.22
Consensus pattern (21 bp):
ATAAACATAAACATCCATAAA
Found at i:764921 original size:16 final size:16
Alignment explanation
Indices: 764897--764939 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
764887 TGCATATATT
764897 AAATATATTAAAACA-A
1 AAATATATTAAAA-ATA
*
764913 AAATTTATTCAAAAATA
1 AAATATATT-AAAAATA
764930 AAATATATTA
1 AAATATATTA
764940 TTTTGTTCGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.33
Consensus pattern (16 bp):
AAATATATTAAAAATA
Found at i:765855 original size:18 final size:17
Alignment explanation
Indices: 765834--765871 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
765824 AAATATCACC
*
765834 TTTTTCATTTTCTTTATT
1 TTTTTCATTTT-TTCATT
765852 TTTTTCATTTTTTCATT
1 TTTTTCATTTTTTCATT
765869 TTT
1 TTT
765872 AAAATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTCATTTTTTCATT
Found at i:767030 original size:3 final size:3
Alignment explanation
Indices: 767016--767095 Score: 117
Period size: 3 Copynumber: 26.7 Consensus size: 3
767006 AAATAAACGT
* * *
767016 TAA TAT TAA TAA TAA TAA TAA TAA -AA AAA AAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
767063 TAA TAA TAA TAA TAAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TA
767096 GGTTTGGGCA
Statistics
Matches: 72, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
2 2 0.03
3 67 0.93
4 3 0.04
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:767576 original size:3 final size:3
Alignment explanation
Indices: 767570--767660 Score: 152
Period size: 3 Copynumber: 31.0 Consensus size: 3
767560 CATCATCATC
767570 ATT ATT ATT ATT ATT A-T ATT ATT ATTT ATT ATT A-T ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT
767614 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -TT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
767661 TGTTTTTCAG
Statistics
Matches: 84, Mismatches: 0, Indels: 8
0.91 0.00 0.09
Matches are distributed among these distances:
2 6 0.07
3 75 0.89
4 3 0.04
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:770062 original size:20 final size:20
Alignment explanation
Indices: 770031--770079 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
770021 TATTGTTCAT
*
770031 TACTATTGACACAGTATCGA
1 TACTATTCACACAGTATCGA
*
770051 TACTGTTCACACAGTATCGA
1 TACTATTCACACAGTATCGA
770071 TACTATTCA
1 TACTATTCA
770080 TACAATACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.33
Consensus pattern (20 bp):
TACTATTCACACAGTATCGA
Found at i:770089 original size:14 final size:14
Alignment explanation
Indices: 770070--770100 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
770060 CACAGTATCG
770070 ATACTATTCATACA
1 ATACTATTCATACA
770084 ATACTATTCATACA
1 ATACTATTCATACA
770098 ATA
1 ATA
770101 TTTTTTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.45, C:0.19, G:0.00, T:0.35
Consensus pattern (14 bp):
ATACTATTCATACA
Found at i:770543 original size:20 final size:20
