Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008558.1 Hibiscus syriacus cultivar Beakdansim tig00111463_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: 2950132
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 14
Found at i:2841689 original size:21 final size:21
Alignment explanation
Indices: 2841663--2841703 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2841653 AATAAGTGTA
*
2841663 CCAAAGTACCGCATATATGTT
1 CCAAAGGACCGCATATATGTT
**
2841684 CCAAAGGATTGCATATATGT
1 CCAAAGGACCGCATATATGT
2841704 CTCGAAGGAC
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:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (21 bp):
CCAAAGGACCGCATATATGTT
Found at i:2842481 original size:19 final size:19
Alignment explanation
Indices: 2842457--2842506 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
2842447 CCCTAGTTGT
2842457 GGTATCGATACCAATCATG
1 GGTATCGATACCAATCATG
2842476 GGTATCGATACCAATCATG
1 GGTATCGATACCAATCATG
2842495 GGTATCGATACC
1 GGTATCGATACC
2842507 CATTTTGCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (19 bp):
GGTATCGATACCAATCATG
Found at i:2845946 original size:27 final size:27
Alignment explanation
Indices: 2845911--2845973 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 27
2845901 AATTCATGAC
* *
2845911 TTCATAAATCACCAAAAAATTAACTAAA
1 TTCA-AAATAACCAAAAAATTAACAAAA
* * *
2845939 TTCAAAATAATCAAATATTTAACAAAA
1 TTCAAAATAACCAAAAAATTAACAAAA
2845966 TGTCAAAA
1 T-TCAAAA
2845974 GTGTATACTA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
27 19 0.66
28 10 0.34
ACGTcount: A:0.57, C:0.14, G:0.02, T:0.27
Consensus pattern (27 bp):
TTCAAAATAACCAAAAAATTAACAAAA
Found at i:2846476 original size:2 final size:2
Alignment explanation
Indices: 2846469--2846498 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2846459 CAACAACAAA
2846469 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2846499 ACCCTAAAAT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2848834 original size:15 final size:15
Alignment explanation
Indices: 2848811--2848840 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2848801 TGTACTTCTG
*
2848811 TACTGAATCATTCAA
1 TACTAAATCATTCAA
2848826 TACTAAATCATTCAA
1 TACTAAATCATTCAA
2848841 AGATACGAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.20, G:0.03, T:0.33
Consensus pattern (15 bp):
TACTAAATCATTCAA
Found at i:2857829 original size:21 final size:20
Alignment explanation
Indices: 2857792--2857831 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2857782 TCAATTGATA
* *
2857792 TAAAATATTTTATTATTATT
1 TAAAACATTTTAATATTATT
2857812 TAAAACATATTTAATATTAT
1 TAAAACAT-TTTAATATTAT
2857832 CTGAATATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (20 bp):
TAAAACATTTTAATATTATT
Found at i:2867441 original size:2 final size:2
Alignment explanation
Indices: 2867428--2867491 Score: 105
Period size: 2 Copynumber: 32.5 Consensus size: 2
2867418 CCTTATTATT
2867428 TA TA TGA TA TA TA T- TA TA TA TA TA TA TA TA -A TA TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2867469 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
2867492 TTAATTATAT
Statistics
Matches: 59, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.03
2 55 0.93
3 2 0.03
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2867508 original size:10 final size:10
Alignment explanation
Indices: 2867421--2867584 Score: 86
Period size: 11 Copynumber: 15.6 Consensus size: 10
2867411 AATTAACCCT
2867421 TATTAT-TTA
1 TATTATATTA
*
2867430 TATGATA-TA
1 TATTATATTA
2867439 TATTATA-TA
1 TATTATATTA
*
2867448 TATATATATAA
1 TAT-TATATTA
2867459 TATATATATATA
1 TAT-TATAT-TA
2867471 TATATATATATA
1 TAT-TATAT-TA
2867483 TATATATATT-
1 TAT-TATATTA
2867493 TAATTATATTA
1 T-ATTATATTA
2867504 TATTATTTATTA
1 TATTA--TATTA
* * *
2867516 TAGTATTTTTT
1 TATTA-TATTA
* * *
2867527 TCATTTTTTTG
1 T-ATTATATTA
**
2867538 CGTTATATTA
1 TATTATATTA
2867548 TATTATATTA
1 TATTATATTA
2867558 TATTTATATTA
1 TA-TTATATTA
2867569 TATATATATT-
1 TAT-TATATTA
2867579 TATTAT
1 TATTAT
2867585 TATTTTTTAT
Statistics
Matches: 127, Mismatches: 17, Indels: 22
0.77 0.10 0.13
Matches are distributed among these distances:
9 21 0.17
10 34 0.27
11 39 0.31
12 33 0.26
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.59
Consensus pattern (10 bp):
TATTATATTA
Found at i:2867545 original size:54 final size:57
Alignment explanation
Indices: 2867487--2867592 Score: 143
Period size: 54 Copynumber: 1.9 Consensus size: 57
2867477 TATATATATA
2867487 TATATT-TAATTATATTATA-TTAT-TTAT-TATAGTATTT-TT-TTCATTTTTTTGCGT
1 TATATTAT-ATTATATTATATTTATATTATATATA-TATTTATTATT-ATTTTTTTGCGT
2867541 TATATTATATTATATTATATTTATATTATATATATATTTATTATTATTTTTT
1 TATATTATATTATATTATATTTATATTATATATATATTTATTATTATTTTTT
2867593 ATCTATGTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
54 17 0.37
55 5 0.11
56 9 0.20
57 13 0.28
58 2 0.04
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (57 bp):
TATATTATATTATATTATATTTATATTATATATATATTTATTATTATTTTTTTGCGT
