Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A10
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: 111961792
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4980000 characters in sequence are not A, C, G, or T
File 322 of 344
Found at i:105352858 original size:17 final size:15
Alignment explanation
Indices: 105352832--105352892 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 15
105352822 TTGATAAATT
*
105352832 AAAAAATAAAGTGTTA
1 AAAAAATAAA-TATTA
105352848 AAAAGAATAAATATTA
1 AAAA-AATAAATATTA
** * **
105352864 AAAATTTAAGTGCTA
1 AAAAAATAAATATTA
105352879 AAAAAATAAATATT
1 AAAAAATAAATATT
105352893 GAATTTAAGT
Statistics
Matches: 33, Mismatches: 11, Indels: 3
0.70 0.23 0.06
Matches are distributed among these distances:
15 15 0.45
16 12 0.36
17 6 0.18
ACGTcount: A:0.62, C:0.02, G:0.08, T:0.28
Consensus pattern (15 bp):
AAAAAATAAATATTA
Found at i:105352887 original size:30 final size:31
Alignment explanation
Indices: 105352829--105352892 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
105352819 TGTTTGATAA
*
105352829 ATTAAAAAATAAAGTGTTAAAAAGAATAAAT
1 ATTAAAAAATAAAGTGCTAAAAAGAATAAAT
* *
105352860 ATTAAAAATTTAAGTGCTAAAAA-AATAAAT
1 ATTAAAAAATAAAGTGCTAAAAAGAATAAAT
105352890 ATT
1 ATT
105352893 GAATTTAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 10 0.33
31 20 0.67
ACGTcount: A:0.61, C:0.02, G:0.08, T:0.30
Consensus pattern (31 bp):
ATTAAAAAATAAAGTGCTAAAAAGAATAAAT
Found at i:105352908 original size:28 final size:30
Alignment explanation
Indices: 105352840--105352909 Score: 81
Period size: 28 Copynumber: 2.4 Consensus size: 30
105352830 TTAAAAAATA
*
105352840 AAGTGTTAAAAAGAATAAATATTAAAAATTT
1 AAGTGATAAAAAGAATAAATATT-AAAATTT
* *
105352871 AAGTGCTAAAAA-AATAAATATT-GAATTT
1 AAGTGATAAAAAGAATAAATATTAAAATTT
*
105352899 AAGTTATAAAA
1 AAGTGATAAAA
105352910 TTATTTAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
28 14 0.40
30 10 0.29
31 11 0.31
ACGTcount: A:0.57, C:0.01, G:0.10, T:0.31
Consensus pattern (30 bp):
AAGTGATAAAAAGAATAAATATTAAAATTT
Found at i:105353240 original size:18 final size:18
Alignment explanation
Indices: 105353207--105353248 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
105353197 TGTGTAAAAA
*
105353207 GGTTAAATTATTTTCAAT
1 GGTTTAATTATTTTCAAT
105353225 GGATTTAATT-TTTTCAAT
1 GG-TTTAATTATTTTCAAT
105353243 GGTTTA
1 GGTTTA
105353249 TCAAACAAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 4 0.18
18 12 0.55
19 6 0.27
ACGTcount: A:0.29, C:0.05, G:0.14, T:0.52
Consensus pattern (18 bp):
GGTTTAATTATTTTCAAT
Found at i:105353612 original size:31 final size:30
Alignment explanation
Indices: 105353525--105353614 Score: 87
Period size: 31 Copynumber: 3.0 Consensus size: 30
105353515 CTGAGTACCG
** * *
105353525 AATTGAATATTGAATCCAAACTTAGGTACTA
1 AATTGAATATT-AAAACAATCTTAAGTACTA
*
105353556 AATTGAGATA--AAAA-AATTTTAAGTACTA
1 AATTGA-ATATTAAAACAATCTTAAGTACTA
105353584 AATTGAATATTAAAGACAATCTTAAGTACTA
1 AATTGAATATTAAA-ACAATCTTAAGTACTA
105353615 TATAGTATAT
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
27 3 0.06
28 17 0.35
29 5 0.10
30 1 0.02
31 19 0.40
32 3 0.06
ACGTcount: A:0.48, C:0.09, G:0.11, T:0.32
Consensus pattern (30 bp):
AATTGAATATTAAAACAATCTTAAGTACTA
Found at i:105354322 original size:14 final size:16
Alignment explanation
Indices: 105354303--105354334 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
105354293 AACTTTTAAG
105354303 TGAATA-AAAAAA-AA
1 TGAATAGAAAAAAGAA
105354317 TGAATAGAAAAAAGAA
1 TGAATAGAAAAAAGAA
105354333 TG
1 TG
105354335 GATACACTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 6 0.38
16 4 0.25
ACGTcount: A:0.69, C:0.00, G:0.16, T:0.16
Consensus pattern (16 bp):
TGAATAGAAAAAAGAA
Found at i:105355534 original size:10 final size:9
Alignment explanation
Indices: 105355500--105355533 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
105355490 CCAAAATGCC
105355500 TTTTTATTG
1 TTTTTATTG
105355509 TTTTTATTG
1 TTTTTATTG
*
105355518 TTTTTAATTT
1 TTTTT-ATTG
105355528 TTTTTA
1 TTTTTA
105355534 ACTGTTTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.15, C:0.00, G:0.06, T:0.79
Consensus pattern (9 bp):
TTTTTATTG
Found at i:105355541 original size:10 final size:10
Alignment explanation
Indices: 105355500--105355542 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
105355490 CCAAAATGCC
105355500 TTTTT-ATTG
1 TTTTTAATTG
105355509 TTTTT-ATTG
1 TTTTTAATTG
*
105355518 TTTTTAATTT
1 TTTTTAATTG
*
105355528 TTTTTAACTG
1 TTTTTAATTG
105355538 TTTTT
1 TTTTT
105355543 CTATGGTGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
9 14 0.47
10 16 0.53
ACGTcount: A:0.14, C:0.02, G:0.07, T:0.77
Consensus pattern (10 bp):
TTTTTAATTG
Found at i:105358662 original size:63 final size:63
Alignment explanation
Indices: 105358480--105358670 Score: 294
Period size: 62 Copynumber: 3.0 Consensus size: 63
105358470 TTTTCAATAT
*
105358480 TTATATCAGTTATAGTTCTGCTGGTAGAGTGCTATCGAAAGAAGTGAATGGGATATCAACAAC
1 TTATATCAGTTATAGTTCTGCTGGTAGAGTGCTATCGAAATAAGTGAATGGGATATCAACAAC
* * * *
105358543 TTATATCAG-TGTAGTTCCGCTGGTAGAGTGCTATCTAAATAAGTGAATGGGCTATCAACAAC
1 TTATATCAGTTATAGTTCTGCTGGTAGAGTGCTATCGAAATAAGTGAATGGGATATCAACAAC
* * * *
105358605 TTATATCAGTTATAATTCTGCTAGTAGAGTGCTATCGAAATAAGTGGATGGAATATCAACAAC
1 TTATATCAGTTATAGTTCTGCTGGTAGAGTGCTATCGAAATAAGTGAATGGGATATCAACAAC
105358668 TTA
1 TTA
105358671 GCATGAATTA
Statistics
Matches: 114, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
62 57 0.50
63 57 0.50
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (63 bp):
TTATATCAGTTATAGTTCTGCTGGTAGAGTGCTATCGAAATAAGTGAATGGGATATCAACAAC
Found at i:105362571 original size:25 final size:25
Alignment explanation
Indices: 105362517--105362576 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
105362507 TTGTCTCTAT
105362517 TATTATATATATTTTAATACCATATG
1 TATTAT-TATATTTTAATACCATATG
*
105362543 TATTATTATCATTTT-ATACTAT-TG
1 TATTATTAT-ATTTTAATACCATATG
105362567 CTATTATTAT
1 -TATTATTAT
105362577 TGTTTTCGTC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
24 2 0.06
25 18 0.58
26 11 0.35
ACGTcount: A:0.33, C:0.08, G:0.03, T:0.55
Consensus pattern (25 bp):
TATTATTATATTTTAATACCATATG
Found at i:105365984 original size:91 final size:91
Alignment explanation
Indices: 105365829--105366010 Score: 364
Period size: 91 Copynumber: 2.0 Consensus size: 91
105365819 TCCTAAGTAG
105365829 TTAATTTTTAACGAAATTTCTTATAGAGTAAGTTTCAAGTGGCATGTCAGTATGAGCAGCCAATA
1 TTAATTTTTAACGAAATTTCTTATAGAGTAAGTTTCAAGTGGCATGTCAGTATGAGCAGCCAATA
105365894 ATTACACTCACCTTCTCCGTCGAAGT
66 ATTACACTCACCTTCTCCGTCGAAGT
105365920 TTAATTTTTAACGAAATTTCTTATAGAGTAAGTTTCAAGTGGCATGTCAGTATGAGCAGCCAATA
1 TTAATTTTTAACGAAATTTCTTATAGAGTAAGTTTCAAGTGGCATGTCAGTATGAGCAGCCAATA
105365985 ATTACACTCACCTTCTCCGTCGAAGT
66 ATTACACTCACCTTCTCCGTCGAAGT
105366011 GGTCCTTTTC
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 91 1.00
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (91 bp):
TTAATTTTTAACGAAATTTCTTATAGAGTAAGTTTCAAGTGGCATGTCAGTATGAGCAGCCAATA
ATTACACTCACCTTCTCCGTCGAAGT
Found at i:105368937 original size:18 final size:19
Alignment explanation
Indices: 105368904--105368941 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
105368894 AGACTCCAGG
*
105368904 TCTGATTCTTTTCAATCAT
1 TCTGATTCTCTTCAATCAT
105368923 TCTGATT-TCTTCAATCAT
1 TCTGATTCTCTTCAATCAT
105368941 T
1 T
105368942 GCTTGCTTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.21, C:0.21, G:0.05, T:0.53
Consensus pattern (19 bp):
TCTGATTCTCTTCAATCAT
Found at i:105378880 original size:12 final size:11
Alignment explanation
Indices: 105378841--105378889 Score: 50
Period size: 12 Copynumber: 4.6 Consensus size: 11
105378831 CAATTTTTAA
105378841 TTTAATTAA-T
1 TTTAATTAATT
*
105378851 TTAAATT--TT
1 TTTAATTAATT
*
105378860 TTAAATTAATAT
1 TTTAATTAAT-T
105378872 TTTAATTAATT
1 TTTAATTAATT
105378883 TTTAATT
1 TTTAATT
105378890 CAATCAATTC
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
9 8 0.24
10 6 0.18
11 9 0.27
12 10 0.30
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTAATTAATT
Found at i:105380606 original size:7 final size:7
Alignment explanation
Indices: 105380594--105380621 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
105380584 CCAGAAAAAC
105380594 ATTAATT
1 ATTAATT
105380601 ATTAATT
1 ATTAATT
105380608 ATTAATT
1 ATTAATT
105380615 ATTAATT
1 ATTAATT
105380622 GTAAAAAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
ATTAATT
Found at i:105381630 original size:11 final size:11
Alignment explanation
Indices: 105381602--105381656 Score: 56
Period size: 11 Copynumber: 5.0 Consensus size: 11
105381592 AAAATGGTAG
105381602 CAAAACAACAA
1 CAAAACAACAA
**
105381613 CCTAACAACAA
