Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001876.1 Hibiscus syriacus cultivar Beakdansim tig00003805_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: 95567
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:8207 original size:2 final size:2
Alignment explanation
Indices: 8202--8241 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
8192 ATTTTTTCTA
8202 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT A- AT A- 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
8241 A
1 A
8242 GAGTTTAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.09
2 32 0.91
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:19455 original size:55 final size:54
Alignment explanation
Indices: 19349--19458 Score: 127
Period size: 55 Copynumber: 2.0 Consensus size: 54
19339 CATAGAATTT
* *
19349 GGCAGGGTAAAAATTCCATGTGGTAACAATGCTAATGGAGACGAGCATATCGCC
1 GGCAGGGTAAAAATTCCATGTGCTAACAATGCTAATGGACACGAGCATATCGCC
* *
19403 GGCAGGGTTAAAAA-TCCATGTGCTAA-ATGATGCTGATGGACAC-AGGCGTATCGCC
1 GGCAGGG-TAAAAATTCCATGTGCTAACA--ATGCTAATGGACACGA-GCATATCGCC
19458 G
1 G
19459 ACCGTGGTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
53 1 0.02
54 19 0.40
55 28 0.58
ACGTcount: A:0.31, C:0.19, G:0.29, T:0.21
Consensus pattern (54 bp):
GGCAGGGTAAAAATTCCATGTGCTAACAATGCTAATGGACACGAGCATATCGCC
Found at i:21894 original size:23 final size:23
Alignment explanation
Indices: 21868--21918 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
21858 GGACCGATTG
*
21868 GTTTTGGTTCAAGTCAACCATTT
1 GTTTCGGTTCAAGTCAACCATTT
21891 GTTTCGGTTCAAGTCAACCATTT
1 GTTTCGGTTCAAGTCAACCATTT
21914 GTTTC
1 GTTTC
21919 TTGGGTAGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.43
Consensus pattern (23 bp):
GTTTCGGTTCAAGTCAACCATTT
Found at i:22589 original size:2 final size:2
Alignment explanation
Indices: 22582--22636 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
22572 TTGCTAGGTC
22582 TA TA TA TA 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 TA TA TA TA
22624 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
22637 TCTTTTTTCA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:28395 original size:2 final size:2
Alignment explanation
Indices: 28326--28378 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
28316 TTTATTATCA
28326 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28368 AT AT AT AT AT A
1 AT AT AT AT AT A
28379 AACAATCAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28760 original size:12 final size:12
Alignment explanation
Indices: 28743--28767 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28733 GTGGAAGGTG
28743 GCGGTGGCGATA
1 GCGGTGGCGATA
28755 GCGGTGGCGATA
1 GCGGTGGCGATA
28767 G
1 G
28768 GTGGGTCAGC
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:0.16, G:0.52, T:0.16
Consensus pattern (12 bp):
GCGGTGGCGATA
Found at i:31381 original size:9 final size:9
Alignment explanation
Indices: 31367--31414 Score: 55
Period size: 9 Copynumber: 5.4 Consensus size: 9
31357 TTAAAATTTC
31367 AAAATATAT
1 AAAATATAT
31376 AAAATATAT
1 AAAATATAT
*
31385 ATAAAT-TGT
1 A-AAATATAT
*
31394 AAAAAAT-T
1 AAAATATAT
31402 AAAATATAT
1 AAAATATAT
31411 AAAA
1 AAAA
31415 ATACGAAGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
8 10 0.30
9 19 0.58
10 4 0.12
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (9 bp):
AAAATATAT
Found at i:31919 original size:2 final size:2
Alignment explanation
Indices: 31912--31945 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
31902 AAACTTGAGA
31912 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
31946 GATACTTAAA
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):
AT
Found at i:32386 original size:7 final size:7
Alignment explanation
Indices: 32374--32407 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
32364 ACAGCTGGTA
32374 CTTTTCC
1 CTTTTCC
32381 CTTTTCC
1 CTTTTCC
32388 CTTTTCC
1 CTTTTCC
32395 CTTTTCC
1 CTTTTCC
32402 CTTTTC
1 CTTTTC
32408 ATTCATATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (7 bp):
CTTTTCC
Found at i:34064 original size:60 final size:61
Alignment explanation
Indices: 33942--34073 Score: 169
Period size: 60 Copynumber: 2.2 Consensus size: 61
33932 ATACGTATAC
* * * *