Found at i:2867560 original size:15 final size:15
Alignment explanation
Indices: 2867540--2867584 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 15
2867530 TTTTTTTGCG
2867540 TTATATTATATTATA
1 TTATATTATATTATA
2867555 TTATATTTATATTATA
1 TTATA-TTATATTATA
2867571 TATATATT-TATTAT
1 T-TATATTATATTAT
2867585 TATTTTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
15 11 0.39
16 13 0.46
17 4 0.14
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTATATTATATTATA
Found at i:2867564 original size:21 final size:21
Alignment explanation
Indices: 2867540--2867582 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
2867530 TTTTTTTGCG
2867540 TTATATTATAT-TATATTATAT
1 TTATATTATATATATATT-TAT
2867561 TTATATTATATATATATTTAT
1 TTATATTATATATATATTTAT
2867582 T
1 T
2867583 ATTATTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TTATATTATATATATATTTAT
Found at i:2867623 original size:8 final size:9
Alignment explanation
Indices: 2867543--2867629 Score: 52
Period size: 10 Copynumber: 9.0 Consensus size: 9
2867533 TTTTGCGTTA
*
2867543 TATTATATTA
1 TATTAT-TTT
*
2867553 TATTATATT
1 TATTATTTT
*
2867562 TA-TATTATA
1 TATTATT-TT
2867571 TATATATTTAT
1 TAT-TATTT-T
2867582 TATTATTTTT
1 TATTA-TTTT
*
2867592 TATCTATGTT
1 TAT-TATTTT
2867602 TACTTATTTAT
1 TA-TTATTT-T
2867613 TATT-TTTT
1 TATTATTTT
2867621 TATTATTTT
1 TATTATTTT
2867630 CCTAACGTTA
Statistics
Matches: 61, Mismatches: 7, Indels: 19
0.70 0.08 0.22
Matches are distributed among these distances:
8 8 0.13
9 13 0.21
10 24 0.39
11 16 0.26
ACGTcount: A:0.29, C:0.02, G:0.01, T:0.68
Consensus pattern (9 bp):
TATTATTTT
Found at i:2867800 original size:21 final size:22
Alignment explanation
Indices: 2867779--2867819 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
2867769 TACATTTTTA
2867779 TATT-TTTT-TTTATA-TATTT
1 TATTATTTTATTTATACTATTT
2867798 TATTATTTTATTTATACTATTT
1 TATTATTTTATTTATACTATTT
2867820 ATTTTCATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 4 0.21
21 6 0.32
22 5 0.26
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (22 bp):
TATTATTTTATTTATACTATTT
Found at i:2867820 original size:21 final size:19
Alignment explanation
Indices: 2867779--2867824 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 19
2867769 TACATTTTTA
2867779 TATTTTTTTTTATATATTT
1 TATTTTTTTTTATATATTT
2867798 TATTATTTTATTTATACTA-TT
1 TATT-TTTT-TTTATA-TATTT
2867819 TATTTT
1 TATTTT
2867825 CATTATATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 4 0.17
20 6 0.25
21 12 0.50
22 2 0.08
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (19 bp):
TATTTTTTTTTATATATTT
Found at i:2868004 original size:15 final size:15
Alignment explanation
Indices: 2867980--2868014 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
2867970 ATTATTTTAT
2867980 GTTTATTA-TTATTG
1 GTTTATTATTTATTG
2867994 GTTTCATTATTTATTG
1 GTTT-ATTATTTATTG
2868010 GTTTA
1 GTTTA
2868015 CTCTTTAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 4 0.21
15 5 0.26
16 10 0.53
ACGTcount: A:0.20, C:0.03, G:0.14, T:0.63
Consensus pattern (15 bp):
GTTTATTATTTATTG
Found at i:2869559 original size:20 final size:21
Alignment explanation
Indices: 2869534--2869573 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2869524 TTTTACCACA
2869534 ATTCAT-CTAGTATCGATACT
1 ATTCATCCTAGTATCGATACT
2869554 ATTCATCCTAGTATCGATAC
1 ATTCATCCTAGTATCGATAC
2869574 CTAGTCCCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.38
Consensus pattern (21 bp):
ATTCATCCTAGTATCGATACT
Found at i:2870050 original size:14 final size:16
Alignment explanation
Indices: 2870006--2870047 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
2869996 ATGAAGCTTG
2870006 GAATGAAGAATGAAGAA
1 GAATGAAGAA-GAAGAA
2870023 GAATTGAAGAAGAAGAA
1 GAA-TGAAGAAGAAGAA
2870040 -AATGAAGA
1 GAATGAAGA
2870048 GAACGGAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 6 0.25
16 2 0.08
17 9 0.38
18 7 0.29
ACGTcount: A:0.60, C:0.00, G:0.29, T:0.12
Consensus pattern (16 bp):
GAATGAAGAAGAAGAA
Found at i:2874956 original size:21 final size:20
Alignment explanation
Indices: 2874910--2874964 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 20
2874900 CCAAAGTGAG
* * *
2874910 TAGTATCGATACTCTATTTG
1 TAGTATCGATACCCTAGTTC
2874930 TAGTATCGATACCCTAAGTTC
1 TAGTATCGATACCCT-AGTTC
*
2874951 TAGTATCCATACCC
1 TAGTATCGATACCC
2874965 CTATGAGTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.36
Consensus pattern (20 bp):
TAGTATCGATACCCTAGTTC
Found at i:2875055 original size:21 final size:21
Alignment explanation
Indices: 2875016--2875056 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2875006 TGGAGCACAA
**
2875016 TATCGATACTGTCACCCTGAG
1 TATCGATACTCCCACCCTGAG
*
2875037 TATCGATACTCCCAGCCTGA
1 TATCGATACTCCCACCCTGA
2875057 AACCTTAATT
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:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (21 bp):
TATCGATACTCCCACCCTGAG
Found at i:2876204 original size:60 final size:61