1 CAAAACAACAA
*
105381624 TAAAACAACAA
1 CAAAACAACAA
* **
105381635 CATAACAGGAA
1 CAAAACAACAA
105381646 CAAAACAACAA
1 CAAAACAACAA
105381657 TGGAAAAAGT
Statistics
Matches: 32, Mismatches: 12, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
11 32 1.00
ACGTcount: A:0.65, C:0.25, G:0.04, T:0.05
Consensus pattern (11 bp):
CAAAACAACAA
Found at i:105381631 original size:22 final size:22
Alignment explanation
Indices: 105381602--105381656 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
105381592 AAAATGGTAG
*
105381602 CAAAACAACAACCTAACAACAA
1 CAAAACAACAACATAACAACAA
* **
105381624 TAAAACAACAACATAACAGGAA
1 CAAAACAACAACATAACAACAA
105381646 CAAAACAACAA
1 CAAAACAACAA
105381657 TGGAAAAAGT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.65, C:0.25, G:0.04, T:0.05
Consensus pattern (22 bp):
CAAAACAACAACATAACAACAA
Found at i:105382988 original size:28 final size:27
Alignment explanation
Indices: 105382956--105383031 Score: 80
Period size: 30 Copynumber: 2.6 Consensus size: 27
105382946 GCTTTTTCCT
*
105382956 AATTTGATACTTAAATTTTTTTGGGTTC
1 AATTTGATA-TTAAATTTTTTTAGGTTC
* *
105382984 AATTTGGTATTTAAGCTTTTTTTTAGGTTC
1 AATTTGATA-TTAA--ATTTTTTTAGGTTC
105383014 AATTTGATATCTAAATTT
1 AATTTGATAT-TAAATTT
105383032 ATTAAATGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
28 15 0.38
29 1 0.03
30 23 0.59
ACGTcount: A:0.26, C:0.07, G:0.13, T:0.54
Consensus pattern (27 bp):
AATTTGATATTAAATTTTTTTAGGTTC
Found at i:105383485 original size:61 final size:58
Alignment explanation
Indices: 105383420--105383576 Score: 170
Period size: 61 Copynumber: 2.6 Consensus size: 58
105383410 AAAATTAGGA
* ** **
105383420 ACCAAATTAGGAAAAAGAGTCAAGTTTAGGTACCAAATTTGACCTCCCAAAAAGTTTAAGT
1 ACCAAATTA-GAAAAAGAGTCAAGTTTAGGTACCAAATTGGA-C-CAAAAAAAGAATAAGT
* * * * *
105383481 ACCAACTTAAGAAAAAGTGTCAAGTTTGGGCACCAAATTGGACCAAAAAAAGAATAGGT
1 ACCAAATT-AGAAAAAGAGTCAAGTTTAGGTACCAAATTGGACCAAAAAAAGAATAAGT
* *
105383540 ACCAAATTAGAAAAAAAGCCAAGTTTAGGTACCAAAT
1 ACCAAATTAGAAAAAGAGTCAAGTTTAGGTACCAAAT
105383577 ATTATATTAA
Statistics
Matches: 79, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
58 24 0.30
59 18 0.23
60 1 0.01
61 35 0.44
62 1 0.01
ACGTcount: A:0.46, C:0.16, G:0.17, T:0.21
Consensus pattern (58 bp):
ACCAAATTAGAAAAAGAGTCAAGTTTAGGTACCAAATTGGACCAAAAAAAGAATAAGT
Found at i:105389711 original size:31 final size:31
Alignment explanation
Indices: 105389676--105389734 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
105389666 TACAGAAGTT
105389676 GGGTTTTAGACAAAAACAT-TTTTTTGTTGTC
1 GGGTTTTAGACAAAAAC-TCTTTTTTGTTGTC
105389707 GGGTTTTAGACAAAAACTCTTTTTTGTT
1 GGGTTTTAGACAAAAACTCTTTTTTGTT
105389735 TTCGATTGGC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 1 0.04
31 26 0.96
ACGTcount: A:0.25, C:0.10, G:0.19, T:0.46
Consensus pattern (31 bp):
GGGTTTTAGACAAAAACTCTTTTTTGTTGTC
Found at i:105391141 original size:7 final size:7
Alignment explanation
Indices: 105391129--105391161 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
105391119 ATTTGTGTTC
105391129 TTATTTT
1 TTATTTT
105391136 TTATTTT
1 TTATTTT
105391143 TTATTTT
1 TTATTTT
*
105391150 TTATTTC
1 TTATTTT
105391157 TTATT
1 TTATT
105391162 ACTTTGCGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (7 bp):
TTATTTT
Found at i:105391148 original size:14 final size:14
Alignment explanation
Indices: 105391126--105391161 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
105391116 AAAATTTGTG
105391126 TTCTTATTTTTTAT
1 TTCTTATTTTTTAT
*
105391140 TTTTTATTTTTTAT
1 TTCTTATTTTTTAT
105391154 TTCTTATT
1 TTCTTATT
105391162 ACTTTGCGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.14, C:0.06, G:0.00, T:0.81
Consensus pattern (14 bp):
TTCTTATTTTTTAT
Found at i:105393368 original size:13 final size:14
Alignment explanation
Indices: 105393352--105393387 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
105393342 CAATCTCATA
105393352 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
105393365 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
105393378 TCTC-ATTTCA
1 TCTCAATTTCA
105393388 TTCCAATAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:105393377 original size:18 final size:19
Alignment explanation
Indices: 105393339--105393379 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
105393329 TGGTTCATGT
105393339 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
105393358 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
105393376 TTTC
1 TTTC
105393380 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:105393624 original size:23 final size:22
Alignment explanation
Indices: 105393541--105393627 Score: 90
Period size: 21 Copynumber: 4.0 Consensus size: 22
105393531 CCTGATCAGT
105393541 ATACGACACATAAAGTGCCTAA
1 ATACGACACATAAAGTGCCTAA
** *
105393563 A-ACGACACACGAGGTGCCT-A
1 ATACGACACATAAAGTGCCTAA
**
105393583 ATACGACACA-CGAGATGCCTGAA
1 ATACGACACATAAAG-TGCCT-AA
105393606 ATACGACACATAAAGTGCCTAA
1 ATACGACACATAAAGTGCCTAA
105393628 TCGGTAAAGC
Statistics
Matches: 52, Mismatches: 8, Indels: 10
0.74 0.11 0.14
Matches are distributed among these distances:
20 3 0.06
21 28 0.54
22 3 0.06
23 16 0.31
24 2 0.04
ACGTcount: A:0.41, C:0.25, G:0.18, T:0.15
Consensus pattern (22 bp):
ATACGACACATAAAGTGCCTAA
Found at i:105393939 original size:15 final size:15
Alignment explanation
Indices: 105393914--105393971 Score: 80
Period size: 15 Copynumber: 3.8 Consensus size: 15
105393904 TCATATATAT
105393914 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
*
105393930 TATAAATTCAATTAA
1 TATAAATTCAATCAA
* *
105393945 AATAATTTCAATCAA
1 TATAAATTCAATCAA
105393960 TATAAATTCAAT
1 TATAAATTCAAT
105393972 AAAACAGATA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
15 32 0.89
16 4 0.11
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:105393956 original size:30 final size:28
Alignment explanation
Indices: 105393917--105393975 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 28
105393907 TATATATTAT
105393917 ATAATTCAATCAATATAAATTCAATTAAA
1 ATAATTCAATCAATATAAATTCAA-TAAA
105393946 ATAATTTCAATCAATATAAATTCAATAAA
1 ATAA-TTCAATCAATATAAATTCAATAAA
105393975 A
1 A
105393976 CAGATATTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 9 0.31
30 20 0.69
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.34
Consensus pattern (28 bp):
ATAATTCAATCAATATAAATTCAATAAA
Found at i:105394134 original size:2 final size:2
Alignment explanation
Indices: 105394127--105394156 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
105394117 ATATCTCATT
105394127 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
105394157 TATATATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:105407855 original size:30 final size:30
Alignment explanation
Indices: 105407819--105407875 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
105407809 ATATATAACC
*
105407819 TTTTGGTAATGATAAAAGCAAAGGAATGAA
1 TTTTGGTAATAATAAAAGCAAAGGAATGAA
*
105407849 TTTTGGTAATAATTAAAGCAAAGGAAT
1 TTTTGGTAATAATAAAAGCAAAGGAAT
105407876 CAATCTCTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.46, C:0.04, G:0.21, T:0.30
Consensus pattern (30 bp):
TTTTGGTAATAATAAAAGCAAAGGAATGAA
Found at i:105409245 original size:19 final size:18
Alignment explanation
Indices: 105409213--105409257 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
105409203 TAAAAAATAA
* * *
105409213 AAAAAAATACTTTCCTTT
1 AAAAAAATAATTTCATAT
105409231 AAAAAAATGAATTTCATAT
1 AAAAAAAT-AATTTCATAT
105409250 AAAAAAAT
1 AAAAAAAT
105409258 TGAAAATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.58, C:0.09, G:0.02, T:0.31
Consensus pattern (18 bp):
AAAAAAATAATTTCATAT
Found at i:105411831 original size:20 final size:20
Alignment explanation
Indices: 105411803--105411843 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
105411793 AAGTACTGAG
105411803 TAATGTATAATAAAA-AATTT
1 TAATGTAT-ATAAAATAATTT
*
105411823 TAATTTATATAAAATAATTT
1 TAATGTATATAAAATAATTT
105411843 T
1 T
105411844 TAAAACTTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (20 bp):
TAATGTATATAAAATAATTT
Found at i:105411938 original size:12 final size:12
Alignment explanation
Indices: 105411921--105411946 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
105411911 TCATAGAGAC
105411921 ATAGTTTAATAG
1 ATAGTTTAATAG
105411933 ATAGTTTAATAG
1 ATAGTTTAATAG
105411945 AT
1 AT
105411947 GTCTTTTTCG
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:0.42, C:0.00, G:0.15, T:0.42
Consensus pattern (12 bp):
ATAGTTTAATAG
Found at i:105412582 original size:11 final size:11
Alignment explanation
Indices: 105412513--105412582 Score: 52
Period size: 11 Copynumber: 6.4 Consensus size: 11
105412503 AAATGATAGC
*
105412513 AAAATGGTAGAA
1 AAAATAGTA-AA