33942 TTTGGGATGAAACTGGAATGTTCAAAATGTTTGGGGACCAATTTAGAATGAAGGTCATAGT
1 TTTGGGATGAAACTGAAATGTTCAAAATGTTTGAGGACCAATTTAGAATGAAAGTCAAAGT
* *
34003 TTTGGGATGAAACTGAAATGTTCACAA-GTTTGAGGACTAATTTAGAAT-AATAGTCAAAGT
1 TTTGGGATGAAACTGAAATGTTCAAAATGTTTGAGGACCAATTTAGAATGAA-AGTCAAAGT
**
34063 TTAAGGATGAA
1 TTTGGGATGAA
34074 TTTCGAATTT
Statistics
Matches: 62, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
59 2 0.03
60 35 0.56
61 25 0.40
ACGTcount: A:0.36, C:0.08, G:0.25, T:0.31
Consensus pattern (61 bp):
TTTGGGATGAAACTGAAATGTTCAAAATGTTTGAGGACCAATTTAGAATGAAAGTCAAAGT
Found at i:36210 original size:28 final size:28
Alignment explanation
Indices: 36165--36219 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
36155 ACTAAAAACA
*
36165 AAATTAGAGAGTTCAATTATAAATATAC
1 AAATTAAAGAGTTCAATTATAAATATAC
36193 AAATTAAAGA-TTCTAATTATAAATATA
1 AAATTAAAGAGTTC-AATTATAAATATA
36220 AAGGTTAGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 3 0.12
28 22 0.88
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35
Consensus pattern (28 bp):
AAATTAAAGAGTTCAATTATAAATATAC
Found at i:37156 original size:29 final size:29
Alignment explanation
Indices: 37112--37186 Score: 141
Period size: 29 Copynumber: 2.6 Consensus size: 29
37102 TAACGGAGGT
*
37112 AGGTCGCCATGTACGCCCGGCGACCAACC
1 AGGTCGCCATGCACGCCCGGCGACCAACC
37141 AGGTCGCCATGCACGCCCGGCGACCAACC
1 AGGTCGCCATGCACGCCCGGCGACCAACC
37170 AGGTCGCCATGCACGCC
1 AGGTCGCCATGCACGCC
37187 ATATACTCAC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.20, C:0.43, G:0.28, T:0.09
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCGGCGACCAACC
Found at i:37230 original size:17 final size:18
Alignment explanation
Indices: 37196--37231 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
37186 CATATACTCA
37196 CCATGCAGACGAGCCATAC
1 CCATGCAGAC-AGCCATAC
37215 CCATGCAGAC-GCCATAC
1 CCATGCAGACAGCCATAC
37232 AAGCCATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
19 10 0.59
ACGTcount: A:0.31, C:0.39, G:0.19, T:0.11
Consensus pattern (18 bp):
CCATGCAGACAGCCATAC
Found at i:37276 original size:28 final size:28
Alignment explanation
Indices: 37245--37300 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
37235 CCATATACTC
37245 ACCATGCAGACGAGCCAGCCAACGGAGA
1 ACCATGCAGACGAGCCAGCCAACGGAGA
37273 ACCATGCAGACGAGCCAGCCAACGGAGA
1 ACCATGCAGACGAGCCAGCCAACGGAGA
37301 GGTCGCCATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.32, G:0.29, T:0.04
Consensus pattern (28 bp):
ACCATGCAGACGAGCCAGCCAACGGAGA
Found at i:37314 original size:28 final size:28
Alignment explanation
Indices: 37283--37339 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
37273 ACCATGCAGA
*
37283 CGAGCCAGCCAACGGAGAGGTCGCCATG
1 CGAGCCAGCCAACAGAGAGGTCGCCATG
*
37311 CGAGCCAGCCAATAGAGAGGTCGCCATG
1 CGAGCCAGCCAACAGAGAGGTCGCCATG
37339 C
1 C
37340 AGTCTGGGCG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.26, C:0.32, G:0.33, T:0.09
Consensus pattern (28 bp):
CGAGCCAGCCAACAGAGAGGTCGCCATG
Found at i:37372 original size:29 final size:29
Alignment explanation
Indices: 37328--37422 Score: 163
Period size: 29 Copynumber: 3.3 Consensus size: 29
37318 GCCAATAGAG
* **
37328 AGGTCGCCATGCAGTCTGGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
37357 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
37386 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
37415 AGGTCGCC
1 AGGTCGCC
37423 CCCTGCAGAC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 63 1.00
ACGTcount: A:0.14, C:0.31, G:0.33, T:0.23
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTGT
Found at i:37454 original size:19 final size:19
Alignment explanation
Indices: 37430--37467 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
37420 GCCCCCTGCA
37430 GACCATGCATGCACCAGCC
1 GACCATGCATGCACCAGCC
37449 GACCATGCATGCACCAGCC
1 GACCATGCATGCACCAGCC
37468 AAATAACTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.42, G:0.21, T:0.11
Consensus pattern (19 bp):
GACCATGCATGCACCAGCC
Found at i:37527 original size:49 final size:48
Alignment explanation
Indices: 37465--37565 Score: 168
Period size: 49 Copynumber: 2.1 Consensus size: 48
37455 GCATGCACCA
*
37465 GCCAAATAACTTCACGTGCTCCTGCT-CCCGCTGCATGCCTGCATGCAT