Alignment explanation
Indices: 2876104--2876232 Score: 208
Period size: 60 Copynumber: 2.1 Consensus size: 61
2876094 TTTTCGAAAC
*
2876104 GTGGATCTTCTAAGTTTTTGACCTAATTGAGACAATACCATATGATATCTCTTGATTTTAT
1 GTGGATCTTATAAGTTTTTGACCTAATTGAGACAATACCATATGATATCTCTTGATTTTAT
**
2876165 GTGGATCTTATAAG-TTTTGACCTAATTGCTACCAA-ACCATATGATATCTCTTGATTTTAT
1 GTGGATCTTATAAGTTTTTGACCTAATTGAGA-CAATACCATATGATATCTCTTGATTTTAT
2876225 GTGGATCT
1 GTGGATCT
2876233 ACTTTATTAT
Statistics
Matches: 64, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
60 48 0.75
61 16 0.25
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.42
Consensus pattern (61 bp):
GTGGATCTTATAAGTTTTTGACCTAATTGAGACAATACCATATGATATCTCTTGATTTTAT
Found at i:2879254 original size:17 final size:17
Alignment explanation
Indices: 2879234--2879268 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
2879224 TCTATTGGCC
2879234 CCCATTGCTTATTAGCA
1 CCCATTGCTTATTAGCA
2879251 CCCATTGCTTATTAGCA
1 CCCATTGCTTATTAGCA
2879268 C
1 C
2879269 TAGCTTGACG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.31, G:0.11, T:0.34
Consensus pattern (17 bp):
CCCATTGCTTATTAGCA
Found at i:2882590 original size:16 final size:17
Alignment explanation
Indices: 2882569--2882602 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2882559 GTCCTTTTCC
2882569 TAAAAA-TAAATAATTA
1 TAAAAATTAAATAATTA
*
2882585 TAAAAATTAACTAATTA
1 TAAAAATTAAATAATTA
2882602 T
1 T
2882603 TACTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (17 bp):
TAAAAATTAAATAATTA
Found at i:2882760 original size:18 final size:17
Alignment explanation
Indices: 2882728--2882773 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
2882718 GAATTATATT
2882728 AGTAAAATATTAAATAA
1 AGTAAAATATTAAATAA
2882745 AGTAAAATACTTAAATAA
1 AGTAAAATA-TTAAATAA
*
2882763 ATTAAATATAT
1 AGTAAA-ATAT
2882774 AATATTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 9 0.35
18 14 0.54
19 3 0.12
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (17 bp):
AGTAAAATATTAAATAA
Found at i:2884064 original size:37 final size:37
Alignment explanation
Indices: 2883998--2884071 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 37
2883988 ATCTAAATCA
* *
2883998 GTCTCAACCTTCCTTCTTTACCGGCAAATTTGCTCCG
1 GTCTCAACCTTCATTCTATACCGGCAAATTTGCTCCG
* *
2884035 GTCTCAACCTTCATTCTATACTGGTAAATTTGCTCCG
1 GTCTCAACCTTCATTCTATACCGGCAAATTTGCTCCG
2884072 ATGGGTAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.19, C:0.31, G:0.14, T:0.36
Consensus pattern (37 bp):
GTCTCAACCTTCATTCTATACCGGCAAATTTGCTCCG
Found at i:2886475 original size:31 final size:31
Alignment explanation
Indices: 2886440--2886537 Score: 97
Period size: 31 Copynumber: 3.1 Consensus size: 31
2886430 AAAGGTAATG
* * * *
2886440 CCTTGGGGCCTTAGAGCCTACCTAATGAATA
1 CCTTGGGGCCTAAGAGCCTACCAAAGGAACA
* *
2886471 CCTTGGGGCCTGACAGCCTACCCAAAGGAACA
1 CCTTGGGGCCTAAGAGCCTA-CCAAAGGAACA
* * * *
2886503 TCTCGGGGCCTAAGAGCCTACCCAAGGGACA
1 CCTTGGGGCCTAAGAGCCTACCAAAGGAACA
2886534 CCTT
1 CCTT
2886538 AGGTCTGTAA
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
31 29 0.55
32 24 0.45
ACGTcount: A:0.26, C:0.32, G:0.24, T:0.18
Consensus pattern (31 bp):
CCTTGGGGCCTAAGAGCCTACCAAAGGAACA
Found at i:2886521 original size:32 final size:32
Alignment explanation
Indices: 2886444--2886536 Score: 91
Period size: 32 Copynumber: 3.0 Consensus size: 32
2886434 GTAATGCCTT
* * * * *
2886444 GGGGCCTTAGAGCCTA-CCTAATGAATACCTT
1 GGGGCCTAAGAGCCTACCCAAAGGAACACCTC
* * *
2886475 GGGGCCTGACAGCCTACCCAAAGGAACATCTC
1 GGGGCCTAAGAGCCTACCCAAAGGAACACCTC
*
2886507 GGGGCCTAAGAGCCTACCC-AAGGGACACCT
1 GGGGCCTAAGAGCCTACCCAAAGGAACACCT
2886537 TAGGTCTGTA
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
31 23 0.46
32 27 0.54
ACGTcount: A:0.27, C:0.31, G:0.26, T:0.16
Consensus pattern (32 bp):
GGGGCCTAAGAGCCTACCCAAAGGAACACCTC
Found at i:2890815 original size:20 final size:20
Alignment explanation
Indices: 2890790--2890827 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2890780 CCACATGCAA
*
2890790 TTATATGATCCTAAATATAT
1 TTATATGAACCTAAATATAT
*
2890810 TTATATGAACGTAAATAT
1 TTATATGAACCTAAATAT
2890828 GCCTTAAGAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (20 bp):
TTATATGAACCTAAATATAT
Found at i:2893168 original size:3 final size:3
Alignment explanation
Indices: 2893160--2893198 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
2893150 TGGAATAAAT
* *
2893160 GAA GAA GAA GAA AAA GAA GAA GAA GAA AAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
2893199 AGTCTAAGCT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:2893180 original size:15 final size:15
Alignment explanation
Indices: 2893160--2893198 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
2893150 TGGAATAAAT
2893160 GAAGAAGAAGAAAAA
1 GAAGAAGAAGAAAAA
2893175 GAAGAAGAAGAAAAA
1 GAAGAAGAAGAAAAA
2893190 GAAGAAGAA
1 GAAGAAGAA
2893199 AGTCTAAGCT
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (15 bp):