* *
105412525 AAAATAATAAG
1 AAAATAGTAAA
* *
105412536 AAAATAGCAAC
1 AAAATAGTAAA
* *
105412547 AAAACAATAAA
1 AAAATAGTAAA
*
105412558 AAAA-AGTAAG
1 AAAATAGTAAA
105412568 AAAATAGTAAA
1 AAAATAGTAAA
105412579 AAAA
1 AAAA
105412583 GAAATATTCT
Statistics
Matches: 44, Mismatches: 13, Indels: 3
0.73 0.22 0.05
Matches are distributed among these distances:
10 8 0.18
11 29 0.66
12 7 0.16
ACGTcount: A:0.71, C:0.04, G:0.11, T:0.13
Consensus pattern (11 bp):
AAAATAGTAAA
Found at i:105414317 original size:21 final size:21
Alignment explanation
Indices: 105414293--105414336 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
105414283 TTAAATTAAA
105414293 AATAAAACCCAAAATAGAGTT
1 AATAAAACCCAAAATAGAGTT
105414314 AATAAAACCCAAAATAGAGTT
1 AATAAAACCCAAAATAGAGTT
105414335 AA
1 AA
105414337 ATATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.59, C:0.14, G:0.09, T:0.18
Consensus pattern (21 bp):
AATAAAACCCAAAATAGAGTT
Found at i:105415174 original size:23 final size:25
Alignment explanation
Indices: 105415144--105415191 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
105415134 ACTTATATAC
105415144 TTTTAATAT-TAT-CATATATTTAT
1 TTTTAATATATATGCATATATTTAT
*
105415167 TTTTAATATATATGTATATATTTAT
1 TTTTAATATATATGCATATATTTAT
105415192 ATAATATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 9 0.41
24 3 0.14
25 10 0.45
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (25 bp):
TTTTAATATATATGCATATATTTAT
Found at i:105415535 original size:21 final size:21
Alignment explanation
Indices: 105415511--105415550 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
105415501 GTATATTCTT
105415511 ACTATTA-TCATTATTATCACC
1 ACTATTATTC-TTATTATCACC
105415532 ACTATTATTCTTATTATCA
1 ACTATTATTCTTATTATCA
105415551 TATTATTGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.33, C:0.20, G:0.00, T:0.47
Consensus pattern (21 bp):
ACTATTATTCTTATTATCACC
Found at i:105415660 original size:3 final size:3
Alignment explanation
Indices: 105415652--105415773 Score: 63
Period size: 3 Copynumber: 41.3 Consensus size: 3
105415642 AATTTCACTT
* * * * * **
105415652 TTA TTA TTA TTA CTA -TA TCA TCA TTG TTA TTA TTA TT- TTC CCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * *
105415698 TTA TTA ATA CTA ATA TTAA TT- TTC TTA TTA TTA TTG TTA TTA GTA
1 TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
105415743 TCA TAA TGTA TTA -TA TTA TTA TTA TTA TTA T
1 TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA T
105415774 CGTCTTTTAT
Statistics
Matches: 91, Mismatches: 22, Indels: 12
0.73 0.18 0.10
Matches are distributed among these distances:
2 8 0.09
3 78 0.86
4 5 0.05
ACGTcount: A:0.32, C:0.07, G:0.03, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:105416540 original size:126 final size:126
Alignment explanation
Indices: 105416315--105416578 Score: 474
Period size: 126 Copynumber: 2.1 Consensus size: 126
105416305 ATTTGGTTTA
*
105416315 AAATAAAGGCAACATTCGGCATTTGAGAATTCGAGAAAACATGCCCTAACTTACTGGGTTTCGAT
1 AAATAAAGGCAACATTCGGCATTTGAGAATTCGAGAAAACATACCCTAACTTACTGGGTTTCGAT
*
105416380 TTCTCTCGTTTACTCTAAATAGTCGAATACCCTTTTAAAAAGGTCAAAATACATGAATTTC
66 TTCTCTCGTTTACTCTAAATAATCGAATACCCTTTTAAAAAGGTCAAAATACATGAATTTC
* * *
105416441 AAATAAAGGCAACATTCGGTATTTGAGAATTCGAGAAAACGTACCCTAACTTACTGGGTTTTGAT
1 AAATAAAGGCAACATTCGGCATTTGAGAATTCGAGAAAACATACCCTAACTTACTGGGTTTCGAT
*
105416506 TTCTCTCGTTTACTCTAAATAATCGAATACCCTTTTAAAAAGGTCAAAATATATGAATTTC
66 TTCTCTCGTTTACTCTAAATAATCGAATACCCTTTTAAAAAGGTCAAAATACATGAATTTC
105416567 AAATAAAGGCAA
1 AAATAAAGGCAA
105416579 GCTCATTCTC
Statistics
Matches: 132, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
126 132 1.00
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (126 bp):
AAATAAAGGCAACATTCGGCATTTGAGAATTCGAGAAAACATACCCTAACTTACTGGGTTTCGAT
TTCTCTCGTTTACTCTAAATAATCGAATACCCTTTTAAAAAGGTCAAAATACATGAATTTC
Found at i:105436083 original size:51 final size:51
Alignment explanation
Indices: 105436012--105436125 Score: 201
Period size: 51 Copynumber: 2.2 Consensus size: 51
105436002 CTGATCACAT
105436012 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
*
105436063 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
* *
105436114 TTGTCGCTTGTC
1 TTATCACTTGTC
105436126 GCTTGTCACT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (51 bp):
TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
Found at i:105447331 original size:43 final size:43
Alignment explanation
Indices: 105447270--105447354 Score: 152
Period size: 43 Copynumber: 2.0 Consensus size: 43
105447260 AATCTACAAG
* *
105447270 ATTTATTGGAGAAGCGTTAGTATAGGGTGTATGATAATTATAA
1 ATTTATTGGAGAAGCGTTAGTATAGAGTGTATAATAATTATAA
105447313 ATTTATTGGAGAAGCGTTAGTATAGAGTGTATAATAATTATA
1 ATTTATTGGAGAAGCGTTAGTATAGAGTGTATAATAATTATA
105447355 GAGCTCACCT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.36, C:0.02, G:0.24, T:0.38
Consensus pattern (43 bp):
ATTTATTGGAGAAGCGTTAGTATAGAGTGTATAATAATTATAA
Found at i:105449933 original size:35 final size:35
Alignment explanation
Indices: 105449894--105449965 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
105449884 TAATAAGGAG
105449894 AAAATCTATTGGATACTTTAAAGAGAAATCAAAAT
1 AAAATCTATTGGATACTTTAAAGAGAAATCAAAAT
105449929 AAAATCTATTGGATACTTTAAAGAGAAATCAAAAT
1 AAAATCTATTGGATACTTTAAAGAGAAATCAAAAT
105449964 AA
1 AA
105449966 TAAGAGAAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.53, C:0.08, G:0.11, T:0.28
Consensus pattern (35 bp):
AAAATCTATTGGATACTTTAAAGAGAAATCAAAAT
Found at i:105458341 original size:13 final size:13
Alignment explanation
Indices: 105458325--105458350 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
105458315 ACTTTATGCA
105458325 AACAAATGGTTTT
1 AACAAATGGTTTT
105458338 AACAAATGGTTTT
1 AACAAATGGTTTT
105458351 TTGGAAACAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (13 bp):
AACAAATGGTTTT
Found at i:105460088 original size:13 final size:13
Alignment explanation
Indices: 105460070--105460095 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
105460060 TAGGGCACAC
105460070 GCCCGTGTGGCCA
1 GCCCGTGTGGCCA
105460083 GCCCGTGTGGCCA
1 GCCCGTGTGGCCA
105460096 ACCCTTGGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.38, G:0.38, T:0.15
Consensus pattern (13 bp):
GCCCGTGTGGCCA
Found at i:105460376 original size:41 final size:41
Alignment explanation
Indices: 105460331--105460409 Score: 99
Period size: 41 Copynumber: 1.9 Consensus size: 41
105460321 ATGTAGGGGA
*
105460331 CACACGGCCT-ATCAACATGCCAGTGTG-CAAGCCGTGTGTCT
1 CACACGG-CTGATC-ACACGCCAGTGTGACAAGCCGTGTGTCT
* *
105460372 CACACGGTTGATCACACGCCCGTGTGACAAGCCGTGTG
1 CACACGGCTGATCACACGCCAGTGTGACAAGCCGTGTG
105460410 GACTTAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 12 0.36
41 21 0.64
ACGTcount: A:0.22, C:0.32, G:0.27, T:0.20
Consensus pattern (41 bp):
CACACGGCTGATCACACGCCAGTGTGACAAGCCGTGTGTCT
Found at i:105462102 original size:16 final size:17
Alignment explanation
Indices: 105462083--105462121 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
105462073 TTTTATTTAC
*
105462083 TTAATAT-ATTATAATA
1 TTAATATAAATATAATA
105462099 TTAATATAAATATAATA
1 TTAATATAAATATAATA
105462116 -TAATAT
1 TTAATAT
105462122 TATTTACTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TTAATATAAATATAATA
Found at i:105463064 original size:20 final size:20
Alignment explanation
Indices: 105463041--105463090 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
105463031 AAATCCAAAT
105463041 TAAAATACTAAAATTCAGGA
1 TAAAATACTAAAATTCAGGA
* *
105463061 TAAAATCCTGAAATTCAGGA
1 TAAAATACTAAAATTCAGGA
105463081 TAAGAATACT
1 TAA-AATACT
105463091 GATGTGGCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 21 0.81
21 5 0.19
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.26
Consensus pattern (20 bp):
TAAAATACTAAAATTCAGGA
Found at i:105465153 original size:23 final size:25
Alignment explanation
Indices: 105465133--105465181 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
105465123 ATTCATTAAT
105465133 ATAATAATATAATATCAATTAAT-TAA
1 ATAATAATA-AATAT-AATTAATATAA
*
105465159 ATAATAATAAATATAATAAATAT
1 ATAATAATAAATATAATTAATAT
105465182 CTATTTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 6 0.29
25 6 0.29
26 9 0.43
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (25 bp):
ATAATAATAAATATAATTAATATAA
Found at i:105465176 original size:15 final size:13
Alignment explanation
Indices: 105465129--105465177 Score: 59
Period size: 12 Copynumber: 3.8 Consensus size: 13
105465119 ATTTATTCAT
105465129 TAATATAATAATA
1 TAATATAATAATA
105465142 TAATATCAATTAAT-
1 TAATAT-AA-TAATA
105465156 TAA-ATAATAATA
1 TAATATAATAATA
105465168 -AATATAATAA
1 TAATATAATAA
105465178 ATATCTATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