1 GCCAAATAACTTCACGTGCTCCTGCTCCCCGCTGCATGCCTACA-GCAT
37513 GCCAAGATAACTTCACGTGCTCCTGCTCCCCGCTGCATGCCTACAGCAT
1 GCCAA-ATAACTTCACGTGCTCCTGCTCCCCGCTGCATGCCTACAGCAT
37562 GCCA
1 GCCA
37566 TGTGATCCTA
Statistics
Matches: 50, Mismatches: 1, Indels: 3
0.93 0.02 0.06
Matches are distributed among these distances:
48 5 0.10
49 29 0.58
50 16 0.32
ACGTcount: A:0.20, C:0.39, G:0.19, T:0.23
Consensus pattern (48 bp):
GCCAAATAACTTCACGTGCTCCTGCTCCCCGCTGCATGCCTACAGCAT
Found at i:37757 original size:16 final size:16
Alignment explanation
Indices: 37722--37763 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
37712 GATTCAGCCG
* *
37722 AGAAAGAAAGAAAGGG
1 AGAAAGAAAGGAAGGA
*
37738 AGAAAGAAAGGAAGTA
1 AGAAAGAAAGGAAGGA
37754 AG-AAGAAAGG
1 AGAAAGAAAGG
37764 GAGATAAGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.62, C:0.00, G:0.36, T:0.02
Consensus pattern (16 bp):
AGAAAGAAAGGAAGGA
Found at i:37794 original size:16 final size:18
Alignment explanation
Indices: 37773--37811 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
37763 GGAGATAAGG
*
37773 TAAATTTGTTTA-TATT-
1 TAAATTAGTTTATTATTA
37789 TAAATTAGTTTATTATTA
1 TAAATTAGTTTATTATTA
37807 TAAAT
1 TAAAT
37812 GTTAATTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 11 0.55
17 4 0.20
18 5 0.25
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (18 bp):
TAAATTAGTTTATTATTA
Found at i:37918 original size:41 final size:41
Alignment explanation
Indices: 37872--37979 Score: 114
Period size: 44 Copynumber: 2.6 Consensus size: 41
37862 GTATACATAA
37872 ATTAAAAATTATTTAATTAGTATATG-TTTG-ATAGTTA-TAT
1 ATTAAAAATTATTTAATTAGT-T-TGTTTTGTATAGTTAGTAT
* *
37912 AGTTAAAAAATAATTAATTAGTTTGTTTTGTTAATAGTTAGTTAT
1 A-TTAAAAATTATTTAATTAGTTTGTTTTG-T-ATAGTTAG-TAT
*
37957 ATAAAAAATTATTTAATTAGTTT
1 ATTAAAAATTATTTAATTAGTTT
37980 TGTTAGTTAA
Statistics
Matches: 56, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
39 2 0.04
40 6 0.11
41 18 0.32
43 7 0.12
44 19 0.34
45 4 0.07
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (41 bp):
ATTAAAAATTATTTAATTAGTTTGTTTTGTATAGTTAGTAT
Found at i:37978 original size:44 final size:45
Alignment explanation
Indices: 37915--38004 Score: 123
Period size: 44 Copynumber: 2.0 Consensus size: 45
37905 GTTATATAGT
*
37915 TAAAAAATAATTAATTAG-TTTGTTTTGTT-AATAGTT-AGTTATA
1 TAAAAAATAATTAATTAGTTTTG-TTAGTTAAATAGTTAAGTTATA
*
37958 TAAAAAATTATTTAATTAGTTTTGTTAGTTAAATAGTTAAGTTATA
1 TAAAAAA-TAATTAATTAGTTTTGTTAGTTAAATAGTTAAGTTATA
38004 T
1 T
38005 TTGTTTGTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
43 7 0.17
44 15 0.37
45 11 0.27
46 8 0.20
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (45 bp):
TAAAAAATAATTAATTAGTTTTGTTAGTTAAATAGTTAAGTTATA
Found at i:37980 original size:40 final size:41
Alignment explanation
Indices: 37875--37984 Score: 107
Period size: 40 Copynumber: 2.6 Consensus size: 41
37865 TACATAAATT
* *
37875 AAAAATTATTTAATTAGTATATGTTTGATAGTTATATAGTTAAA
1 AAAAATTATTTAATTAGT-TTTG-TTAATAGTTATATAG-TAAA
* * * *
37919 AAATAATTAATTAGTTTGTTTTGTTAATAGTTAGT-TA-TATA
1 AAA-AATTATTTAATTAGTTTTGTTAATAGTTA-TATAGTAAA
37960 AAAAATTATTTAATTAGTTTTGTTA
1 AAAAATTATTTAATTAGTTTTGTTA
37985 GTTAAATAGT
Statistics
Matches: 55, Mismatches: 9, Indels: 8
0.76 0.12 0.11
Matches are distributed among these distances:
40 19 0.35
41 6 0.11
43 11 0.20
44 7 0.13
45 12 0.22
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (41 bp):
AAAAATTATTTAATTAGTTTTGTTAATAGTTATATAGTAAA
Found at i:38047 original size:12 final size:12
Alignment explanation
Indices: 38030--38073 Score: 61
Period size: 12 Copynumber: 3.5 Consensus size: 12
38020 ATATATAAAA
38030 ATTAGTTAGTTT
1 ATTAGTTAGTTT
38042 ATTAGTTAGTTTT
1 ATTAGTTAG-TTT
*
38055 AGTTAGTAAGTTT
1 A-TTAGTTAGTTT
38068 ATTAGT
1 ATTAGT
38074 ATATTATAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 14 0.48
13 8 0.28
14 7 0.24
ACGTcount: A:0.27, C:0.00, G:0.18, T:0.55
Consensus pattern (12 bp):
ATTAGTTAGTTT
Found at i:38204 original size:15 final size:15
Alignment explanation
Indices: 38186--38223 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
38176 AGTTTGTTAG
* *
38186 TTATTAGTTCTTATA
1 TTATAAGTTATTATA
38201 TTATAAGTTATTATA
1 TTATAAGTTATTATA
38216 TTA-AAGTT
1 TTATAAGTT