GAAGAAGAAGAAAAA
Found at i:2896590 original size:66 final size:63
Alignment explanation
Indices: 2896483--2896605 Score: 158
Period size: 66 Copynumber: 1.9 Consensus size: 63
2896473 TTTGTTGAAG
* * *
2896483 GTGCATCGATGCACATGGAGTGTATCGATGCACTCATTTAAAATAAATAAACATCGAATGCCATT
1 GTGCATCGATGCACAAGGAGTGCATCGATGCACTCA-TTAAAAT--ACAAACATCGAATGCCATT
2896548 A
63 A
*
2896549 GTGCATCGATGCATAAGGAGTGCATCGATGCACCTGC-TTAAAATACAAACATCGAAT
1 GTGCATCGATGCACAAGGAGTGCATCGATGCA-CT-CATTAAAATACAAACATCGAAT
2896606 AGGATTTCTG
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
64 12 0.24
66 36 0.71
67 2 0.04
68 1 0.02
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.25
Consensus pattern (63 bp):
GTGCATCGATGCACAAGGAGTGCATCGATGCACTCATTAAAATACAAACATCGAATGCCATTA
Found at i:2897225 original size:22 final size:22
Alignment explanation
Indices: 2897200--2897251 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
2897190 ATATTAGTCC
2897200 TTCGGGATGTATCCAGTGGTCA
1 TTCGGGATGTATCCAGTGGTCA
* *
2897222 TTCGAGATGTATCCAGTGGTCC
1 TTCGGGATGTATCCAGTGGTCA
2897244 TTCGGGAT
1 TTCGGGAT
2897252 ATAGTGGTCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (22 bp):
TTCGGGATGTATCCAGTGGTCA
Found at i:2904159 original size:22 final size:22
Alignment explanation
Indices: 2904134--2904190 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
2904124 GGGTATATTA
*
2904134 GTCCTTCGGGACGTATCCAGTG
1 GTCCTTCGGGACATATCCAGTG
2904156 GTCCTTCGGGACATATCCAGTG
1 GTCCTTCGGGACATATCCAGTG
*
2904178 ATCCTTCGGGACA
1 GTCCTTCGGGACA
2904191 AAAACTGAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.18, C:0.28, G:0.28, T:0.26
Consensus pattern (22 bp):
GTCCTTCGGGACATATCCAGTG
Found at i:2925282 original size:36 final size:36
Alignment explanation
Indices: 2925240--2925315 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
2925230 TATAGCTAAA
*
2925240 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
2925276 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
2925312 AAAA
1 AAAA
2925316 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:2929812 original size:15 final size:15
Alignment explanation
Indices: 2929794--2929822 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2929784 CCACGGTGCT
2929794 CCGGAATCCTGCGCC
1 CCGGAATCCTGCGCC
2929809 CCGGAATCCTGCGC
1 CCGGAATCCTGCGC
2929823 GATTGTGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.45, G:0.28, T:0.14
Consensus pattern (15 bp):
CCGGAATCCTGCGCC
Found at i:2930296 original size:36 final size:36
Alignment explanation
Indices: 2930246--2930321 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
2930236 ATAGCTAAAA
*
2930246 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
2930282 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
2930318 AAAA
1 AAAA
2930322 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:2932390 original size:14 final size:14
Alignment explanation
Indices: 2932371--2932413 Score: 68
Period size: 14 Copynumber: 3.1 Consensus size: 14
2932361 TTATGAGTGT
2932371 TTATTGGGGTAAAA
1 TTATTGGGGTAAAA
2932385 TTATTGGGGTAAAA
1 TTATTGGGGTAAAA
* *
2932399 TTATTCGGATAAAA
1 TTATTGGGGTAAAA
2932413 T
1 T
2932414 GCTTTTGACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.37, C:0.02, G:0.23, T:0.37
Consensus pattern (14 bp):
TTATTGGGGTAAAA
Found at i:2932482 original size:21 final size:21
Alignment explanation
Indices: 2932456--2932512 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
2932446 AAATTAGTGA
2932456 ATATTTTTTAAGATTTTGAAT
1 ATATTTTTTAAGATTTTGAAT
2932477 ATATTTTTTAAGATTTTGAAT
1 ATATTTTTTAAGATTTTGAAT
2932498 ATATTTTTTAA-ATTT
1 ATATTTTTTAAGATTT
2932513 AGTATTTACA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 4 0.11
21 32 0.89
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (21 bp):
ATATTTTTTAAGATTTTGAAT
Found at i:2933225 original size:20 final size:20
Alignment explanation
Indices: 2933200--2933392 Score: 246
Period size: 20 Copynumber: 9.6 Consensus size: 20
2933190 GATTTTCCAG
* ** *
2933200 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
2933220 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
2933240 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2933260 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
2933280 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2933300 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2933320 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
2933340 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGTATCCGT-A
2933361 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
2933381 AATCGCAACGCG
1 AATCGCAACGCG
2933393 ATTTTTAAAG
Statistics
Matches: 151, Mismatches: 17, Indels: 10
0.85 0.10 0.06
Matches are distributed among these distances:
19 1 0.01
20 131 0.87
21 19 0.13
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:2933808 original size:32 final size:32
Alignment explanation
Indices: 2933770--2933838 Score: 120