11 6 0.19
12 9 0.28
13 8 0.25
14 5 0.16
15 4 0.12
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (13 bp):
TAATATAATAATA
Found at i:105468349 original size:19 final size:21
Alignment explanation
Indices: 105468322--105468362 Score: 68
Period size: 19 Copynumber: 2.0 Consensus size: 21
105468312 ATGGACATTT
105468322 GGACTTTTAATTTTG-TTTTG
1 GGACTTTTAATTTTGATTTTG
105468342 GGAC-TTTAATTTTGATTTTG
1 GGACTTTTAATTTTGATTTTG
105468362 G
1 G
105468363 TATTTACTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.17, C:0.05, G:0.22, T:0.56
Consensus pattern (21 bp):
GGACTTTTAATTTTGATTTTG
Found at i:105469772 original size:24 final size:24
Alignment explanation
Indices: 105469735--105469786 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
105469725 AAGATTGAAC
* *
105469735 ATTTATTAGCATAATATATTTGGT
1 ATTTATTAACATAAAATATTTGGT
* * *
105469759 ATTTATTAATATAAAATCTTTGTT
1 ATTTATTAACATAAAATATTTGGT
105469783 ATTT
1 ATTT
105469787 CTTTTTATAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.54
Consensus pattern (24 bp):
ATTTATTAACATAAAATATTTGGT
Found at i:105482284 original size:29 final size:31
Alignment explanation
Indices: 105482228--105482287 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 31
105482218 TTTTTATTAA
* **
105482228 TTATTTAAATTTTAAAATTAATTAAACATAT
1 TTATTTAAATTTTAAAATCAACAAAACATAT
105482259 TTATTTAAA-TTT-AAATCAACAAAACATAT
1 TTATTTAAATTTTAAAATCAACAAAACATAT
105482288 AAAATAAAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 14 0.54
30 3 0.12
31 9 0.35
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (31 bp):
TTATTTAAATTTTAAAATCAACAAAACATAT
Found at i:105496544 original size:43 final size:43
Alignment explanation
Indices: 105496483--105496632 Score: 138
Period size: 44 Copynumber: 3.4 Consensus size: 43
105496473 TTCACAAGCA
* *
105496483 TTAACCCCCTAAGCAGTAGGGTAACAGGTTGAATTTATAGATC
1 TTAACCCCCTAAGCAGTAGGGTAACAGGTCGAAATTATAGATC
* * * * * * **
105496526 TTAACCCCCTAAGTAGTAGGGAAACAGATCGAAGGTGATGGGCC
1 TTAACCCCCTAAGCAGTAGGGTAACAGGTCGAA-ATTATAGATC
* * *
105496570 TTAAACCCCTAAGCAGTAGGGTAACAGGCTGGAAATTACAGATC
1 TTAACCCCCTAAGCAGTAGGGTAACAGG-TCGAAATTATAGATC
** *
105496614 TTGTCTCCCTAAGCAGTAG
1 TTAACCCCCTAAGCAGTAG
105496633 CGGAGTAGAT
Statistics
Matches: 81, Mismatches: 24, Indels: 3
0.75 0.22 0.03
Matches are distributed among these distances:
43 29 0.36
44 48 0.59
45 4 0.05
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.23
Consensus pattern (43 bp):
TTAACCCCCTAAGCAGTAGGGTAACAGGTCGAAATTATAGATC
Found at i:105496643 original size:88 final size:88
Alignment explanation
Indices: 105496483--105496887 Score: 499
Period size: 88 Copynumber: 4.6 Consensus size: 88
105496473 TTCACAAGCA
* * * ** * *
105496483 TTAACCCCCTAAGCAGTAGGGTAACAGGTTG-AATTTATAGATCTTAACCCCCTAAGTAGTAG-G
1 TTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAAATTACAGATCTTGTCTCCCTAAGCAGTAGTG
* ** *
105496546 GAAACAGATCGAAGGTGATGGGCC
66 G-AGCAGATCGAAGACGAAGGGCC
* * *
105496570 TTAAACCCCTAAGCAGTAGGGTAACAGGCTGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCG
1 TTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAAATTACAGATCTTGTCTCCCTAAGCAGTAGTG
* * ** *
105496635 GAGTAGATCGAAGAGGGTGAGCC
66 GAGCAGATCGAAGACGAAGGGCC
* * * *
105496658 TTGACCCCCTAAGCAATAGGGTAACAGGCTAAAAATTACAGATCTTGTCTCCCTAAGCAATAGTG
1 TTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAAATTACAGATCTTGTCTCCCTAAGCAGTAGTG
105496723 GAGCAGATCGAAGACGAAGGGCC
66 GAGCAGATCGAAGACGAAGGGCC
* * * * *
105496746 TTAACCCCCTAAACAGTAGGGTAACAAGTTGAAAATTACAAATCTTGTCTCCCTAAGCAGTTGTG
1 TTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAAATTACAGATCTTGTCTCCCTAAGCAGTAGTG
105496811 GAGCAGATCGAAGACGAAGGGCC
66 GAGCAGATCGAAGACGAAGGGCC
* * * *
105496834 TTAACCCACTAAGTAGTAGGGTAACAGGCTGAAAATTACAAATCTTATCTCCCT
1 TTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAAATTACAGATCTTGTCTCCCT
105496888 GAAGTTGCAG
Statistics
Matches: 275, Mismatches: 41, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
87 29 0.11
88 244 0.89
89 2 0.01
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.22
Consensus pattern (88 bp):
TTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAAATTACAGATCTTGTCTCCCTAAGCAGTAGTG
GAGCAGATCGAAGACGAAGGGCC
Found at i:105497311 original size:21 final size:20
Alignment explanation
Indices: 105497278--105497317 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
105497268 GTGTCCTAAC
*
105497278 TTACTGGATATGACATCTTG
1 TTACTGGAGATGACATCTTG
*
105497298 TTACTTGGAGATGAGATCTT
1 TTAC-TGGAGATGACATCTT
105497318 TGCAAACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.25, C:0.12, G:0.23, T:0.40
Consensus pattern (20 bp):
TTACTGGAGATGACATCTTG
Found at i:105498849 original size:12 final size:12
Alignment explanation
Indices: 105498832--105498858 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
105498822 TCCTGTTTCT
105498832 TTTTTTATTTAA
1 TTTTTTATTTAA
105498844 TTTTTTATTTAA
1 TTTTTTATTTAA
105498856 TTT
1 TTT
105498859 CATCCTTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTTTATTTAA
Found at i:105503613 original size:16 final size:16
Alignment explanation
Indices: 105503585--105503624 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
105503575 ATCGAATCGG
105503585 ATTTTTTATTTTTAATA
1 ATTTTTTATTTTTAA-A
105503602 ATTTTTTA-TTTTAAA
1 ATTTTTTATTTTTAAA
*
105503617 ATATTTTA
1 ATTTTTTA
105503625 ATGATTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
16 6 0.27
17 8 0.36
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
ATTTTTTATTTTTAAA
Found at i:105512676 original size:25 final size:25
Alignment explanation
Indices: 105512633--105512684 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 25
105512623 AATATTTAGT
105512633 TTAAACTACTTTATATAGTATTCATTC
1 TTAAACTA-TTTATATAGTATTC-TTC
*
105512660 TTAAACT-TTTATTTAGTATTCTTC
1 TTAAACTATTTATATAGTATTCTTC
105512684 T
1 T
105512685 CAAATTGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 4 0.17
25 13 0.54
27 7 0.29
ACGTcount: A:0.29, C:0.13, G:0.04, T:0.54
Consensus pattern (25 bp):
TTAAACTATTTATATAGTATTCTTC
Found at i:105513042 original size:7 final size:7
Alignment explanation
Indices: 105513030--105513054 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
105513020 AATTTCAAAG
105513030 TATTATA
1 TATTATA
105513037 TATTATA
1 TATTATA
105513044 TATTATA
1 TATTATA
105513051 TATT
1 TATT
105513055 GTAAGTTGCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
TATTATA
Found at i:105515434 original size:30 final size:31
Alignment explanation
Indices: 105515361--105515431 Score: 142
Period size: 31 Copynumber: 2.3 Consensus size: 31
105515351 TCTTTAAATT
105515361 TTTTTAAAAATTTTAATTAGCCTCCTCAAAA
1 TTTTTAAAAATTTTAATTAGCCTCCTCAAAA
105515392 TTTTTAAAAATTTTAATTAGCCTCCTCAAAA
1 TTTTTAAAAATTTTAATTAGCCTCCTCAAAA
105515423 TTTTTAAAA
1 TTTTTAAAA
105515432 TTTACTATTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.39, C:0.14, G:0.03, T:0.44
Consensus pattern (31 bp):
TTTTTAAAAATTTTAATTAGCCTCCTCAAAA
Found at i:105519747 original size:17 final size:17
Alignment explanation
Indices: 105519702--105519747 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
105519692 TAGTCATGAC
105519702 AAAATAAATT-AAAATTA
1 AAAAT-AATTAAAAATTA
*
105519719 GAAA-AATATAAAAATTA
1 AAAATAAT-TAAAAATTA
105519736 AAAATAATTAAA
1 AAAATAATTAAA
105519748 TTAAAATACA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
15 3 0.12
16 1 0.04
17 17 0.71
18 3 0.12
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (17 bp):
AAAATAATTAAAAATTA
Found at i:105528250 original size:30 final size:30
Alignment explanation
Indices: 105528212--105528285 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
105528202 TCTTAATAAA
*
105528212 TTTAAATTTAAATTATTAT-CTTTTTACTT
1 TTTAAATTTAAATTATTATACTTTTTACAT
* * *
105528241 TTTAGAATTT-AATTTTTATATTTTTTAGAT
1 TTTA-AATTTAAATTATTATACTTTTTACAT
105528271 TTTAAAATTTAAATT
1 TTT-AAATTTAAATT
105528286 TAATTATTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
29 12 0.32
30 20 0.54
31 5 0.14
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (30 bp):
TTTAAATTTAAATTATTATACTTTTTACAT
Found at i:105528281 original size:23 final size:23
Alignment explanation
Indices: 105528239--105528286 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
105528229 ATCTTTTTAC
** *
105528239 TTTTTAGAATTTAATTTTTATAT
1 TTTTTAGAATTTAAAATTTAAAT
*
105528262 TTTTTAGATTTTAAAATTTAAAT
1 TTTTTAGAATTTAAAATTTAAAT
105528285 TT
1 TT
105528287 AATTATTAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (23 bp):
TTTTTAGAATTTAAAATTTAAAT
Found at i:105532725 original size:28 final size:28
Alignment explanation