38224 TAGTGTTGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 5 0.24
15 16 0.76
ACGTcount: A:0.34, C:0.03, G:0.08, T:0.55
Consensus pattern (15 bp):
TTATAAGTTATTATA
Found at i:40390 original size:17 final size:17
Alignment explanation
Indices: 40368--40400 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
40358 CAATGATGTT
40368 TAGTATCAAATAATTAC
1 TAGTATCAAATAATTAC
40385 TAGTATCAAATAATTA
1 TAGTATCAAATAATTA
40401 GTATTAAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.09, G:0.06, T:0.36
Consensus pattern (17 bp):
TAGTATCAAATAATTAC
Found at i:40404 original size:14 final size:14
Alignment explanation
Indices: 40367--40417 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
40357 ACAATGATGT
40367 TTAGTATCAAATAA
1 TTAGTATCAAATAA
40381 TTACTAGTATCAAATAA
1 -T--TAGTATCAAATAA
* *
40398 TTAGTATTAAATCA
1 TTAGTATCAAATAA
40412 TTAGTA
1 TTAGTA
40418 ATAATTAGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 17 0.53
15 1 0.03
16 1 0.03
17 13 0.41
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (14 bp):
TTAGTATCAAATAA
Found at i:40419 original size:21 final size:21
Alignment explanation
Indices: 40395--40438 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
40385 TAGTATCAAA
* *
40395 TAATTAGTATTAAATCATTAG
1 TAATAAGTAGTAAATCATTAG
*
40416 TAATAATTAGTAAATCATTAG
1 TAATAAGTAGTAAATCATTAG
40437 TA
1 TA
40439 TCAAATCATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.41
Consensus pattern (21 bp):
TAATAAGTAGTAAATCATTAG
Found at i:40437 original size:11 final size:11
Alignment explanation
Indices: 40405--40438 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
40395 TAATTAGTAT
40405 TAAATCATTAG
1 TAAATCATTAG
*
40416 T-AATAATTAG
1 TAAATCATTAG
40426 TAAATCATTAG
1 TAAATCATTAG
40437 TA
1 TA
40439 TCAAATCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (11 bp):
TAAATCATTAG
Found at i:40446 original size:14 final size:13
Alignment explanation
Indices: 40385--40449 Score: 50
Period size: 14 Copynumber: 5.2 Consensus size: 13
40375 AAATAATTAC
*
40385 TAGTATCAAATAAT
1 TAGTAT-AAATCAT
40399 TAGTATTAAATCAT
1 TAGTA-TAAATCAT
*
40413 TAG--T-AATAAT
1 TAGTATAAATCAT
40423 TAG--TAAATCAT
1 TAGTATAAATCAT
40434 TAGTATCAAATCAT
1 TAGTAT-AAATCAT
40448 TA
1 TA
40450 AATATTTAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
10 9 0.21
11 9 0.21
13 1 0.02
14 23 0.53
15 1 0.02
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
TAGTATAAATCAT
Found at i:40529 original size:19 final size:22
Alignment explanation
Indices: 40507--40551 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
40497 TCATCAAATC
40507 ATTAAAT-A-TTTA-AATCATT
1 ATTAAATCATTTTATAATCATT
*
40526 ATTAAATCATTTTATAATGATT
1 ATTAAATCATTTTATAATCATT
40548 ATTA
1 ATTA
40552 CTAAATCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 7 0.32
20 1 0.05
21 4 0.18
22 10 0.45
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.49
Consensus pattern (22 bp):
ATTAAATCATTTTATAATCATT
Found at i:40569 original size:7 final size:7
Alignment explanation
Indices: 40557--40583 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
40547 TATTACTAAA
40557 TCATTGT
1 TCATTGT
40564 TCATTGT
1 TCATTGT
40571 TCATTGT
1 TCATTGT
40578 TCATTG
1 TCATTG
40584 AACCAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.56
Consensus pattern (7 bp):
TCATTGT
Found at i:40675 original size:14 final size:14
Alignment explanation
Indices: 40656--40703 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
40646 TTCAAGTCGT
40656 AAATCATTACTATC
1 AAATCATTACTATC
40670 AAATCATTAC--T-
1 AAATCATTACTATC
*
40681 AAATCATTAATATC
1 AAATCATTACTATC
40695 AAATCATTA
1 AAATCATTA
40704 AATATTAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 9 0.30
12 1 0.03
13 1 0.03
14 19 0.63
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.35
Consensus pattern (14 bp):
AAATCATTACTATC
Found at i:40737 original size:48 final size:49
Alignment explanation
Indices: 40675--41025 Score: 182
Period size: 60 Copynumber: 6.3 Consensus size: 49
40665 CTATCAAATC
*
40675 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATT-ATT
1 ATTACT-AATCATTAATATCAAATCATTAAAAATTAATAATAAATTCATT
* *
40724 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTAATATCAAATCATTAAAAATTAATAATAAATTCATT