Alignment explanation
Indices: 770514--770556 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
770504 TAAAAAATAT
*
770514 TGTATGAATAGTATT-GATAC
1 TGTATAAATAGT-TTCGATAC
770534 TGTATAAATAGTTTCGATAC
1 TGTATAAATAGTTTCGATAC
770554 TGT
1 TGT
770557 GTGAACATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.33, C:0.07, G:0.19, T:0.42
Consensus pattern (20 bp):
TGTATAAATAGTTTCGATAC
Found at i:771837 original size:15 final size:15
Alignment explanation
Indices: 771817--771858 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
771807 TTTGAAAATC
771817 AAAATGAAATTTTGA
1 AAAATGAAATTTTGA
771832 AAAATG--ATTTTGA
1 AAAATGAAATTTTGA
771845 AAAA-GAAAATTTTG
1 AAAATG-AAATTTTG
771859 GTTTAAAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
12 1 0.04
13 11 0.46
15 12 0.50
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.33
Consensus pattern (15 bp):
AAAATGAAATTTTGA
Found at i:772911 original size:20 final size:20
Alignment explanation
Indices: 772886--772957 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 20
772876 GAATAGTACC
*
772886 GTATGAATAGTATTGATATT
1 GTATGAATAGTATCGATATT
*
772906 GTATGAATAGTATCGATACT
1 GTATGAATAGTATCGATATT
*** *
772926 ACGTGAATAGTATCGATACT
1 GTATGAATAGTATCGATATT
* *
772946 GTGTGAACAGTA
1 GTATGAATAGTA
772958 ATGAACAGTA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.35, C:0.08, G:0.22, T:0.35
Consensus pattern (20 bp):
GTATGAATAGTATCGATATT
Found at i:776253 original size:9 final size:9
Alignment explanation
Indices: 776227--776341 Score: 60
Period size: 9 Copynumber: 12.8 Consensus size: 9
776217 GTGAAGATAC
776227 TATT-TTTT
1 TATTATTTT
*
776235 TATCCATTTT
1 TAT-TATTTT
776245 T-TTATTTT
1 TATTATTTT
* *
776253 TAATATTAT
1 TATTATTTT
776262 TATTA-TTT
1 TATTATTTT
*
776270 TATTTATACTAT
1 TA-TTAT--TTT
776282 TATTA-TTT
1 TATTATTTT
*
776290 TATTA-TTA
1 TATTATTTT
* * *
776298 TAATACTAT
1 TATTATTTT
776307 TATTTATTTT
1 TA-TTATTTT
*
776317 TATTATTAT
1 TATTATTTT
*
776326 TATTATTAT
1 TATTATTTT
776335 TATTATT
1 TATTATT
776342 ATTACAAACA
Statistics
Matches: 82, Mismatches: 16, Indels: 17
0.71 0.14 0.15
Matches are distributed among these distances:
8 26 0.32
9 38 0.46
10 11 0.13
11 3 0.04
12 4 0.05
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (9 bp):
TATTATTTT
Found at i:776262 original size:3 final size:3
Alignment explanation
Indices: 776246--776345 Score: 100
Period size: 3 Copynumber: 34.0 Consensus size: 3
776236 ATCCATTTTT
* * *
776246 TTA TTT TTA ATA TTA TTA TTA TT- TTA TT- TATA CTA TTA TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
* * *
776289 TTA TTA TTA -TA ATA CTA TTA TTTA TTT TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
776334 TTA TTA TTA TTA
1 TTA TTA TTA TTA
776346 CAAACAGGCT
Statistics
Matches: 81, Mismatches: 10, Indels: 12
0.79 0.10 0.12
Matches are distributed among these distances:
2 7 0.09
3 71 0.88
4 3 0.04
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:778081 original size:151 final size:149
Alignment explanation
Indices: 777883--778172 Score: 435
Period size: 151 Copynumber: 1.9 Consensus size: 149
777873 AAAAATAATC
* * * *
777883 ATATTTTAAATATTTATTTATTTTTTAATATTAAGAAATAGGTTGTCTTAAATCACCTAGAAGTC
1 ATATTTTAAATATTTATTTATTTATTAATATTAAGAAATAGGCTGTCTTAAAGCACCTAAAAGTC
* * *
777948 CTTTTCTGATA-TTCTTAAATAAATAAATATCTTACTTTTATAAAATATATATATTAATATATTT
66 ATTTTCTGATATTTC-TAAATAAATAAATATCTTA--TTTATAAAATATAAAAATTAATATATTT
778012 T-TTAAA-TTATTTTTAGATAA
128 TCTTAAAGTTATTTTTAGATAA
778032 ATATTTTATTAATATTTATTTATTTATTAATATTAAGAAA-AGAGCTGTCTTAAAGCACCTAAAA
1 ATATTTTA--AATATTTATTTATTTATTAATATTAAGAAATAG-GCTGTCTTAAAGCACCTAAAA
778096 GTCATTTTCTGATATTTCTAAATAAATAAATATCTTATTTATAAAATATAAAAATTAATATATTT
63 GTCATTTTCTGATATTTCTAAATAAATAAATATCTTATTTATAAAATATAAAAATTAATATATTT
778161 TCTTAAAGTTAT
128 TCTTAAAGTTAT
778173 ACTAATAAAA
Statistics
Matches: 128, Mismatches: 7, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
149 35 0.27
150 7 0.05
151 83 0.65
152 3 0.02
ACGTcount: A:0.41, C:0.07, G:0.06, T:0.47
Consensus pattern (149 bp):
ATATTTTAAATATTTATTTATTTATTAATATTAAGAAATAGGCTGTCTTAAAGCACCTAAAAGTC
ATTTTCTGATATTTCTAAATAAATAAATATCTTATTTATAAAATATAAAAATTAATATATTTTCT
TAAAGTTATTTTTAGATAA
Found at i:789582 original size:15 final size:15
Alignment explanation
Indices: 789550--789592 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 15
789540 AGAGCCTCTT
789550 AATCATTCAGACTGCTA
1 AATCATTCAG--TGCTA
789567 AATCATTCAGTGCTA
1 AATCATTCAGTGCTA
*
789582 AACCATTCAGT
1 AATCATTCAGT
789593 TTTAACAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 15 0.60
17 10 0.40
ACGTcount: A:0.35, C:0.23, G:0.12, T:0.30
Consensus pattern (15 bp):
AATCATTCAGTGCTA
Found at i:799643 original size:15 final size:15
Alignment explanation
Indices: 799623--799661 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
799613 GTTATATAAT
799623 TGATAATAATTTTGG
1 TGATAATAATTTTGG
799638 TGATAATAATTTTGG
1 TGATAATAATTTTGG
799653 TGATAATAA
1 TGATAATAA
799662 AAAATATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.18, T:0.44
Consensus pattern (15 bp):
TGATAATAATTTTGG
Found at i:804895 original size:66 final size:66
Alignment explanation
Indices: 804789--804916 Score: 193
Period size: 66 Copynumber: 1.9 Consensus size: 66
804779 TAGGTCCGTA
* *
804789 AGGAATTACCAGTCGATGCTGAACCTATAAAATGAATTACCAACAACAACTAAACCTGCCAGAGA
1 AGGAATTACCAGTCGATGCAGAACCTATAAAAAGAATTACCAACAACAACTAAACCTGCCAGAGA
804854 T
66 T
* * * * *
804855 AGGAATTACTAGTCGGTGCAGAACTTATAAAAAGAATTACCCACAACAACTGAACCTGCCAG
1 AGGAATTACCAGTCGATGCAGAACCTATAAAAAGAATTACCAACAACAACTAAACCTGCCAG
804917 TGTCTTTATA
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
66 55 1.00
ACGTcount: A:0.41, C:0.23, G:0.16, T:0.20