Indices: 105532661--105532718 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
105532651 CAATTGGTCC
**
105532661 TTATATTTTTTTCATTTTGAGTAATTTT
1 TTATATTTTTTTCATTTTGAACAATTTT
105532689 TTATATTTTTTTCATTTTGAACAATTTT
1 TTATATTTTTTTCATTTTGAACAATTTT
105532717 TT
1 TT
105532719 TCCTTTTATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.22, C:0.05, G:0.05, T:0.67
Consensus pattern (28 bp):
TTATATTTTTTTCATTTTGAACAATTTT
Found at i:105532789 original size:17 final size:17
Alignment explanation
Indices: 105532749--105532791 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
105532739 TGGAGAAGGG
*
105532749 AGAAAAATAGAAGGAAA
1 AGAAAAAGAGAAGGAAA
*
105532766 AGTAAAAGAGAATGGAAA
1 AGAAAAAGAGAA-GGAAA
*
105532784 AAAAAAAG
1 AGAAAAAG
105532792 GAAAGTTAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.70, C:0.00, G:0.23, T:0.07
Consensus pattern (17 bp):
AGAAAAAGAGAAGGAAA
Found at i:105533176 original size:33 final size:33
Alignment explanation
Indices: 105533134--105533196 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
105533124 TGAGCAAAAG
105533134 TGAGAATTTCACAATAGAATAATTATAGTAGAA
1 TGAGAATTTCACAATAGAATAATTATAGTAGAA
105533167 TGAGAATTTCACAATAGAATAATTATAGTA
1 TGAGAATTTCACAATAGAATAATTATAGTA
105533197 CAATATTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.48, C:0.06, G:0.14, T:0.32
Consensus pattern (33 bp):
TGAGAATTTCACAATAGAATAATTATAGTAGAA
Found at i:105533186 original size:19 final size:19
Alignment explanation
Indices: 105533134--105533186 Score: 53
Period size: 19 Copynumber: 3.1 Consensus size: 19
105533124 TGAGCAAAAG
105533134 TGAGAATTTCACAATAGAA
1 TGAGAATTTCACAATAGAA
* *
105533153 T---AA-TT-ATAGTAGAA
1 TGAGAATTTCACAATAGAA
105533167 TGAGAATTTCACAATAGAA
1 TGAGAATTTCACAATAGAA
105533186 T
1 T
105533187 AATTATAGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 10
0.64 0.10 0.26
Matches are distributed among these distances:
14 8 0.32
15 2 0.08
16 2 0.08
17 2 0.08
18 2 0.08
19 9 0.36
ACGTcount: A:0.47, C:0.08, G:0.15, T:0.30
Consensus pattern (19 bp):
TGAGAATTTCACAATAGAA
Found at i:105533199 original size:19 final size:19
Alignment explanation
Indices: 105533144--105533201 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
105533134 TGAGAATTTC
105533144 ACAATAGAATAATTATAGT
1 ACAATAGAATAATTATAGT
* * *
105533163 AGAAT-G-AGAATT-T--C
1 ACAATAGAATAATTATAGT
105533177 ACAATAGAATAATTATAGT
1 ACAATAGAATAATTATAGT
105533196 ACAATA
1 ACAATA
105533202 TTTTAAAAGT
Statistics
Matches: 28, Mismatches: 6, Indels: 10
0.64 0.14 0.23
Matches are distributed among these distances:
14 4 0.14
15 1 0.04
16 6 0.21
17 6 0.21
18 1 0.04
19 10 0.36
ACGTcount: A:0.52, C:0.07, G:0.12, T:0.29
Consensus pattern (19 bp):
ACAATAGAATAATTATAGT
Found at i:105547296 original size:12 final size:12
Alignment explanation
Indices: 105547279--105547311 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
105547269 AGGCCCGCCC
105547279 ATATTAATTTTT
1 ATATTAATTTTT
105547291 ATATT-ATTTTT
1 ATATTAATTTTT
105547302 ATA-TAATTTT
1 ATATTAATTTT
105547312 AAAATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:105547351 original size:18 final size:20
Alignment explanation
Indices: 105547312--105547352 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
105547302 ATATAATTTT
*
105547312 AAAATATATATAATACATCA
1 AAAATATATATAATACAGCA
105547332 AAAATAT-TATAA-ACAGCA
1 AAAATATATATAATACAGCA
105547350 AAA
1 AAA
105547353 TAAGTATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
19 5 0.25
20 7 0.35
ACGTcount: A:0.63, C:0.10, G:0.02, T:0.24
Consensus pattern (20 bp):
AAAATATATATAATACAGCA
Found at i:105547479 original size:30 final size:30
Alignment explanation
Indices: 105547435--105547497 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
105547425 ACTTAACAAG
* *
105547435 CAAATGTCTCTAAAATAATAACAAAATTGA
1 CAAATATCTCTAAAATAATAACAAAATTAA
*
105547465 CAAATATCTTTAAAATAATAACAAAATTAA
1 CAAATATCTCTAAAATAATAACAAAATTAA
105547495 CAA
1 CAA
105547498 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.57, C:0.13, G:0.03, T:0.27
Consensus pattern (30 bp):
CAAATATCTCTAAAATAATAACAAAATTAA
Found at i:105549056 original size:69 final size:72
Alignment explanation
Indices: 105548845--105549078 Score: 314
Period size: 69 Copynumber: 3.3 Consensus size: 72
105548835 ATATAGATAA
* * * *
105548845 AAAG-AGTAATATTGCAAATTACAACAACAACAAAAAAAAACAAATTTGAAGTTAATAACTACTT
1 AAAGTAGTAATCTTGCAAATT---ACGACAACAAAAACATACAAATTTGAAGTTAATAACTACTT
105548909 AAGTCCCTAG
63 AAGTCCCTAG
* * *
105548919 AAAGTAGTAATATTGCAAATTACGACAAAAAAAACATACAAATTTGAAGTTAATAACTACTTAGG
1 AAAGTAGTAATCTTGCAAATTACGACAACAAAAACATACAAATTTGAAGTTAATAACTACTTAAG
*
105548984 TCCCTAC
66 TCCCTAG
* * *
105548991 AATGTAGTAATCCTGCAAA-T-C-ACAACAAAAACATACACATTTGAAGTTAATAACTACTTAAG
1 AAAGTAGTAATCTTGCAAATTACGACAACAAAAACATACAAATTTGAAGTTAATAACTACTTAAG
105549053 TCCCTAG
66 TCCCTAG
105549060 AAAGTAGTAATCTTGCAAA
1 AAAGTAGTAATCTTGCAAA
105549079 GAAACTCGAC
Statistics
Matches: 144, Mismatches: 15, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
69 61 0.42
70 1 0.01
71 1 0.01
72 61 0.42
74 4 0.03
75 16 0.11
ACGTcount: A:0.48, C:0.16, G:0.11, T:0.25
Consensus pattern (72 bp):
AAAGTAGTAATCTTGCAAATTACGACAACAAAAACATACAAATTTGAAGTTAATAACTACTTAAG
TCCCTAG
Found at i:105549894 original size:22 final size:23
Alignment explanation
Indices: 105549867--105549913 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
105549857 CTTATCTTAT
* *
105549867 TTTAATTAC-TTAAAAAAATTAA
1 TTTAATCACTTTAAAAAAAATAA
105549889 TTTAATCACTTTAAAAAAAATAA
1 TTTAATCACTTTAAAAAAAATAA
105549912 TT
1 TT
105549914 GTATAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.40
Consensus pattern (23 bp):
TTTAATCACTTTAAAAAAAATAA
Found at i:105550728 original size:23 final size:23
Alignment explanation
Indices: 105550702--105550745 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
105550692 AAAAAATTAT
*
105550702 AAAAGTAGTATTTAAATTATTTA
1 AAAAATAGTATTTAAATTATTTA
**
105550725 AAAAATTTTATTTAAATTATT
1 AAAAATAGTATTTAAATTATT
105550746 GGGCTGATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (23 bp):
AAAAATAGTATTTAAATTATTTA
Found at i:105551740 original size:14 final size:14
Alignment explanation
Indices: 105551721--105551747 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
105551711 TTAATTTTAA
105551721 ATAAAAGAAAAACG
1 ATAAAAGAAAAACG
105551735 ATAAAAGAAAAAC
1 ATAAAAGAAAAAC
105551748 CCTCACCCTC
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:0.74, C:0.07, G:0.11, T:0.07
Consensus pattern (14 bp):
ATAAAAGAAAAACG
Found at i:105562176 original size:78 final size:78
Alignment explanation
Indices: 105562047--105562202 Score: 303
Period size: 78 Copynumber: 2.0 Consensus size: 78
105562037 CAAGCTCTTG
105562047 TCTAATTTCTTATTGAGGCAATAGAAATTATATAGTCTTTAACAACAATATTATCAAAACCATTT
1 TCTAATTTCTTATTGAGGCAATAGAAATTATATAGTCTTTAACAACAATATTATCAAAACCATTT
105562112 TTAACCAAAATTA
66 TTAACCAAAATTA
*
105562125 TCTAATTTCTTATTGAGGCAATAGAAATTATATAGTCTTTAACAACAATATTATCGAAACCATTT
1 TCTAATTTCTTATTGAGGCAATAGAAATTATATAGTCTTTAACAACAATATTATCAAAACCATTT
105562190 TTAACCAAAATTA
66 TTAACCAAAATTA
105562203 GTGGGATTAT
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 77 1.00
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.37
Consensus pattern (78 bp):
TCTAATTTCTTATTGAGGCAATAGAAATTATATAGTCTTTAACAACAATATTATCAAAACCATTT
TTAACCAAAATTA
Found at i:105569303 original size:22 final size:22
Alignment explanation
Indices: 105569264--105569305 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
105569254 GCGAAATCAC
*
105569264 AGCAAAATAGTAACAAAACAGT
1 AGCAAAACAGTAACAAAACAGT
* *
105569286 AGCAAAACAGTGATAAAACA
1 AGCAAAACAGTAACAAAACA
105569306 ACAACAATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.60, C:0.14, G:0.14, T:0.12
Consensus pattern (22 bp):
AGCAAAACAGTAACAAAACAGT
Found at i:105571183 original size:16 final size:16
Alignment explanation
Indices: 105571148--105571177 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
105571138 AACAAAAGAG
105571148 TAATTATAAGATGGTA
1 TAATTATAAGATGGTA
105571164 TAATTATAA-ATGGT
1 TAATTATAAGATGGT
105571178 TTTAATCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.43, C:0.00, G:0.17, T:0.40
Consensus pattern (16 bp):
TAATTATAAGATGGTA
Found at i:105576447 original size:23 final size:24
Alignment explanation
Indices: 105576420--105576498 Score: 76
Period size: 23 Copynumber: 3.4 Consensus size: 24
105576410 ACTAACATTG
105576420 TTTAA-TTTCTAACAAACATACAA
1 TTTAAGTTTCTAACAAACATACAA
** * **
105576443 TTTAAGTTGATACACTAACAT--TG
1 TTTAAGTTTCTA-ACAAACATACAA
105576466 TTTAA-TTTCTAACAAACATACAA
1 TTTAAGTTTCTAACAAACATACAA
105576489 TTTAAGTTTC
1 TTTAAGTTTC
105576499 ATTAGCACAT
Statistics
Matches: 41, Mismatches: 10, Indels: 9