Period size: 32 Copynumber: 2.2 Consensus size: 32
2933760 ATTTCACTTA
2933770 GATTTCATTTCGCGTTACGATTCTCTCGTTGC
1 GATTTCATTTCGCGTTACGATTCTCTCGTTGC
* *
2933802 GATTTCATTTCGCGTTGCTATTCTCTCGTTGC
1 GATTTCATTTCGCGTTACGATTCTCTCGTTGC
2933834 GATTT
1 GATTT
2933839 TCAAGTTAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.12, C:0.23, G:0.19, T:0.46
Consensus pattern (32 bp):
GATTTCATTTCGCGTTACGATTCTCTCGTTGC
Found at i:2933819 original size:18 final size:18
Alignment explanation
Indices: 2933770--2933819 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 18
2933760 ATTTCACTTA
*
2933770 GATTTCATTTCGCGTTAC
1 GATTTCATTTCGCGTTGC
*
2933788 GA-TTC---TCTCGTTGC
1 GATTTCATTTCGCGTTGC
2933802 GATTTCATTTCGCGTTGC
1 GATTTCATTTCGCGTTGC
2933820 TATTCTCTCG
Statistics
Matches: 25, Mismatches: 3, Indels: 8
0.69 0.08 0.22
Matches are distributed among these distances:
14 9 0.36
15 3 0.12
17 3 0.12
18 10 0.40
ACGTcount: A:0.12, C:0.24, G:0.20, T:0.44
Consensus pattern (18 bp):
GATTTCATTTCGCGTTGC
Found at i:2933947 original size:21 final size:20
Alignment explanation
Indices: 2933921--2933994 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 20
2933911 TGCAGAAGAG
2933921 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* **
2933942 TCGCAACGTGAAAATGACTA
1 TCGCAACGAGAAAATGAAAA
2933962 TCTGCAACGAGAAAAATGAAAA
1 TC-GCAACGAG-AAAATGAAAA
2933984 TCGCAACGAGA
1 TCGCAACGAGA
2933995 GAATCGCAAC
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
20 10 0.22
21 25 0.56
22 10 0.22
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:2934092 original size:21 final size:21
Alignment explanation
Indices: 2934066--2934130 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
2934056 CGCGTTGCGA
2934066 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
2934087 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
2934107 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
2934128 TTC
1 TTC
2934131 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:2934127 original size:20 final size:20
Alignment explanation
Indices: 2934022--2934128 Score: 97
Period size: 19 Copynumber: 5.7 Consensus size: 20
2934012 CAAAATTGCA
2934022 TTGCGATTTTCATT-T-TGCG
1 TTGCGATTTTCATTCTCT-CG
*
2934041 TTGCGATTTTCATT-TCGCG
1 TTGCGATTTTCATTCTCTCG
2934060 TTGCG------ATTCTCTCG
1 TTGCGATTTTCATTCTCTCG
2934074 TTGCGATTTTCATTTCTCTCG
1 TTGCGATTTTCA-TTCTCTCG
***
2934095 TTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCATTCTCTCG
2934115 TTGCGATTTTCATT
1 TTGCGATTTTCATT
2934129 TCAACCAAAA
Statistics
Matches: 71, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
13 3 0.04
14 9 0.13
19 22 0.31
20 20 0.28
21 17 0.24
ACGTcount: A:0.11, C:0.22, G:0.19, T:0.48
Consensus pattern (20 bp):
TTGCGATTTTCATTCTCTCG
Found at i:2936053 original size:93 final size:93
Alignment explanation
Indices: 2935816--2936130 Score: 596
Period size: 93 Copynumber: 3.4 Consensus size: 93
2935806 TAGATTGCTT
* *
2935816 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTATGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2935881 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
2935909 AGT-AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTATGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2935973 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2936001 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2936066 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2936094 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
2936131 AATACCCTGA
Statistics
Matches: 217, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
92 89 0.41
93 128 0.59
ACGTcount: A:0.23, C:0.14, G:0.18, T:0.45
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:2936264 original size:14 final size:14
Alignment explanation
Indices: 2936245--2936301 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
2936235 ACGAAACTTA
2936245 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
2936259 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
2936278 AATCGCAACGACAG
1 AATCGCAACGAGAG
2936292 AATCGCAACG
1 AATCGCAACG
2936302 CGAAACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:2936265 original size:33 final size:33
Alignment explanation
Indices: 2936228--2936350 Score: 167
Period size: 33 Copynumber: 3.7 Consensus size: 33
2936218 TAGTTTACTT
* * *
2936228 TCGCAACACGAAACTTAAATCGCAACGAGAGAA
1 TCGCAACGCGAAACTAAAATCGCAACGACAGAA
2936261 TCGCAACGCGAAA-TGAAAATCGCAACGACAGAA
1 TCGCAACGCGAAACT-AAAATCGCAACGACAGAA
* *
2936294 TCGCAACGCGAAACCAAAATCGCAACGACAAAA
1 TCGCAACGCGAAACTAAAATCGCAACGACAGAA
* *
2936327 TCGCAACGCAAAACCAAAATCGCA
1 TCGCAACGCGAAACTAAAATCGCA
2936351 TTGCGATTTT
Statistics
Matches: 82, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
32 1 0.01
33 81 0.99
ACGTcount: A:0.46, C:0.28, G:0.17, T:0.09
Consensus pattern (33 bp):
TCGCAACGCGAAACTAAAATCGCAACGACAGAA
Found at i:2936283 original size:19 final size:18