Consensus pattern (66 bp):
AGGAATTACCAGTCGATGCAGAACCTATAAAAAGAATTACCAACAACAACTAAACCTGCCAGAGA
T
Found at i:805964 original size:28 final size:27
Alignment explanation
Indices: 805933--805986 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
805923 TTAAAGGTAC
*
805933 TTTTGGTCATTTAACACTTTAGGGGCA
1 TTTTTGTCATTTAACACTTTAGGGGCA
*
805960 TTTTTGTCATTTTACACTTTAGGGGCA
1 TTTTTGTCATTTAACACTTTAGGGGCA
805987 AATATGTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.20, C:0.15, G:0.20, T:0.44
Consensus pattern (27 bp):
TTTTTGTCATTTAACACTTTAGGGGCA
Found at i:805998 original size:27 final size:27
Alignment explanation
Indices: 805941--806000 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
805931 ACTTTTGGTC
* ** * *
805941 ATTTAACACTTTAGGGGCATTTTTGTC
1 ATTTTACACTTTAGGGGCAAATATGTA
805968 ATTTTACACTTTAGGGGCAAATATGTA
1 ATTTTACACTTTAGGGGCAAATATGTA
805995 ATTTTA
1 ATTTTA
806001 TTCAATTGAG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.28, C:0.12, G:0.17, T:0.43
Consensus pattern (27 bp):
ATTTTACACTTTAGGGGCAAATATGTA
Found at i:813061 original size:2 final size:2
Alignment explanation
Indices: 813054--813080 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
813044 ATTTATTTAA
813054 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
813081 ATAAATAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:813678 original size:2 final size:2
Alignment explanation
Indices: 813673--813706 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
813663 GTAGTGTGTG
813673 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
813707 ACAGATAGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:815325 original size:44 final size:44
Alignment explanation
Indices: 815276--815438 Score: 150
Period size: 44 Copynumber: 3.8 Consensus size: 44
815266 AAGAAAGAAT
815276 AATAAAATAAATAAATGAAGAAAAT-TTAAATTTTAAAGGAAGTA
1 AATAAAATAAATAAA-GAAGAAAATGTTAAATTTTAAAGGAAGTA
* *
815320 AAT-AAATAAATAAATGAAGAAAATGTTAATTTTTAAAAAGGGAA-AA
1 AATAAAATAAATAAA-GAAGAAAATGTTAAATTTT--AAA-GGAAGTA
815366 AATAAAAT-AA-AAAGAA-AGAAATGTTAAATTTT---GGAAGTA
1 AATAAAATAAATAAAGAAGA-AAATGTTAAATTTTAAAGGAAGTA
815405 AA-AAAATAGAATAAA-AAGAAAAAGTGTTAAATTT
1 AATAAAATA-AATAAAGAAG-AAAA-TGTTAAATTT
815439 AAAAAAAACG
Statistics
Matches: 102, Mismatches: 4, Indels: 28
0.76 0.03 0.21
Matches are distributed among these distances:
38 9 0.09
39 3 0.03
40 4 0.04
41 6 0.06
42 11 0.11
43 22 0.22
44 27 0.26
45 3 0.03
46 9 0.09
47 8 0.08
ACGTcount: A:0.61, C:0.00, G:0.13, T:0.26
Consensus pattern (44 bp):
AATAAAATAAATAAAGAAGAAAATGTTAAATTTTAAAGGAAGTA
Found at i:815374 original size:43 final size:41
Alignment explanation
Indices: 815279--815376 Score: 126
Period size: 43 Copynumber: 2.3 Consensus size: 41
815269 AAAGAATAAT
*
815279 AAAATAAATAAATGAAGAAAATTTAAATTTTAAAGGAAGTAA
1 AAAATAAATAAATGAAGAAAATTTAAATTTTAAA-GAAGGAA
*