* * *
40773 ATTACTAATCATTACTAAATCATTACTATCAAATCATACATAATTAATAATAATTTCATT
1 ATTACTAATCATTA--ATATCA--A--ATC--AT--TA-AAAATTAATAATAAATTCATT
* * *
40833 ATTACTAATCATTACTAAATCATTACTATCAAATCATACATAATTAATAATAATTTCATT
1 ATTACTAATCATTA--ATATCA--A--ATC--AT--TA-AAAATTAATAATAAATTCATT
* * *
40893 ATTACTAATCATTACTAAGTCATTACTATCAATCATACATAATTAATAATAATTTCATT
1 ATTACTAATCATTAAT-A-TCA--A--ATC-AT--TA-AAAATTAATAATAAATTCATT
*
40952 ATTACTAATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATC---A-T---T-A--A-TATCAAATCATTAAAAATTAATAATAAATTCATT
41012 ATTACTAATCATTA
1 ATTACTAATCATTA
41026 CTAAATCATT
Statistics
Matches: 267, Mismatches: 10, Indels: 47
0.82 0.03 0.15
Matches are distributed among these distances:
48 36 0.13
49 23 0.09
51 4 0.01
52 1 0.00
53 2 0.01
55 3 0.01
56 1 0.00
57 3 0.01
59 42 0.16
60 135 0.51
61 2 0.01
62 1 0.00
63 3 0.01
64 3 0.01
66 2 0.01
67 1 0.00
68 3 0.01
69 1 0.00
70 1 0.00
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.40
Consensus pattern (49 bp):
ATTACTAATCATTAATATCAAATCATTAAAAATTAATAATAAATTCATT
Found at i:40799 original size:60 final size:60
Alignment explanation
Indices: 40724--41152 Score: 751
Period size: 60 Copynumber: 7.2 Consensus size: 60
40714 ATAAATTATT
*
40724 ATTACT-AATCATTACTATCAAATCATTA-AAAATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCA-TACATAATTAATAATAATTTCATTATTACTAATC
40783 ATTACTAAATCATTACTATCAAATCATACATAATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATACATAATTAATAATAATTTCATTATTACTAATC
40843 ATTACTAAATCATTACTATCAAATCATACATAATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATACATAATTAATAATAATTTCATTATTACTAATC
*
40903 ATTACTAAGTCATTACTATC-AATCATACATAATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATACATAATTAATAATAATTTCATTATTACTAATC
*
40962 ATTACTAAATCATTACTATCAAATCATTA-AAAATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCA-TACATAATTAATAATAATTTCATTATTACTAATC
41022 ATTACTAAATCATTACTATCAAATCATACATAATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATACATAATTAATAATAATTTCATTATTACTAATC
* *
41082 ATTACTAAATCATTACTATCAAATCATTA-AAAATTAATAATAATTTCATCATTACTAATC
1 ATTACTAAATCATTACTATCAAATCA-TACATAATTAATAATAATTTCATTATTACTAATC
41142 ATTACTAAATC
1 ATTACTAAATC
41153 TTATAAATAC
Statistics
Matches: 357, Mismatches: 7, Indels: 11
0.95 0.02 0.03
Matches are distributed among these distances:
59 68 0.19
60 285 0.80
61 4 0.01
ACGTcount: A:0.45, C:0.15, G:0.00, T:0.40
Consensus pattern (60 bp):
ATTACTAAATCATTACTATCAAATCATACATAATTAATAATAATTTCATTATTACTAATC
Found at i:40855 original size:179 final size:179
Alignment explanation
Indices: 40724--41152 Score: 774
Period size: 179 Copynumber: 2.4 Consensus size: 179
40714 ATAAATTATT
40724 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACT
*
40789 AAATCATTACTATCAAATCA-TACATAATTAATAATAATTTCATTATTACTAATCATTACTAAAT
66 AAATCATTACTATCAAATCATTA-AAAATTAATAATAATTTCATTATTACTAATCATTACTAAAT
40853 CATTACTATCAAATCATACATAATTAATAATAATTTCATTATTACTAATC
130 CATTACTATCAAATCATACATAATTAATAATAATTTCATTATTACTAATC
*
40903 ATTACTAAGTCATTACTATC-AATCA-TACATAATTAATAATAATTTCATTATTACTAATCATTA
1 ATTACTAA-TCATTACTATCAAATCATTA-AAAATTAATAATAATTTCATTATTACTAATCATTA
40966 CTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAA
64 CTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAA
41031 TCATTACTATCAAATCATACATAATTAATAATAATTTCATTATTACTAATC
129 TCATTACTATCAAATCATACATAATTAATAATAATTTCATTATTACTAATC
*
41082 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATCATTACTAATCATTAC
1 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
41147 TAAATC
65 TAAATC
41153 TTATAAATAC
Statistics
Matches: 240, Mismatches: 4, Indels: 11
0.94 0.02 0.04
Matches are distributed among these distances:
178 2 0.01
179 176 0.73
180 60 0.25
181 2 0.01
ACGTcount: A:0.45, C:0.15, G:0.00, T:0.40
Consensus pattern (179 bp):
ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACT
AAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATC
ATTACTATCAAATCATACATAATTAATAATAATTTCATTATTACTAATC
Found at i:40917 original size:11 final size:10
Alignment explanation
Indices: 40893--41099 Score: 58
Period size: 10 Copynumber: 20.7 Consensus size: 10
40883 TAATTTCATT
40893 ATTACTAATC
1 ATTACTAATC
40903 ATTACTAAGTC