Alignment explanation
Indices: 2936259--2936320 Score: 60
Period size: 19 Copynumber: 3.6 Consensus size: 18
2936249 GCAACGAGAG
2936259 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAA-GAA
*
2936278 AATCGCAA--CGACAG--
1 AATCGCAACGCGAAAGAA
*
2936292 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-GAA
2936311 AATCGCAACG
1 AATCGCAACG
2936321 ACAAAATCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 8 0.23
16 5 0.14
17 4 0.11
19 18 0.51
ACGTcount: A:0.45, C:0.27, G:0.19, T:0.08
Consensus pattern (18 bp):
AATCGCAACGCGAAAGAA
Found at i:2936327 original size:14 final size:14
Alignment explanation
Indices: 2936276--2936339 Score: 67
Period size: 14 Copynumber: 4.3 Consensus size: 14
2936266 ACGCGAAATG
2936276 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
2936290 AGAATCGCAACGCGAAACC
1 AAAATCGCAA--CG--A-C
2936309 AAAATCGCAACGAC
1 AAAATCGCAACGAC
2936323 AAAATCGCAACG-C
1 AAAATCGCAACGAC
2936336 AAAA
1 AAAA
2936340 CCAAAATCGC
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
13 5 0.12
14 22 0.51
15 1 0.02
16 2 0.05
17 2 0.05
18 1 0.02
19 10 0.23
ACGTcount: A:0.50, C:0.28, G:0.16, T:0.06
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:2936336 original size:19 final size:19
Alignment explanation
Indices: 2936292--2936350 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
2936282 GCAACGACAG
*
2936292 AATCGCAACGCGAAACCAA
1 AATCGCAACGCAAAACCAA
2936311 AATCGCAACG----A-CAA
1 AATCGCAACGCAAAACCAA
2936325 AATCGCAACGCAAAACCAA
1 AATCGCAACGCAAAACCAA
2936344 AATCGCA
1 AATCGCA
2936351 TTGCGATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 13 0.37
15 1 0.03
18 1 0.03
19 20 0.57
ACGTcount: A:0.49, C:0.31, G:0.14, T:0.07
Consensus pattern (19 bp):
AATCGCAACGCAAAACCAA
Found at i:2936368 original size:19 final size:19
Alignment explanation
Indices: 2936346--2936504 Score: 157
Period size: 19 Copynumber: 8.6 Consensus size: 19
2936336 AAAACCAAAA
*
2936346 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2936365 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
2936384 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
*
2936400 T--CGTTACGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
2936417 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* **
2936436 TCGCGTTACGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
2936455 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
2936474 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
2936494 TCGTGTTGCGA
1 TCGCGTTGCGA
2936505 AAGTAAACTA
Statistics
Matches: 115, Mismatches: 19, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
14 6 0.05
16 5 0.04
17 5 0.04
19 87 0.76
20 12 0.10
ACGTcount: A:0.12, C:0.19, G:0.23, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2936416 original size:52 final size:54
Alignment explanation
Indices: 2936354--2936488 Score: 166
Period size: 52 Copynumber: 2.5 Consensus size: 54
2936344 AATCGCATTG
*
2936354 CGATTTTCATTTCGCGTTGCGATTTTCATTTCGCATTGCGATTCT-G-TCGTTA
1 CGATTTTCATTTCGCGTTGCGATTTTCATTTCGCATTACGATTCTGGTTCGTTA
** * * *
2936406 CGATTTTCATTTCGCGTTGCGATTTTGGTTTCGCGTTACGATTTTGGTTTCTCGTTG
1 CGATTTTCATTTCGCGTTGCGATTTTCATTTCGCATTACGATTCTGG--T-TCGTTA
*
2936463 CGATTCTCATTTCGCGTTGCGATTTT
1 CGATTTTCATTTCGCGTTGCGATTTT
2936489 AAGTTTCGTG
Statistics
Matches: 71, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
52 40 0.56
53 1 0.01
57 30 0.42
ACGTcount: A:0.11, C:0.20, G:0.21, T:0.47
Consensus pattern (54 bp):
CGATTTTCATTTCGCGTTGCGATTTTCATTTCGCATTACGATTCTGGTTCGTTA
Found at i:2938434 original size:14 final size:14
Alignment explanation
Indices: 2938415--2938450 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2938405 ACTGTTTAAT
2938415 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
2938429 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
2938443 TGATTTGT
1 TGATTTGT
2938451 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2938633 original size:20 final size:19
Alignment explanation
Indices: 2938557--2938654 Score: 127
Period size: 19 Copynumber: 5.4 Consensus size: 19
2938547 AAAAATGACT
2938557 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2938576 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2938595 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
2938609 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
2938629 ATCGCAATGCGGAAATG-AA
1 ATCGCAATGC-GAAATGAAA
2938648 ATCGCAA
1 ATCGCAA
2938655 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 12
0.84 0.02 0.14
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 1 0.01
17 3 0.04
19 36 0.51
20 20 0.28
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2938636 original size:53 final size:53
Alignment explanation
Indices: 2938557--2938672 Score: 209
Period size: 53 Copynumber: 2.2 Consensus size: 53
2938547 AAAAATGACT
2938557 ATCGCAATGC-GAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGGAAATGAAAATCGCAATGCGGAAATG-AAATCGCAACGAGAGA