815321 ATAAATAAATAAATGAAGAAAATGTTAATTTTTAAA-AAGGGAA
1 A-AAATAAATAAATGAAGAAAAT-TTAAATTTTAAAGAA-GGAA
815364 AAAATAAAATAAA
1 AAAAT-AAATAAA
815377 AAGAAAGAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
42 7 0.14
43 32 0.64
44 11 0.22
ACGTcount: A:0.63, C:0.00, G:0.11, T:0.26
Consensus pattern (41 bp):
AAAATAAATAAATGAAGAAAATTTAAATTTTAAAGAAGGAA
Found at i:816940 original size:39 final size:39
Alignment explanation
Indices: 816831--817151 Score: 256
Period size: 37 Copynumber: 8.6 Consensus size: 39
816821 TTTAAAACCA
*
816831 TTTT-AAAAACTATATA-CTATATGTTTTCAAAAATA--
1 TTTTCAAAAACTATATATATATATGTTTTCAAAAATATG
816866 TTTT-AAAAACTATATATTATATATGATTTTCAAAAATATG
1 TTTTCAAAAACTATATA-TATATATG-TTTTCAAAAATATG
* *
816906 TTTTCAAACACTATATTATATATATGTTTT-AAAAA-ATA
1 TTTTCAAAAACTATA-TATATATATGTTTTCAAAAATATG
* **
816944 TTTT-AAAATC-ATATAT-TATATGTTTTTC-AAAA-CCG
1 TTTTCAAAAACTATATATATATATG-TTTTCAAAAATATG
*
816979 ATTTT-AAAAACTATGTATTATATATGTTTTCAAAAATATG
1 -TTTTCAAAAACTATATA-TATATATGTTTTCAAAAATATG
* *
817019 TTTTC-AAAACTATATAT-TAAATGTTTT-AAAACT-TG
1 TTTTCAAAAACTATATATATATATGTTTTCAAAAATATG
* * *
817054 TTTTCAAAACCATATTATATATATAT-ATTTCAAAAACTA-A
1 TTTTCAAAAAC-TA-TATATATATATGTTTTCAAAAA-TATG
* * *
817094 TTTTAAAAAAAT-TATATATTATATGTTTTC-AAAAT-TA
1 TTTTCAAAAACTATATATA-TATATGTTTTCAAAAATATG
817131 TTTTCAAAAACTATAT-TATAT
1 TTTTCAAAAACTATATATATAT
817152 TATTATATAT
Statistics
Matches: 233, Mismatches: 26, Indels: 53
0.75 0.08 0.17
Matches are distributed among these distances:
34 6 0.03
35 34 0.15
36 24 0.10
37 45 0.19
38 45 0.19
39 42 0.18
40 18 0.08
41 17 0.07
42 2 0.01
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.45
Consensus pattern (39 bp):
TTTTCAAAAACTATATATATATATGTTTTCAAAAATATG
Found at i:816998 original size:114 final size:111
Alignment explanation
Indices: 816830--817151 Score: 352
Period size: 113 Copynumber: 2.9 Consensus size: 111
816820 TTTTAAAACC
* *
816830 ATTTTAAAAACTATATACTATATG-TTTTCAAAA-ATATTTTAAAAACTATATATTATATATGAT
1 ATTTTAAAAAC-ATATATTATATGTTTTTCAAAACAAATTTTAAAAACTAT-TATTATATATG-T
*
816893 TTTCAAAAATATGTTTTCAAACACTATATTATATATATGTTTTAAAAAAT
63 TTTCAAAAATATGTTTTCAAA-ACTATATTATATAAATGTTTTAAAAAAT
* **
816943 ATTTTAAAATCATATATTATATGTTTTTCAAAACCGATTTTAAAAACTATGTATTATATATGTTT
1 ATTTTAAAAACATATATTATATGTTTTTCAAAACAAATTTTAAAAACTAT-TATTATATATGTTT
**
817008 TCAAAAATATGTTTTCAAAACTATA-TAT-TAAATGTTTTAAAACTT
65 TCAAAAATATGTTTTCAAAACTATATTATATAAATGTTTTAAAAAAT
* * * * * *
817053 GTTTTCAAAACCATATTATATATATATATTTCAAAAACTAATTTTAAAAA-AATTATATATTATA
1 ATTTT-AAAAACATA-TAT-TATATGTTTTTC-AAAACAAATTTTAAAAACTATTAT-TA-TATA
*
817117 TGTTTTC-AAAAT-TATTTTCAAAAACTATATTATAT
60 TGTTTTCAAAAATATGTTTTC-AAAACTATATTATAT
817152 TATTATATAT
Statistics
Matches: 182, Mismatches: 16, Indels: 20
0.83 0.07 0.09
Matches are distributed among these distances:
110 18 0.10
111 11 0.06
112 29 0.16
113 69 0.38
114 54 0.30