1 ATTACTAA-TC
40914 ATTACT-ATC
1 ATTACTAATC
* *
40923 AAT-CATACATA
1 ATTAC-TA-ATC
* *
40934 ATTAATAATA
1 ATTACTAATC
* *
40944 ATT--TCATT
1 ATTACTAATC
40952 ATTACTAATC
1 ATTACTAATC
40962 ATTACTAAATC
1 ATTACT-AATC
40973 ATTACT-ATC
1 ATTACTAATC
* * **
40982 AAATCATTAAAA
1 --ATTACTAATC
* *
40994 ATTAATAATA
1 ATTACTAATC
* *
41004 ATT--TCATT
1 ATTACTAATC
41012 ATTACTAATC
1 ATTACTAATC
41022 ATTACTAAATC
1 ATTACT-AATC
41033 ATTACT-ATC
1 ATTACTAATC
* *
41042 A-AATCATACATA
1 ATTA-C-TA-ATC
* *
41054 ATTAATAATA
1 ATTACTAATC
* *
41064 ATT--TCATT
1 ATTACTAATC
41072 ATTACTAATC
1 ATTACTAATC
41082 ATTACTAAATC
1 ATTACT-AATC
41093 ATTACTA
1 ATTACTA
41100 TCAAATCATT
Statistics
Matches: 148, Mismatches: 27, Indels: 44
0.68 0.12 0.20
Matches are distributed among these distances:
8 20 0.14
9 13 0.09
10 60 0.41
11 50 0.34
12 4 0.03
13 1 0.01
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.40
Consensus pattern (10 bp):
ATTACTAATC
Found at i:44247 original size:28 final size:28
Alignment explanation
Indices: 44216--44269 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
44206 ATAATCTAAT
*
44216 ATATAACTTAAACTAACAAATTAATATA
1 ATATAACTTAAACTAACAAACTAATATA
44244 ATATAACTTAAACTAACAAACTAATA
1 ATATAACTTAAACTAACAAACTAATA
44270 ATTTATACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (28 bp):
ATATAACTTAAACTAACAAACTAATATA
Found at i:44276 original size:28 final size:28
Alignment explanation
Indices: 44212--44276 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 28
44202 TTATATAATC
*
44212 TAATATATAACTTAAACTAACAAATTAA
1 TAATATATAACTTAAACTAACAAACTAA
44240 T-ATAATATAACTTAAACTAACAAACTAA
1 TAAT-ATATAACTTAAACTAACAAACTAA
*
44268 TAATTTATA
1 TAATATATA
44277 CTAACAAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 29 0.88
29 2 0.06
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (28 bp):
TAATATATAACTTAAACTAACAAACTAA
Found at i:44279 original size:21 final size:21
Alignment explanation
Indices: 44246--44294 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
44236 TTAATATAAT
44246 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
44267 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
44288 ATTAACT
1 A-TAACT
44295 AAATTTCTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:44929 original size:20 final size:20
Alignment explanation
Indices: 44904--45020 Score: 82
Period size: 20 Copynumber: 5.8 Consensus size: 20
44894 TTTGGCGAGC
44904 TGGGCGTGCATGGAGGT-CGT
1 TGGGCGTGCATGGAGGTGC-T
** *
44924 TGGGCGTGCATGGCCGTGCA
1 TGGGCGTGCATGGAGGTGCT
* * *
44944 TGGAG-GT-CGTTGGACGTGCC
1 TGG-GCGTGC-ATGGAGGTGCT
*
44964 TGGGCATGCATGGAGGT-CGT
1 TGGGCGTGCATGGAGGTGC-T
*
44984 TGGGCGTGCATGG-GCGTGCA
1 TGGGCGTGCATGGAG-GTGCT
45004 TGGGCGTGCATGGAGGT
1 TGGGCGTGCATGGAGGT
45021 CGTGGGGTAG
Statistics
Matches: 76, Mismatches: 12, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
19 4 0.05
20 67 0.88
21 5 0.07
ACGTcount: A:0.11, C:0.18, G:0.48, T:0.23
Consensus pattern (20 bp):
TGGGCGTGCATGGAGGTGCT
Found at i:44944 original size:30 final size:30
Alignment explanation
Indices: 44904--45006 Score: 170
Period size: 30 Copynumber: 3.4 Consensus size: 30
44894 TTTGGCGAGC
44904 TGGGCGTGCATGGAGGTCGTTGGGCGTGCA
1 TGGGCGTGCATGGAGGTCGTTGGGCGTGCA
* * *
44934 TGGCCGTGCATGGAGGTCGTTGGACGTGCC
1 TGGGCGTGCATGGAGGTCGTTGGGCGTGCA
*
44964 TGGGCATGCATGGAGGTCGTTGGGCGTGCA
1 TGGGCGTGCATGGAGGTCGTTGGGCGTGCA
44994 TGGGCGTGCATGG
1 TGGGCGTGCATGG
45007 GCGTGCATGG
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 65 1.00
ACGTcount: A:0.11, C:0.18, G:0.48, T:0.23
Consensus pattern (30 bp):
TGGGCGTGCATGGAGGTCGTTGGGCGTGCA
Found at i:44999 original size:10 final size:10
Alignment explanation
Indices: 44984--45016 Score: 66
Period size: 10 Copynumber: 3.3 Consensus size: 10
44974 TGGAGGTCGT
44984 TGGGCGTGCA
1 TGGGCGTGCA
44994 TGGGCGTGCA
1 TGGGCGTGCA
45004 TGGGCGTGCA
1 TGGGCGTGCA
45014 TGG
1 TGG
45017 AGGTCGTGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.09, C:0.18, G:0.52, T:0.21
Consensus pattern (10 bp):
TGGGCGTGCA
Found at i:45071 original size:29 final size:29
Alignment explanation
Indices: 45030--45170 Score: 264
Period size: 29 Copynumber: 4.9 Consensus size: 29
45020 TCGTGGGGTA
*