2938609 ATCGCAATGCGGAAATGAAAATCGCAATGCGGAAATGAAATCGCAACGAGAGA
1 ATCGCAATGCGGAAATGAAAATCGCAATGCGGAAATGAAATCGCAACGAGAGA
2938662 ATCGCAATGCG
1 ATCGCAATGCG
2938673 ATTTTCATTT
Statistics
Matches: 62, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
52 10 0.16
53 46 0.74
54 6 0.10
ACGTcount: A:0.43, C:0.18, G:0.25, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGGAAATGAAAATCGCAATGCGGAAATGAAATCGCAACGAGAGA
Found at i:2938691 original size:19 final size:19
Alignment explanation
Indices: 2938663--2938923 Score: 303
Period size: 19 Copynumber: 14.7 Consensus size: 19
2938653 AACGAGAGAA
*
2938663 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
2938682 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
2938701 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
2938718 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
2938735 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
2938754 TCGCATTGCGA--TTC-TA
1 TCGCATTGCGATTTTCATT
2938770 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
2938787 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
2938806 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
2938823 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
2938840 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
2938859 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
2938878 TCCGCATTGCGA-TTTCA--
1 T-CGCATTGCGATTTTCATT
*
2938895 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
2938911 TCGCATTGCGATT
1 TCGCATTGCGATT
2938924 CTCTCGTTGC
Statistics
Matches: 209, Mismatches: 9, Indels: 48
0.79 0.03 0.18
Matches are distributed among these distances:
13 5 0.02
14 23 0.11
15 1 0.00
16 18 0.09
17 21 0.10
18 6 0.03
19 105 0.50
20 30 0.14
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:2938812 original size:105 final size:104
Alignment explanation
Indices: 2938669--2938937 Score: 418
Period size: 105 Copynumber: 2.6 Consensus size: 104
2938659 AGAATCGCAA
2938669 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
2938734 TTCGCATTGCGATTTTCATTTCGCATTGCGATTCTATC-GT
66 TTCGCATTGCGATTTTCATTTCGCATTGCGATT-T-TCAGT
2938774 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
*
2938839 TTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATT
66 TTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCAGT
* * *** *
2938878 TCCGCA-TTGCGATTTCATGTTGGGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATT
1 TGCG-ATTTTC-ATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATT
2938938 GTAATTTCCG
Statistics
Matches: 154, Mismatches: 7, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
103 2 0.01
104 34 0.22
105 118 0.77
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (104 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
TTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCAGT
Found at i:2938945 original size:52 final size:52
Alignment explanation
Indices: 2938669--2938937 Score: 400
Period size: 52 Copynumber: 5.1 Consensus size: 52
2938659 AGAATCGCAA
2938669 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
*
2938722 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTATCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
2938774 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
*
2938827 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATT-T-TCATT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC-GT
* * *** *
2938878 TCCGCA-TTGCGATTTCATGTTGGGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCG-ATTTTC-ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
2938931 TGCGATT
1 TGCGATT
2938938 GTAATTTCCG
Statistics
Matches: 198, Mismatches: 11, Indels: 14
0.89 0.05 0.06
Matches are distributed among these distances:
50 2 0.01
51 8 0.04
52 96 0.48
53 90 0.45
54 2 0.01
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (52 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:2941220 original size:12 final size:12
Alignment explanation
Indices: 2941203--2941227 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2941193 TCTTCGGGGA
2941203 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2941215 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2941227 C
1 C
2941228 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:2942165 original size:20 final size:20
Alignment explanation
Indices: 2942137--2942365 Score: 235
Period size: 20 Copynumber: 11.4 Consensus size: 20
2942127 AAATTTCAGT
* * *
2942137 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
2942157 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
2942177 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
2942197 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
2942217 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
2942237 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
2942257 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
2942277 GTTGCTATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