115 1 0.01
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.45
Consensus pattern (111 bp):
ATTTTAAAAACATATATTATATGTTTTTCAAAACAAATTTTAAAAACTATTATTATATATGTTTT
CAAAAATATGTTTTCAAAACTATATTATATAAATGTTTTAAAAAAT
Found at i:817019 original size:14 final size:14
Alignment explanation
Indices: 817000--817027 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
816990 TATGTATTAT
817000 ATATGTTTTCAAAA
1 ATATGTTTTCAAAA
817014 ATATGTTTTCAAAA
1 ATATGTTTTCAAAA
817028 CTATATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (14 bp):
ATATGTTTTCAAAA
Found at i:817152 original size:39 final size:37
Alignment explanation
Indices: 816808--817154 Score: 227
Period size: 39 Copynumber: 9.2 Consensus size: 37
816798 ACTATATAAC
* **
816808 ATATATTATAT-TTTTTAAAACCATTTTAAAAAC--T
1 ATATATTATATGTTTTCAAAATTATTTTAAAAACTAT
* *
816842 ATATACTATATGTTTTCAAAAATATTTTAAAAACTAT
1 ATATATTATATGTTTTCAAAATTATTTTAAAAACTAT
* *
816879 ATAT-TATATATGATTTTCAAAAATATGTTTTCAAACACTAT
1 ATATAT-TATATG-TTTTC-AAAAT-TATTTT-AAAAACTAT
* * *
816920 AT-TATATATATGTTTTAAAAAATATTTT-AAAA-T-C
1 ATATAT-TATATGTTTTCAAAATTATTTTAAAAACTAT
**
816954 ATATATTATATGTTTTTCAAAACCGATTTTAAAAACTAT
1 ATATATTATATG-TTTTCAAAA-TTATTTTAAAAACTAT
* * *
816993 GTAT-TATATATGTTTTCAAAAATATGTTTTCAAAAC--T
1 ATATAT-TATATGTTTTC-AAAAT-TATTTTAAAAACTAT
* * * *
817030 ATATATTAAATGTTTT-AAAACTTGTTTTCAAAACCAT
1 ATATATTATATGTTTTCAAAA-TTATTTTAAAAACTAT
* * *
817067 ATTATATATATAT-ATTTCAAAAACTAATTTTAAAAA-AATT
1 A-TATAT-TATATGTTTTC-AAAA-TTATTTTAAAAACTA-T
817107 ATATATTATATGTTTTCAAAATTATTTTCAAAAACTAT
1 ATATATTATATGTTTTCAAAATTATTTT-AAAAACTAT
817145 ATTATATTAT
1 A-TATATTAT
817155 TATATATACT
Statistics
Matches: 249, Mismatches: 33, Indels: 57
0.73 0.10 0.17
Matches are distributed among these distances:
34 18 0.07
35 47 0.19
36 9 0.04
37 36 0.14
38 42 0.17
39 53 0.21
40 26 0.10
41 18 0.07
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (37 bp):
ATATATTATATGTTTTCAAAATTATTTTAAAAACTAT
Found at i:823294 original size:32 final size:32
Alignment explanation
Indices: 823257--823319 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
823247 TAATGTCAAT
*
823257 CTTCTTATAATATGATCTTTATTCACTAAATC
1 CTTCTTATAATATGATATTTATTCACTAAATC
*
823289 CTTCTTATCATATGATATTTATTCACTAAAT
1 CTTCTTATAATATGATATTTATTCACTAAAT
823320 GTGTACATCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.32, C:0.17, G:0.03, T:0.48
Consensus pattern (32 bp):
CTTCTTATAATATGATATTTATTCACTAAATC
Found at i:826775 original size:31 final size:31
Alignment explanation
Indices: 826658--826781 Score: 108
Period size: 31 Copynumber: 4.0 Consensus size: 31
826648 CCCAAATGAC
* * *
826658 CTATCCATATGTTCCAAAAAACATAGGTAACA
1 CTATCCATATGTCCCGAAAGACATAGGTAA-A
* * * *
826690 CTGTCCTTTTG-CCCG-AAGAACATAGGTAAT
1 CTATCCATATGTCCCGAAAG-ACATAGGTAAA
* * *
826720 CTTGTCCATATATCCCGAATGACATAGGTAAA
1 C-TATCCATATGTCCCGAAAGACATAGGTAAA