45030 GGTCGCAGGGCGTGCATGGCGACCTGGTT
1 GGTCGCCGGGCGTGCATGGCGACCTGGTT
45059 GGTCGCCGGGCGTGCATGGCGACCTGGTT
1 GGTCGCCGGGCGTGCATGGCGACCTGGTT
45088 GGTCGCCGGGCGTGCATGGCGACCTGGTT
1 GGTCGCCGGGCGTGCATGGCGACCTGGTT
45117 GGTCGCCGGGCGTGCATGGCGACCTGGTT
1 GGTCGCCGGGCGTGCATGGCGACCTGGTT
*
45146 GGTCGCCGGGCGTACATGGCGACCT
1 GGTCGCCGGGCGTGCATGGCGACCT
45171 ACCCCCGTTA
Statistics
Matches: 110, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 110 1.00
ACGTcount: A:0.09, C:0.28, G:0.44, T:0.20
Consensus pattern (29 bp):
GGTCGCCGGGCGTGCATGGCGACCTGGTT
Found at i:47458 original size:60 final size:60
Alignment explanation
Indices: 47359--47531 Score: 151
Period size: 60 Copynumber: 2.9 Consensus size: 60
47349 ATGATCCATT
* * * *
47359 TTCTAAATTGGTCTTTAAACTTTTAA-ATGTTCTAATTTCAT-TTCTAAACTATGAT-TACCA
1 TTCTAAATTAGTCCTCAAACTTTTAACAT-TTCTAATTTCATCCTC-AAACTAT-ATCTACCA
* * ***
47419 TTCTAAATTTGTCCTCAAACTTTTGAACATTT-TATTTTCATCCTCAAACTATATCTTTTA
1 TTCTAAATTAGTCCTCAAACTTTT-AACATTTCTAATTTCATCCTCAAACTATATCTACCA
* * *
47479 TTATAAATTAGTCCTCAAACTTTTCAACATTTC-AATTTTATCC-CAAATTATAT
1 TTCTAAATTAGTCCTCAAACTTTT-AACATTTCTAATTTCATCCTCAAACTATAT
47532 GTATACACTA
Statistics
Matches: 94, Mismatches: 14, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
59 11 0.12
60 75 0.80
61 6 0.06
62 2 0.02
ACGTcount: A:0.32, C:0.18, G:0.04, T:0.46
Consensus pattern (60 bp):
TTCTAAATTAGTCCTCAAACTTTTAACATTTCTAATTTCATCCTCAAACTATATCTACCA
Found at i:49017 original size:21 final size:22
Alignment explanation
Indices: 48993--49033 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
48983 AAACATCCTC
48993 AAGACACCGG-AAATCCCAAAT
1 AAGACACCGGTAAATCCCAAAT
* *
49014 AAGACGCCGGTAGATCCCAA
1 AAGACACCGGTAAATCCCAA
49034 GCAAGACCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.41, C:0.29, G:0.20, T:0.10
Consensus pattern (22 bp):
AAGACACCGGTAAATCCCAAAT
Found at i:49039 original size:22 final size:21
Alignment explanation
Indices: 48992--49040 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 21
48982 CAAACATCCT
48992 CAAGACACCGGAAATCCCAAA
1 CAAGACACCGGAAATCCCAAA
* * * *
49013 TAAGACGCCGGTAGATCCCAAG
1 CAAGACACCGG-AAATCCCAAA
49035 CAAGAC
1 CAAGAC
49041 CCAAAAAAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.41, C:0.31, G:0.20, T:0.08
Consensus pattern (21 bp):
CAAGACACCGGAAATCCCAAA
Found at i:51001 original size:22 final size:22
Alignment explanation
Indices: 50968--51014 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
50958 TGCGTTTTCG
*
50968 CTTTTCATTTTTACTGTTATAT
1 CTTTTCATTTTTACAGTTATAT
*
50990 CTTTCTCA-TTTTACAGTTTTAT
1 CTTT-TCATTTTTACAGTTATAT
51012 CTT
1 CTT
51015 AGAATCACAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.17, C:0.17, G:0.04, T:0.62
Consensus pattern (22 bp):
CTTTTCATTTTTACAGTTATAT
Found at i:55209 original size:21 final size:21
Alignment explanation
Indices: 55183--55248 Score: 66
Period size: 21 Copynumber: 3.1 Consensus size: 21
55173 AAGGGTTAAA
55183 TTTTAATTATATGAAGATTTT
1 TTTTAATTATATGAAGATTTT
* *
55204 TTTTAA--ATGA-GAAAATTGAAT
1 TTTTAATTAT-ATGAAGATT--TT
55225 TTTTAATTATATGAAGATTTT
1 TTTTAATTATATGAAGATTTT
55246 TTT
1 TTT
55249 AAAATGAGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 12
0.69 0.08 0.24
Matches are distributed among these distances:
19 8 0.23
20 1 0.03
21 17 0.49
22 1 0.03
23 8 0.23
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (21 bp):
TTTTAATTATATGAAGATTTT
Found at i:55261 original size:40 final size:41
Alignment explanation
Indices: 55183--55272 Score: 155
Period size: 42 Copynumber: 2.2 Consensus size: 41
55173 AAGGGTTAAA
*
55183 TTTTAATTATATGAAGATTTTTTTTAAATGAGAAAATTGAAT
1 TTTTAATTATATGAAGATTTTTTTAAAATGAG-AAATTGAAT
55225 TTTTAATTATATGAAGATTTTTTTAAAATGAG-AATTGAAT
1 TTTTAATTATATGAAGATTTTTTTAAAATGAGAAATTGAAT
55265 TTTTAATT
1 TTTTAATT
55273 TTATTTTAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 16 0.34
42 31 0.66
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (41 bp):
TTTTAATTATATGAAGATTTTTTTAAAATGAGAAATTGAAT
Found at i:63373 original size:30 final size:31
Alignment explanation
Indices: 63337--63412 Score: 84
Period size: 30 Copynumber: 2.5 Consensus size: 31
63327 ATGGTCCCCG
*
63337 ACTATAGGATATTACTTTGTTGAGTCC-TCA