0.68 0.17 0.15
Matches are distributed among these distances:
21 7 0.17
22 4 0.10
23 15 0.37
24 8 0.20
25 7 0.17
ACGTcount: A:0.41, C:0.15, G:0.05, T:0.39
Consensus pattern (24 bp):
TTTAAGTTTCTAACAAACATACAA
Found at i:105576458 original size:46 final size:46
Alignment explanation
Indices: 105576405--105576496 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
105576395 GTGCTGCAAA
105576405 GATACACTAACATTGTTTAATTTCTAACAAACATACAATTTAAGTT
1 GATACACTAACATTGTTTAATTTCTAACAAACATACAATTTAAGTT
105576451 GATACACTAACATTGTTTAATTTCTAACAAACATACAATTTAAGTT
1 GATACACTAACATTGTTTAATTTCTAACAAACATACAATTTAAGTT
105576497 TCATTAGCAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (46 bp):
GATACACTAACATTGTTTAATTTCTAACAAACATACAATTTAAGTT
Found at i:105576484 original size:21 final size:21
Alignment explanation
Indices: 105576413--105576484 Score: 63
Period size: 21 Copynumber: 3.2 Consensus size: 21
105576403 AAGATACACT
105576413 AACATTGTTTAATTTCTAACA
1 AACATTGTTTAATTTCTAACA
** ** *
105576434 AACATACAATTTAAGTTGATACACT
1 AACAT--TGTTTAA-TTTCTA-ACA
105576459 AACATTGTTTAATTTCTAACA
1 AACATTGTTTAATTTCTAACA
105576480 AACAT
1 AACAT
105576485 ACAATTTAAG
Statistics
Matches: 37, Mismatches: 10, Indels: 8
0.67 0.18 0.15
Matches are distributed among these distances:
21 12 0.32
22 4 0.11
23 10 0.27
24 4 0.11
25 7 0.19
ACGTcount: A:0.42, C:0.15, G:0.06, T:0.38
Consensus pattern (21 bp):
AACATTGTTTAATTTCTAACA
Found at i:105590646 original size:20 final size:20
Alignment explanation
Indices: 105590614--105590656 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 20
105590604 TGATTTTAAA
105590614 TTAATTCTAAAAGAAATATTT
1 TTAATTCTAAAAGAAA-ATTT
105590635 TTAATT-TAAAAGAAAATTT
1 TTAATTCTAAAAGAAAATTT
105590654 TTA
1 TTA
105590657 TTTGTGTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 7 0.32
20 9 0.41
21 6 0.27
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (20 bp):
TTAATTCTAAAAGAAAATTT
Found at i:105591578 original size:19 final size:16
Alignment explanation
Indices: 105591554--105591596 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 16
105591544 ACCCAAGCCC
105591554 AAAAAGAAAAATGATGAAA
1 AAAAAGAAAAA-GA--AAA
*
105591573 AAAAAGAAGAAGAAAA
1 AAAAAGAAAAAGAAAA
105591589 AAAAAGAA
1 AAAAAGAA
105591597 CCCCACGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 11 0.48
18 2 0.09
19 10 0.43
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (16 bp):
AAAAAGAAAAAGAAAA
Found at i:105591748 original size:32 final size:32
Alignment explanation
Indices: 105591705--105591773 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
105591695 ATCAAGTTGT
*
105591705 CGCCGTTAACCCCATTCGCCGTCTTACGTCAC
1 CGCCGTCAACCCCATTCGCCGTCTTACGTCAC
* *
105591737 CGCCGTCAACCCCTTTCGTCGTCTTACGTCAC
1 CGCCGTCAACCCCATTCGCCGTCTTACGTCAC
105591769 CGCCG
1 CGCCG
105591774 ACAATCGTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.13, C:0.45, G:0.17, T:0.25
Consensus pattern (32 bp):
CGCCGTCAACCCCATTCGCCGTCTTACGTCAC
Found at i:105594188 original size:17 final size:18
Alignment explanation
Indices: 105594152--105594194 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
105594142 CACCTTATTT
* *
105594152 TTTTTTTCTATTTTTTCA
1 TTTTTTTCTATCTTTCCA
105594170 TTTTTTTCT-TCTTTCCA
1 TTTTTTTCTATCTTTCCA
*
105594187 TTTATTTC
1 TTTTTTTC
105594195 CCTTAGCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTTTCTATCTTTCCA
Found at i:105597166 original size:13 final size:14
Alignment explanation
Indices: 105597148--105597177 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
105597138 CTATAATTAG
105597148 TTTAAA-TTTGATT
1 TTTAAATTTTGATT
105597161 TTTAAATTTTGATT
1 TTTAAATTTTGATT
105597175 TTT
1 TTT
105597178 CTAGTGATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (14 bp):
TTTAAATTTTGATT
Found at i:105599125 original size:17 final size:16
Alignment explanation
Indices: 105599103--105599145 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
105599093 ATTTTCAACT
105599103 TTAATTTATTCATAATA
1 TTAATTTATTCAT-ATA
*
105599120 TTAA-TTATTTATATA
1 TTAATTTATTCATATA
105599135 TTAATATTATT
1 TTAAT-TTATT
105599146 ATTTTTAGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 7 0.30
16 7 0.30
17 9 0.39
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (16 bp):
TTAATTTATTCATATA
Found at i:105602542 original size:36 final size:36
Alignment explanation
Indices: 105602502--105602581 Score: 101
Period size: 36 Copynumber: 2.2 Consensus size: 36
105602492 ATACATATAA
*
105602502 ATATATATACT-TATAAAAATAAAAAT-ATGTATATGT
1 ATATATATA-TATATAAAAAGAAAAATGA-GTATATGT
* *
105602538 ATATAGATATATATAAAAAGAAATATGAGTATATGT
1 ATATATATATATATAAAAAGAAAAATGAGTATATGT
105602574 ATATATAT
1 ATATATAT
105602582 TAAACAAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
35 1 0.03
36 36 0.95
37 1 0.03
ACGTcount: A:0.53, C:0.01, G:0.09, T:0.38
Consensus pattern (36 bp):
ATATATATATATATAAAAAGAAAAATGAGTATATGT
Found at i:105602723 original size:3 final size:3
Alignment explanation
Indices: 105602712--105602799 Score: 133
Period size: 3 Copynumber: 29.3 Consensus size: 3
105602702 CAATAATACC
* * *
105602712 AAT ACT AAT AAT AGT AA- AGAT GAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
105602757 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
105602800 GCAAAAGTAC
Statistics
Matches: 77, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
2 1 0.01
3 76 0.99
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:105603865 original size:31 final size:29
Alignment explanation
Indices: 105603830--105603898 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 29
105603820 TTGTTTGTAA
*
105603830 TTGGGCTGAGGGTCTATTTTGGGTCTTGGGT
1 TTGGGCTGAGGGT-TATTTT-GGTCATGGGT
* * *
105603861 TTGGGCTGGTGGGTTGTTTTGGTGATGGGT
1 TTGGGCT-GAGGGTTATTTTGGTCATGGGT
105603891 TTGGGCTG
1 TTGGGCTG
105603899 GGTTAAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 1 0.03
30 15 0.45
31 12 0.36
32 5 0.15
ACGTcount: A:0.04, C:0.07, G:0.46, T:0.42
Consensus pattern (29 bp):
TTGGGCTGAGGGTTATTTTGGTCATGGGT
Found at i:105604545 original size:29 final size:30
Alignment explanation
Indices: 105604478--105604555 Score: 95
Period size: 29 Copynumber: 2.6 Consensus size: 30
105604468 AGTACAAGAA
*
105604478 TAGTCACTTAACTATTTAATTTGTTCTATTT
1 TAGTCACTCAACTATTT-ATTTGTTCTATTT
* * *
105604509 TAGGCACTCAACTATTTATTT-TTTTGTTT
1 TAGTCACTCAACTATTTATTTGTTCTATTT
*
105604538 TAGTCACTCAACTTTTTA
1 TAGTCACTCAACTATTTA
105604556 AAAATTAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 22 0.54
30 4 0.10
31 15 0.37
ACGTcount: A:0.24, C:0.15, G:0.08, T:0.53
Consensus pattern (30 bp):
TAGTCACTCAACTATTTATTTGTTCTATTT
Found at i:105609665 original size:14 final size:14
Alignment explanation
Indices: 105609643--105609681 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
105609633 ATCATTTTAC
* *
105609643 TATTATATTGTTAT
1 TATTTTATTATTAT
105609657 TATTTTATTATTAT
1 TATTTTATTATTAT
*
105609671 TATTTGATTAT
1 TATTTTATTAT
105609682 CGTATAACTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (14 bp):
TATTTTATTATTAT
Found at i:105617718 original size:7 final size:7
Alignment explanation
Indices: 105617706--105617730 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
105617696 AAAAGATTTT
105617706 AAAAATA
1 AAAAATA
105617713 AAAAATA
1 AAAAATA
105617720 AAAAATA
1 AAAAATA
105617727 AAAA
1 AAAA
105617731 CATAGTGGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:105620703 original size:156 final size:156
Alignment explanation
Indices: 105620487--105620810 Score: 450
Period size: 156 Copynumber: 2.1 Consensus size: 156
105620477 ACAAGTTCAA
* * *
105620487 AAGTTTCATTATAGTCAATTTCTTCCACCTAGTGATTACCAAAAACAACAACAAGAGTTTTAATT
1 AAGTGTCATTATAGTCAATTCCTTCCACCTAGTGATTACCAAAAACAACAACAAGAGTTTTAAGT
* * * *
105620552 CTCTCCATACTTCCATCAGAGTTATATTTAATCTTGTACACCTATTTACTACCCAGTGCTATCTT
66 CTCTCAATACTTCCATCAGAGTTATATTTAACCTTGTACACCCACTTACTACCCAGTGCTATCTT
*
105620617 TCCAGGAGGAAGTATTTCTATAGACC
131 TCCAGGAGGAAGTATTTCCATAGACC
* * ** * *
105620643 AAGTGTCATTATAGTCAGTTCCTTCTACCTAGTGATTATTAAAAACAACAAGATGAGTTTTAAGT
1 AAGTGTCATTATAGTCAATTCCTTCCACCTAGTGATTACCAAAAACAACAACAAGAGTTTTAAGT
* * * * *
105620708 CTCTTAATACTTCCATCGGAGTTATATTTAACCTTGTACACCCACTTACTACCTAGTGTTTTCTT
66 CTCTCAATACTTCCATCAGAGTTATATTTAACCTTGTACACCCACTTACTACCCAGTGCTATCTT
* * *
105620773 TCTATGAGGAAGTGTTTCCATAGACC
131 TCCAGGAGGAAGTATTTCCATAGACC
105620799 AAGTGTCATTAT
1 AAGTGTCATTAT
105620811 CCTCCAGAGC
Statistics
Matches: 146, Mismatches: 22, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
156 146 1.00
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (156 bp):
AAGTGTCATTATAGTCAATTCCTTCCACCTAGTGATTACCAAAAACAACAACAAGAGTTTTAAGT