*
826752 CTATCCATATGTCTCGAAAGACATAGGTAA
1 CTATCCATATGTCCCGAAAGACATAGGTAA
826782 CCCTTCGACT
Statistics
Matches: 72, Mismatches: 16, Indels: 9
0.74 0.16 0.09
Matches are distributed among these distances:
30 3 0.04
31 44 0.61
32 23 0.32
33 2 0.03
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.27
Consensus pattern (31 bp):
CTATCCATATGTCCCGAAAGACATAGGTAAA
Found at i:830068 original size:24 final size:24
Alignment explanation
Indices: 830041--830086 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
830031 CTTTCTTCAC
*
830041 TATACCACATTA-CTATGATCCAAA
1 TATACAACATTATCTA-GATCCAAA
*
830065 TATACAACTTTATCTAGATCCA
1 TATACAACATTATCTAGATCCA
830087 CTTCGTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 16 0.84
25 3 0.16
ACGTcount: A:0.39, C:0.24, G:0.04, T:0.33
Consensus pattern (24 bp):
TATACAACATTATCTAGATCCAAA
Found at i:831644 original size:31 final size:32
Alignment explanation
Indices: 831585--831663 Score: 106
Period size: 31 Copynumber: 2.5 Consensus size: 32
831575 TTCTTTTGCT
* *
831585 CGAAGGACATAGGTAATCCTGTCCATATGTCC
1 CGAAGGACATAGGTAATACTATCCATATGTCC
*
831617 CGAAGGACATAGGTAA-ACTATCCATATGTCT
1 CGAAGGACATAGGTAATACTATCCATATGTCC
* *
831648 CGAAAGATATAGGTAA
1 CGAAGGACATAGGTAA
831664 CCCTCGACTC
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
31 26 0.62
32 16 0.38
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (32 bp):
CGAAGGACATAGGTAATACTATCCATATGTCC
Found at i:834437 original size:12 final size:12
Alignment explanation
Indices: 834420--834445 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
834410 AAGAATAATA
834420 AAATAAAAAATG
1 AAATAAAAAATG
834432 AAATAAAAAATG
1 AAATAAAAAATG
834444 AA
1 AA
834446 GAAAATTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (12 bp):
AAATAAAAAATG
Found at i:834440 original size:40 final size:39
Alignment explanation
Indices: 834336--834440 Score: 90
Period size: 40 Copynumber: 2.6 Consensus size: 39
834326 TATATTAGAT
*
834336 TATAAAATAGAACAAAT-AAATAAATATTAAATAAAAAGAA
1 TATAAAATA-AA-AAATGAAATAAAAATTAAATAAAAAGAA
* * * * *
834376 TTTAAAAAAAAAAAGGTTAAA-AAAAGTTAAA-AGAAAGAA
1 TATAAAATAAAAAA--TGAAATAAAAATTAAATAAAAAGAA
834415 TAATAAAATAAAAAATGAAATAAAAA
1 T-ATAAAATAAAAAATGAAATAAAAA
834441 ATGAAGAAAA
Statistics
Matches: 51, Mismatches: 9, Indels: 11
0.72 0.13 0.15
Matches are distributed among these distances:
38 7 0.14
39 14 0.27
40 27 0.53
41 3 0.06
ACGTcount: A:0.71, C:0.01, G:0.08, T:0.20
Consensus pattern (39 bp):
TATAAAATAAAAAATGAAATAAAAATTAAATAAAAAGAA
Found at i:835369 original size:12 final size:12
Alignment explanation
Indices: 835352--835376 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
835342 TTAAATTTTC
835352 TCATTTTTTATT
1 TCATTTTTTATT
835364 TCATTTTTTATT
1 TCATTTTTTATT
835376 T
1 T
835377 TATTATTTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTTTATT
Done.