* *
2942297 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
2942317 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
2942337 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
2942357 GTTGCGATT
1 GTTGCGATT
2942366 CTTGAAAATC
Statistics
Matches: 181, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 180 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:2942418 original size:21 final size:20
Alignment explanation
Indices: 2942333--2942429 Score: 79
Period size: 21 Copynumber: 4.7 Consensus size: 20
2942323 ATTTATGTGT
* *
2942333 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCAAAA
*
2942353 TCGCGTTGCGATTCTTGAAAA
1 TCGCGTTGCGATT-TTCAAAA
** **
2942374 TCGCAATGCGAATTTGT-ACTA
1 TCGCGTTGCG-ATTT-TCAAAA
*
2942395 TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTTCAA-AA
2942416 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
2942430 GGAAACTGAT
Statistics
Matches: 61, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
19 1 0.02
20 18 0.30
21 38 0.62
22 4 0.07
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.37
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCAAAA
Found at i:2942426 original size:42 final size:42
Alignment explanation
Indices: 2942333--2942430 Score: 105
Period size: 42 Copynumber: 2.4 Consensus size: 42
2942323 ATTTATGTGT
* *
2942333 TCGCGTTGCGATTT-TCATATTCGCGTTGCGATTCTTGAAAA
1 TCGCGTTGCGATTTGTCATATTCGCATTGCGATTCTTCAAAA
**
2942374 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATT-TTCAAGAA
1 TCGCGTTGCG-ATTTGTCA-TATTCGCATTGCGATTCTTCAA-AA
2942416 TCGCGTTGCGATTTG
1 TCGCGTTGCGATTTG
2942431 GAAACTGATT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
41 17 0.36
42 27 0.57
43 3 0.06
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.37
Consensus pattern (42 bp):
TCGCGTTGCGATTTGTCATATTCGCATTGCGATTCTTCAAAA
Found at i:2943828 original size:20 final size:21
Alignment explanation
Indices: 2943789--2943828 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2943779 AGCGCTACCT
*
2943789 AAAATATTATTTTTTCTATCG
1 AAAATATTATATTTTCTATCG
*
2943810 AAAATATTA-ATTTTGTATC
1 AAAATATTATATTTTCTATC
2943829 TAATTTTAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.50
Consensus pattern (21 bp):
AAAATATTATATTTTCTATCG
Found at i:2944201 original size:50 final size:50
Alignment explanation
Indices: 2944133--2944255 Score: 144
Period size: 50 Copynumber: 2.5 Consensus size: 50
2944123 TTAGCAGAAA
* *
2944133 AGCGCG-CCCCTGCACCGCGCTATATGCTGATTTGACGT-CACGTGGGTAT
1 AGCGCGCCCCCTGCACCGCGCTATACGCTGATCTGAC-TCCACGTGGGTAT
* * * *
2944182 AGCGCGCCCCCTGCCCCGCGATATACGGTGATCTGGCTCCACGTGGGTAT
1 AGCGCGCCCCCTGCACCGCGCTATACGCTGATCTGACTCCACGTGGGTAT
*
2944232 AGCGCGCCCCTTG-ATCCGCGCTAT
1 AGCGCGCCCCCTGCA-CCGCGCTAT
2944256 CCCTGGATAT
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
49 7 0.11
50 55 0.89
ACGTcount: A:0.15, C:0.35, G:0.28, T:0.22
Consensus pattern (50 bp):
AGCGCGCCCCCTGCACCGCGCTATACGCTGATCTGACTCCACGTGGGTAT
Found at i:2944403 original size:9 final size:10
Alignment explanation
Indices: 2944378--2944417 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
2944368 TTTATCACAC
*
2944378 CAAATTCTTT
1 CAAATTCTCT
2944388 CAAATTCTCT
1 CAAATTCTCT
2944398 -AAATTCTCT
1 CAAATTCTCT
*
2944407 CAAATACTCT
1 CAAATTCTCT
2944417 C
1 C
2944418 TTTTTAAGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
9 9 0.33
10 18 0.67
ACGTcount: A:0.33, C:0.28, G:0.00, T:0.40
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:2944403 original size:19 final size:19
Alignment explanation
Indices: 2944379--2944416 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2944369 TTATCACACC
* *
2944379 AAATTCTTTCAAATTCTCT
1 AAATTCTCTCAAATACTCT
2944398 AAATTCTCTCAAATACTCT
1 AAATTCTCTCAAATACTCT
2944417 CTTTTTAAGG
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:0.34, C:0.24, G:0.00, T:0.42
Consensus pattern (19 bp):
AAATTCTCTCAAATACTCT
Found at i:2944666 original size:110 final size:110
Alignment explanation
Indices: 2944546--2944757 Score: 354
Period size: 110 Copynumber: 1.9 Consensus size: 110
2944536 TCATATCTCT
* *
2944546 ACACTTTGCTGATACGGTAACATTTTAACATTTTAATTTAATTTTAATTATAAGTAATATTTAGT
1 ACACTTTGCTGATACGGTAACATTTTAACATTTTAATTTAATTTAAATTATAAGTAATAATTAGT
* *
2944611 TGATTTATTATGTGCATGATTATTAGATTAA-AATTAAATATATCG
66 TGATTCATTA-ATGCATGATTATTAGATTAAGAATTAAATATATCG
* *
2944656 ACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
1 ACACTTTGCTGATACGGTAACATTTTAACATTTTAATTTAATTTAAATTATAAGTAATAATTAGT
2944721 TGATTCATTAATGCATGATTATTAGATTAAGAATTAA
66 TGATTCATTAATGCATGATTATTAGATTAAGAATTAA
2944758 TTTTTGTAAT
Statistics
Matches: 95, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
109 19 0.20
110 76 0.80
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.44
Consensus pattern (110 bp):
ACACTTTGCTGATACGGTAACATTTTAACATTTTAATTTAATTTAAATTATAAGTAATAATTAGT
TGATTCATTAATGCATGATTATTAGATTAAGAATTAAATATATCG
Done.