CTCTCAATACTTCCATCAGAGTTATATTTAACCTTGTACACCCACTTACTACCCAGTGCTATCTT
TCCAGGAGGAAGTATTTCCATAGACC
Found at i:105622312 original size:43 final size:42
Alignment explanation
Indices: 105622251--105622353 Score: 152
Period size: 43 Copynumber: 2.4 Consensus size: 42
105622241 AATATCTCAT
* *
105622251 AATAATATTCTATAATATCTCATTAGGAATCAAACTGCTAAGA
1 AATAATATCCTATAATATCCCATTAGGAATCAAACTGCTAA-A
*
105622294 AATAATATCCTATAATATCCCATTAGGAATCAAATTGCTAAA
1 AATAATATCCTATAATATCCCATTAGGAATCAAACTGCTAAA
*
105622336 AGATAATATCCCATAATA
1 A-ATAATATCCTATAATA
105622354 ATATCCTAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
42 2 0.04
43 53 0.96
ACGTcount: A:0.46, C:0.16, G:0.08, T:0.31
Consensus pattern (42 bp):
AATAATATCCTATAATATCCCATTAGGAATCAAACTGCTAAA
Found at i:105624500 original size:255 final size:246
Alignment explanation
Indices: 105624033--105624530 Score: 565
Period size: 255 Copynumber: 2.0 Consensus size: 246
105624023 TATTAATACA
* * * *
105624033 TATATATAACTATTATTATACTATAGATTATAATAAAATATATAGTATAAATGATATTATAATGT
1 TATATATAACTATAATTATACTATAAATTAAAATAAAAAATATAGTATAAATGATATTATAATGT
* *
105624098 TTAATTATCAGTGCATATATATAAATTATTAATTTATTATATGATATGATATAACACTATATAAT
66 TTAATCATCAGTGCATATATATAAACTATTAATTTATTATATGATATGATATAACACTATATAAT
* ** * * * * **
105624163 ATATTAGGAGGGATAATTTTTAAATATACAAAAAGTATAGGGACTTATATCATATTTTGACCAAT
131 ATAGTAAAAGGGATAACTTTCAAATATACAAAAAGTATAGGGACTTAAAGCATATTTCAACCAAT
* *
105624228 ATAATAGTAAACAATAATGT-T-TAATAATTAATATATAATGTACTACTGT
196 ATAATAATAAACAATAATATATATAATAATTAATATATAATGTACTACTGT
* ***
105624277 TATATATAACTATAATTATATTATAAATTAAAATAAAAAATATAGTATTGCGTGATATTATAATG
1 TATATATAACTATAATTATACTATAAATTAAAATAAAAAATATAGTA-TAAATGATATTATAATG
*
105624342 TTTAATCATTTA-TGCATATATATAAACTATTAATATATATTATAT-ACTATACCGTATGATGTA
65 TTTAATCA-TCAGTGCATATATATAAACTATTAAT-T-TATTATATGA-TAT---G-AT-A--TA
* * * **
105624405 GA-AGTAATATAATATAGTAAAAGGGTTAACTTTCAAATGTATGAAAAGTATAGGGACTTAAAGC
119 -ACACT-ATATAATATAGTAAAAGGGATAACTTTCAAATATACAAAAAGTATAGGGACTTAAAGC
* *
105624469 ATATTTCAACCAATATAATAATAAGCAATAATATATGATAATAATTAATATATTATGTACTA
182 ATATTTCAACCAATATAATAATAAACAATAATATAT-ATAATAATTAATATATAATGTACTA
105624531 TTTTTATAAT
Statistics
Matches: 208, Mismatches: 29, Indels: 20
0.81 0.11 0.08
Matches are distributed among these distances:
244 42 0.20
245 42 0.20
246 4 0.02
247 11 0.05
250 1 0.00
251 2 0.01
252 1 0.00
254 4 0.02
255 77 0.37
256 1 0.00
258 23 0.11
ACGTcount: A:0.45, C:0.06, G:0.09, T:0.39
Consensus pattern (246 bp):
TATATATAACTATAATTATACTATAAATTAAAATAAAAAATATAGTATAAATGATATTATAATGT
TTAATCATCAGTGCATATATATAAACTATTAATTTATTATATGATATGATATAACACTATATAAT
ATAGTAAAAGGGATAACTTTCAAATATACAAAAAGTATAGGGACTTAAAGCATATTTCAACCAAT
ATAATAATAAACAATAATATATATAATAATTAATATATAATGTACTACTGT
Found at i:105624550 original size:15 final size:15
Alignment explanation
Indices: 105624530--105624560 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
105624520 ATTATGTACT
105624530 ATTTTTATAATTAAA
1 ATTTTTATAATTAAA
*
105624545 ATTTTTATTATTAAA
1 ATTTTTATAATTAAA
105624560 A
1 A
105624561 AGCAAATTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTTTTATAATTAAA
Found at i:105626958 original size:17 final size:17
Alignment explanation
Indices: 105626936--105626969 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
105626926 ATGGGGTCCT
105626936 GTCCAAAGACATAATTC
1 GTCCAAAGACATAATTC
105626953 GTCCAAAGACATAATTC
1 GTCCAAAGACATAATTC
105626970 ATTATCTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.24, G:0.12, T:0.24
Consensus pattern (17 bp):
GTCCAAAGACATAATTC
Found at i:105629325 original size:15 final size:15
Alignment explanation
Indices: 105629305--105629358 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
105629295 ATACTACAAA
105629305 ATATTTATTATTAAT
1 ATATTTATTATTAAT
*
105629320 ATATTTATAATTGTAAT
1 ATATTTATTA-T-TAAT
*
105629337 AAATATTTATTATTAAA
1 --ATATTTATTATTAAT
105629354 ATATT
1 ATATT
105629359 AATATTGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 14 0.44
16 1 0.03
17 7 0.22
18 1 0.03
19 9 0.28
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:105630426 original size:33 final size:33
Alignment explanation
Indices: 105630388--105630456 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 33
105630378 AACCCTTATC
*
105630388 AAATTAACTATTAA-TTTT-TAAATTTAATGTTAA
1 AAATTAA--ATTAATTTTTGTAAATTTAATATTAA
*
105630421 AAATTAAATTAATTTTTGTAATTTTAATATTAA
1 AAATTAAATTAATTTTTGTAAATTTAATATTAA
105630454 AAA
1 AAA
105630457 CTATTTTTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 5 0.16
32 4 0.12
33 23 0.72
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (33 bp):
AAATTAAATTAATTTTTGTAAATTTAATATTAA
Found at i:105654770 original size:11 final size:9
Alignment explanation
Indices: 105654743--105654798 Score: 51
Period size: 10 Copynumber: 5.8 Consensus size: 9
105654733 TACTTCATGC
105654743 TAATTTTTA
1 TAATTTTTA
105654752 TAAATTTTTA
1 T-AATTTTTA
105654762 TGAACTTTTTA
1 T-AA-TTTTTA
105654773 TAATTTTT-
1 TAATTTTTA
*
105654781 TGAATTTTAAA
1 T-AATTTT-TA
105654792 TAATTTT
1 TAATTTT
105654799 ATTTTTATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
8 1 0.03
9 12 0.30
10 19 0.47
11 8 0.20
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.61
Consensus pattern (9 bp):
TAATTTTTA
Found at i:105654784 original size:19 final size:19
Alignment explanation
Indices: 105654744--105654798 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
105654734 ACTTCATGCT
105654744 AATTTTTATAAATTTTTATG
1 AATTTTTAT-AATTTTTATG
105654764 AACTTTTTATAATTTTT-TG
1 AA-TTTTTATAATTTTTATG
*
105654783 AATTTTAAATAATTTT
1 AATTTT-TATAATTTT
105654799 ATTTTTATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
18 4 0.12
19 12 0.38
20 9 0.28
21 7 0.22
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.60
Consensus pattern (19 bp):
AATTTTTATAATTTTTATG
Found at i:105654786 original size:9 final size:10
Alignment explanation
Indices: 105654744--105654788 Score: 58
Period size: 10 Copynumber: 4.6 Consensus size: 10
105654734 ACTTCATGCT
*
105654744 AATTTTTATA
1 AATTTTTATG
105654754 AATTTTTATG
1 AATTTTTATG
105654764 AACTTTTTAT-
1 AA-TTTTTATG
105654774 AATTTTT-TG
1 AATTTTTATG
105654783 AATTTT
1 AATTTT
105654789 AAATAATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
8 1 0.03
9 11 0.34
10 13 0.41
11 7 0.22
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.62
Consensus pattern (10 bp):
AATTTTTATG
Found at i:105656311 original size:20 final size:19
Alignment explanation
Indices: 105656266--105656311 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 19
105656256 TTTTGGTTGG
105656266 TTAATTATTGAATTAATTA
1 TTAATTATTGAATTAATTA
*
105656285 TTCAATTATTGAGTTAATTA
1 TT-AATTATTGAATTAATTA
105656305 CTTAATT
1 -TTAATT
105656312 TAGTGCTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 2 0.08
20 20 0.83
21 2 0.08
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.52
Consensus pattern (19 bp):
TTAATTATTGAATTAATTA
Found at i:105656847 original size:22 final size:22
Alignment explanation
Indices: 105656822--105656865 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
105656812 AAGCATCAAC
*
105656822 TGTTAAATGCATTAAAGCCCAA
1 TGTTAAATGCATTAAAACCCAA
105656844 TGTTAAATGCATTAAAACCCAA
1 TGTTAAATGCATTAAAACCCAA
105656866 CTTCAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.18, G:0.11, T:0.27
Consensus pattern (22 bp):
TGTTAAATGCATTAAAACCCAA
Found at i:105659656 original size:18 final size:18
Alignment explanation
Indices: 105659635--105659669 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
105659625 AATCAGTAAT
* *
105659635 CAGTAACGGTAGCAGTAG
1 CAGTAACAGTAACAGTAG
105659653 CAGTAACAGTAACAGTA
1 CAGTAACAGTAACAGTA
105659670 TTCAACACAC
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:0.40, C:0.17, G:0.26, T:0.17
Consensus pattern (18 bp):
CAGTAACAGTAACAGTAG
Found at i:105659711 original size:45 final size:45
Alignment explanation
Indices: 105659656--105659755 Score: 146
Period size: 45 Copynumber: 2.2 Consensus size: 45
105659646 GCAGTAGCAG
* *
105659656 TAACAGTAACAGTATTCAACACACAAAGTGCTGAATCTGTAACAA
1 TAACGGTAACAGTATTCAACACACAAAGTGCTGAATCGGTAACAA
* * * *
105659701 TAGCGGTAACAGTATTCGACACACAAAGTGTTGAATCGGTAACAG
1 TAACGGTAACAGTATTCAACACACAAAGTGCTGAATCGGTAACAA
105659746 TAACGGTAAC
1 TAACGGTAAC
105659756 GGTAACAGTA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (45 bp):
TAACGGTAACAGTATTCAACACACAAAGTGCTGAATCGGTAACAA
Found at i:105659714 original size:51 final size:49
Alignment explanation
Indices: 105659641--105659765 Score: 123
Period size: 45 Copynumber: 2.6 Consensus size: 49
105659631 TAATCAGTAA
* *
105659641 CGGTAGCAGTAGCAGTAACAGTAACAGTATTCAACACACAAAGTGCTGAAT