1 ACTATAGGATATTACTTTATTGAGTCCTTCA
* *
63367 ACTATAGAGA-GTTACTTTATTGAGTCCTTCG
1 ACTATAG-GATATTACTTTATTGAGTCCTTCA
* *
63398 ACTATTGAATATTAC
1 ACTATAGGATATTAC
63413 AAAATGATCA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
30 23 0.62
31 14 0.38
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (31 bp):
ACTATAGGATATTACTTTATTGAGTCCTTCA
Found at i:68781 original size:13 final size:14
Alignment explanation
Indices: 68744--68781 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
68734 TAACCAAAAA
*
68744 TATTAAATATATAT
1 TATTAAATACATAT
68758 TATTAAATACATAT
1 TATTAAATACATAT
*
68772 T-TTAAGTACA
1 TATTAAATACA
68782 AACTCATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 8 0.36
14 14 0.64
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (14 bp):
TATTAAATACATAT
Found at i:72255 original size:18 final size:18
Alignment explanation
Indices: 72229--72263 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
72219 TTGAAATGAC
*
72229 TGGAATAAATGATAAGTT
1 TGGAATAAATAATAAGTT
*
72247 TGGATTAAATAATAAGT
1 TGGAATAAATAATAAGT
72264 CCGAACAGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.20, T:0.34
Consensus pattern (18 bp):
TGGAATAAATAATAAGTT
Found at i:73624 original size:154 final size:154
Alignment explanation
Indices: 73344--73651 Score: 616
Period size: 154 Copynumber: 2.0 Consensus size: 154
73334 CTTGCAGTAA
73344 ATCTGAATTTAGAATTATTATGTATAAAGGTTCCTGAACGTTTTCCTAATGCACACGAAAATATA
1 ATCTGAATTTAGAATTATTATGTATAAAGGTTCCTGAACGTTTTCCTAATGCACACGAAAATATA
73409 GTGGGATTCTAATGTATCAACCTTAAATGTCTGGCTAGATCGGTTAGTAATCGATTCTCCTCAAT
66 GTGGGATTCTAATGTATCAACCTTAAATGTCTGGCTAGATCGGTTAGTAATCGATTCTCCTCAAT
73474 AGGACCTTGTTCTTGGAATTCGAT
131 AGGACCTTGTTCTTGGAATTCGAT
73498 ATCTGAATTTAGAATTATTATGTATAAAGGTTCCTGAACGTTTTCCTAATGCACACGAAAATATA
1 ATCTGAATTTAGAATTATTATGTATAAAGGTTCCTGAACGTTTTCCTAATGCACACGAAAATATA
73563 GTGGGATTCTAATGTATCAACCTTAAATGTCTGGCTAGATCGGTTAGTAATCGATTCTCCTCAAT
66 GTGGGATTCTAATGTATCAACCTTAAATGTCTGGCTAGATCGGTTAGTAATCGATTCTCCTCAAT
73628 AGGACCTTGTTCTTGGAATTCGAT
131 AGGACCTTGTTCTTGGAATTCGAT
73652 CAAATTTCAT
Statistics
Matches: 154, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
154 154 1.00
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (154 bp):
ATCTGAATTTAGAATTATTATGTATAAAGGTTCCTGAACGTTTTCCTAATGCACACGAAAATATA
GTGGGATTCTAATGTATCAACCTTAAATGTCTGGCTAGATCGGTTAGTAATCGATTCTCCTCAAT
AGGACCTTGTTCTTGGAATTCGAT
Found at i:80898 original size:31 final size:31
Alignment explanation
Indices: 80860--80920 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
80850 ATTACAAAAG
80860 TTAACAAATAACAACATTTAAATTTCTTTTA
1 TTAACAAATAACAACATTTAAATTTCTTTTA
*
80891 TTAACAAATAATAACATTTAAATTTCTTTT
1 TTAACAAATAACAACATTTAAATTTCTTTT
80921 TTTTAGTCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (31 bp):
TTAACAAATAACAACATTTAAATTTCTTTTA
Found at i:84593 original size:17 final size:17
Alignment explanation
Indices: 84571--84613 Score: 68
Period size: 19 Copynumber: 2.4 Consensus size: 17
84561 ATCCAAGAGT
84571 TGATTAAGTATGGGAAA
1 TGATTAAGTATGGGAAA
84588 TGATTATAAGTATGGGAAA
1 TGA-T-TAAGTATGGGAAA
84607 TGATTAA
1 TGATTAA
84614 CACTTTTACA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.25
18 2 0.08
19 16 0.67
ACGTcount: A:0.42, C:0.00, G:0.26, T:0.33
Consensus pattern (17 bp):
TGATTAAGTATGGGAAA
Found at i:84599 original size:19 final size:19
Alignment explanation
Indices: 84575--84612 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
84565 AAGAGTTGAT
84575 TAAGTATGGGAAATGATTA
1 TAAGTATGGGAAATGATTA
84594 TAAGTATGGGAAATGATTA
1 TAAGTATGGGAAATGATTA
84613 ACACTTTTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.26, T:0.32
Consensus pattern (19 bp):
TAAGTATGGGAAATGATTA
Found at i:94762 original size:29 final size:30
Alignment explanation
Indices: 94718--94778 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 30
94708 ATATTACCTC
*
94718 TTTTATTAATTTTTAGACACAAATTTAGAA
1 TTTTATTAATTTTTAGACACAAATTCAGAA
*
94748 TTTTATT-TTTTTTAGACACAAATTCAGAA
1 TTTTATTAATTTTTAGACACAAATTCAGAA
94777 TT
1 TT
94779 CTGTAATTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 22 0.76
30 7 0.24
ACGTcount: A:0.36, C:0.08, G:0.07, T:0.49
Consensus pattern (30 bp):
TTTTATTAATTTTTAGACACAAATTCAGAA
Done.