1 CGGTAACAATAGC-GTAAC-GTAACAGTATTCAACACACAAAGTGCTGAAT
* * *
105659692 CTGTAACAATAGCG----GTAACAGTATTCGACACACAAAGTGTTGAAT
1 CGGTAACAATAGCGTAACGTAACAGTATTCAACACACAAAGTGCTGAAT
* *
105659737 CGGTAACAGTAACGGTAACGGTAACAGTA
1 CGGTAACAATAGC-GTAAC-GTAACAGTA
105659766 GTCGGCACAT
Statistics
Matches: 60, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
45 39 0.65
46 1 0.02
50 1 0.02
51 19 0.32
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.21
Consensus pattern (49 bp):
CGGTAACAATAGCGTAACGTAACAGTATTCAACACACAAAGTGCTGAAT
Found at i:105660153 original size:21 final size:22
Alignment explanation
Indices: 105660126--105660182 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
105660116 ATATATTAAA
105660126 TTATTATTATTATTTATTATAG
1 TTATTATTATTATTTATTATAG
* *
105660148 TT-TTA-TATTTAATTATTATTG
1 TTATTATTA-TTATTTATTATAG
*
105660169 TTATTGTTATTATT
1 TTATTATTATTATT
105660183 ATTTAAATTG
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
20 2 0.07
21 16 0.57
22 8 0.29
23 2 0.07
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (22 bp):
TTATTATTATTATTTATTATAG
Found at i:105660820 original size:23 final size:21
Alignment explanation
Indices: 105660773--105660813 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
105660763 TTTGGTTAAA
105660773 AATTGAATAGAAATGAAGTATG
1 AATTGAATAGAAA-GAAGTATG
105660795 AATTGAGATAGAAA-AAGTA
1 AATTGA-ATAGAAAGAAGTA
105660814 AGTGAATCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.28
22 6 0.33
23 7 0.39
ACGTcount: A:0.54, C:0.00, G:0.22, T:0.24
Consensus pattern (21 bp):
AATTGAATAGAAAGAAGTATG
Found at i:105661181 original size:15 final size:15
Alignment explanation
Indices: 105661139--105661189 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
105661129 TGAATTTATC
105661139 AAATTTATATTGATT
1 AAATTTATATTGATT
* * *
105661154 AAAATCATTTTGATT
1 AAATTTATATTGATT
105661169 AAATTTATATTGATT
1 AAATTTATATTGATT
105661184 GAAATT
1 -AAATT
105661190 ATAATATATA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
15 24 0.83
16 5 0.17
ACGTcount: A:0.41, C:0.02, G:0.08, T:0.49
Consensus pattern (15 bp):
AAATTTATATTGATT
Found at i:105664034 original size:5 final size:5
Alignment explanation
Indices: 105663998--105664052 Score: 51
Period size: 5 Copynumber: 10.6 Consensus size: 5
105663988 TATTTGTTTG
105663998 TTTTA -TTTA TTTTA TGCTTTA TTTCT- TTTTA TTTTA TTTTA TTTATA
1 TTTTA TTTTA TTTTA T--TTTA TTT-TA TTTTA TTTTA TTTTA TTT-TA
*
105664045 TTATA TTT
1 TTTTA TTT
105664053 AATTAATAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
4 5 0.12
5 27 0.64
6 5 0.12
7 5 0.12
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:105664561 original size:20 final size:19
Alignment explanation
Indices: 105664534--105664575 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
105664524 ATATAAAACC
105664534 ATAACAATTA-ATAATTATA
1 ATAACAATTATATAA-TATA
105664553 ATAATCAATTATATAATATA
1 ATAA-CAATTATATAATATA
105664573 ATA
1 ATA
105664576 TAATATAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
20 13 0.62
21 4 0.19
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
ATAACAATTATATAATATA
Found at i:105664568 original size:12 final size:12
Alignment explanation
Indices: 105664542--105664590 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
105664532 CCATAACAAT
105664542 TAATAATTATAA
1 TAATAATTATAA
105664554 TAATCAATTAT-A
1 TAAT-AATTATAA
*
105664566 TAATATAATATAA
1 TAATA-ATTATAA
105664579 T-ATAA-TATAA
1 TAATAATTATAA
105664589 TA
1 TA
105664591 TATATATAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
10 6 0.19
11 2 0.06
12 16 0.50
13 8 0.25
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (12 bp):
TAATAATTATAA
Found at i:105664573 original size:5 final size:5
Alignment explanation
Indices: 105664563--105664600 Score: 67
Period size: 5 Copynumber: 7.4 Consensus size: 5
105664553 ATAATCAATT
105664563 ATATA ATATA ATATA ATATA ATATA ATATA TATATA AT
1 ATATA ATATA ATATA ATATA ATATA ATATA -ATATA AT
105664601 TTAAATAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 27 0.84
6 5 0.16
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:105668226 original size:54 final size:53
Alignment explanation
Indices: 105668139--105668315 Score: 185
Period size: 54 Copynumber: 3.3 Consensus size: 53
105668129 GATGAGGTTT
* * *
105668139 GGGGGAAAGCAAAAGGAAAAAAGTTTTGGGGGGTTTGGGGGAAGTAAAAGTTTT-
1 GGGGGAAAGTAAAAGGAAAAAA-ATTT-AGGGGTTTGGGGGAAGTAAAAGTTTTA
* * * * *
105668193 GGGAGAAAAGTAAAAGGAAAAAAATTTAAGGGGTTTTGAGAAAGTAAATGTTTTA
1 GGG-GGAAAGTAAAAGGAAAAAAATTT-AGGGGTTTGGGGGAAGTAAAAGTTTTA
* * * * *
105668248 AGGGGAAAGTAAAAGGAAAAAAGTTTTGGAGGTTTGGGGGAAGTACAATTTTTA
1 GGGGGAAAGTAAAAGGAAAAAAATTTAGG-GGTTTGGGGGAAGTAAAAGTTTTA
105668302 GGGGGAAAGTAAAA
1 GGGGGAAAGTAAAA
105668316 AGGTTTGAAA
Statistics
Matches: 100, Mismatches: 20, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
53 2 0.02
54 79 0.79
55 19 0.19
ACGTcount: A:0.41, C:0.01, G:0.34, T:0.23
Consensus pattern (53 bp):
GGGGGAAAGTAAAAGGAAAAAAATTTAGGGGTTTGGGGGAAGTAAAAGTTTTA
Found at i:105669838 original size:23 final size:24
Alignment explanation
Indices: 105669801--105669891 Score: 68
Period size: 23 Copynumber: 4.0 Consensus size: 24
105669791 AATATATACG
*
105669801 CATACATATTAAAAATATATACATA
1 CATA-ATATTAAAAAAATATACATA
* * *
105669826 TATAATATT-AAAAAATGTATATA
1 CATAATATTAAAAAAATATACATA
* *
105669849 CATAATA-TATATAAA-A-ACATA
1 CATAATATTAAAAAAATATACATA
*
105669870 -AT-ATAGTAAAAAAATATACATA
1 CATAATATTAAAAAAATATACATA
105669892 ATATAAGAAT
Statistics
Matches: 51, Mismatches: 11, Indels: 11
0.70 0.15 0.15
Matches are distributed among these distances:
19 3 0.06
20 8 0.16
21 5 0.10
22 6 0.12
23 21 0.41
24 5 0.10
25 3 0.06
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.32
Consensus pattern (24 bp):
CATAATATTAAAAAAATATACATA
Found at i:105669870 original size:17 final size:17
Alignment explanation
Indices: 105669848--105669897 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
105669838 AAATGTATAT
105669848 ACATAATATATATAAAA
1 ACATAATATATATAAAA
*
105669865 ACATAATATAGTAAAAAA
1 ACATAATATA-TATAAAA
*
105669883 ATATACATA-ATATAA
1 ACATA-ATATATATAA
105669898 GAATGTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
17 14 0.50
18 11 0.39
19 3 0.11
ACGTcount: A:0.64, C:0.06, G:0.02, T:0.28
Consensus pattern (17 bp):
ACATAATATATATAAAA
Found at i:105671592 original size:56 final size:57
Alignment explanation
Indices: 105671468--105671604 Score: 137
Period size: 56 Copynumber: 2.5 Consensus size: 57
105671458 TATAACGTAG
* *
105671468 AAAATA-ATG-ATAATAATA-TA-TGAATTTAAAATATATATATACATACATATACCA
1 AAAATATATGCATAATAATAGTATTGAATTTAAAATATATATATACATA-AGAGACCA
* * *
105671522 AAGACATATTCATAATAATAGTATTGAATATTAAAAGTATATATATA-AT-AGAGA-CA
1 AAAATATATGCATAATAATAGTATTGAAT-TTAAAA-TATATATATACATAAGAGACCA
*
105671578 AAAATATATGCATAAT-GTAGTATTGAA
1 AAAATATATGCATAATAATAGTATTGAA
105671605 AGTATTTACA
Statistics
Matches: 68, Mismatches: 9, Indels: 11
0.77 0.10 0.12
Matches are distributed among these distances:
54 4 0.06
55 12 0.18
56 24 0.35
57 5 0.07
58 5 0.07
59 8 0.12
60 10 0.15
ACGTcount: A:0.53, C:0.06, G:0.09, T:0.33
Consensus pattern (57 bp):
AAAATATATGCATAATAATAGTATTGAATTTAAAATATATATATACATAAGAGACCA
Found at i:105671724 original size:36 final size:36
Alignment explanation
Indices: 105671658--105671727 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
105671648 TGATATTAAA
* *
105671658 AATATATACATAAAAATATAATAGATATATATATCT
1 AATATATACATAAAAATATAATAAAAATATATATCT
* *
105671694 AATATATACAT-AATATAGTATTAAAAATATATAT
1 AATATATACATAAAAATA-TAATAAAAATATATAT
105671728 AATACATACA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 5 0.17
36 24 0.83
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (36 bp):
AATATATACATAAAAATATAATAAAAATATATATCT
Found at i:105673613 original size:3 final size:3
Alignment explanation
Indices: 105673605--105673637 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
105673595 AGTTAAGAAA
105673605 AAT AAT AAT AAT AAT AAT AAT AAT AAT AGAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AA
105673638 AAAGAAAACT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:105673749 original size:22 final size:22
Alignment explanation
Indices: 105673716--105673768 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
105673706 TGCTAATAAA
*
105673716 TAAT-AAACATAATA-ATGATAG
1 TAATAAAATATAATACAT-ATAG
105673737 TAATAAAATATAATAGCATATAG
1 TAATAAAATATAATA-CATATAG
*
105673760 TATTAAAAT
1 TAATAAAAT
105673769 TAAAATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 4 0.15
22 9 0.33
23 12 0.44
24 2 0.07
ACGTcount: A:0.57, C:0.04, G:0.08, T:0.32
Consensus pattern (22 bp):
TAATAAAATATAATACATATAG
Done.