Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004188.1 Hibiscus syriacus cultivar Beakdansim tig00009160_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: 84254
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:6842 original size:20 final size:20
Alignment explanation
Indices: 6804--6843 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
6794 TAAAGTTAGT
*
6804 GCAAAGATTTCCTTGTGATA
1 GCAAAGATTTCCTTATGATA
*
6824 GCAAAGATTTCTTTATGATA
1 GCAAAGATTTCCTTATGATA
6844 TAGGTGGCAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (20 bp):
GCAAAGATTTCCTTATGATA
Found at i:10398 original size:36 final size:36
Alignment explanation
Indices: 10332--10400 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 36
10322 GATATGCTTT
* * *
10332 GTTTCTATTTTGGGCTTTCGTACGAAGGGTATCTTA
1 GTTTCTATGTTGGGCTGTCCTACGAAGGGTATCTTA
* *
10368 GTTTCTATGTTGGGCTGTCCTATGATGGGTATC
1 GTTTCTATGTTGGGCTGTCCTACGAAGGGTATC
10401 CTAGGAAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 28 1.00
ACGTcount: A:0.14, C:0.14, G:0.28, T:0.43
Consensus pattern (36 bp):
GTTTCTATGTTGGGCTGTCCTACGAAGGGTATCTTA
Found at i:11883 original size:30 final size:30
Alignment explanation
Indices: 11824--11883 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
11814 GAAGGGATTT
*
11824 AATAATTTTTTAGTTATATTTTATGTTTTA
1 AATAATTTTTTAGTTATATTTTATCTTTTA
*
11854 AATAATTATTTT-TTTA-ATTTTAATCTTTTA
1 AATAATT-TTTTAGTTATATTTT-ATCTTTTA
11884 GGTTTGATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
29 5 0.19
30 17 0.65
31 4 0.15
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (30 bp):
AATAATTTTTTAGTTATATTTTATCTTTTA
Found at i:11981 original size:56 final size:57
Alignment explanation
Indices: 11856--11981 Score: 157
Period size: 58 Copynumber: 2.2 Consensus size: 57
11846 ATGTTTTAAA
* *
11856 TAATTATTTTTTTAATTTTAATCTTTTAGGTTTGATCAAAACAGACCAAATAATAAGT
1 TAATTATTTTTGTAATTTTAATCTTTTAGGTTTGACCAAAACAGA-CAAATAATAAGT
* * * * *
11914 TAATTAATTTTGTACTTTTAATGTTTTGGGTTTGGACCAAAACA-A-ACATAATAAGT
1 TAATTATTTTTGTAATTTTAATCTTTTAGGTTT-GACCAAAACAGACAAATAATAAGT
11970 TAATTATTTTTG
1 TAATTATTTTTG
11982 GGATTTGATA
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
56 21 0.36
58 29 0.49
59 9 0.15
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.45
Consensus pattern (57 bp):
TAATTATTTTTGTAATTTTAATCTTTTAGGTTTGACCAAAACAGACAAATAATAAGT
Found at i:20345 original size:22 final size:22
Alignment explanation
Indices: 20317--20364 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
20307 ATAACTCAAC
20317 TATTCATATGTTTCAAATTCAT
1 TATTCATATGTTTCAAATTCAT
20339 TATTCATATGTTTCAAATTCAT
1 TATTCATATGTTTCAAATTCAT
20361 TATT
1 TATT
20365 TTTTATTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.31, C:0.12, G:0.04, T:0.52
Consensus pattern (22 bp):
TATTCATATGTTTCAAATTCAT
Found at i:22127 original size:60 final size:58
Alignment explanation
Indices: 22026--22192 Score: 185
Period size: 60 Copynumber: 2.9 Consensus size: 58
22016 ACATATCAAC
* *** * *
22026 TTAGGGATGAAATTTGAATATTTAAAAGTTTGGGGATTAATTTAGAAA-GAGGGTCATAGT
1 TTAGGGATGAAATTAGAATATTTAAAAGTTTAAAGACTAATTTA-AAATGA--GTCATAAT
*
22086 TTAGGGATGAAGTTAGAATATTTAAAAGTTTAAAGACTAATTTAAAATGAGTCATAAT
1 TTAGGGATGAAATTAGAATATTTAAAAGTTTAAAGACTAATTTAAAATGAGTCATAAT
* * ** *
22144 TTAGAGA-AAAATTAGAATATCCAAAAATTTAAAGACTAATTTAAAATGA
1 TTAGGGATGAAATTAGAATATTTAAAAGTTTAAAGACTAATTTAAAATGA
22193 AGGTTATAAC
Statistics
Matches: 93, Mismatches: 13, Indels: 5
0.84 0.12 0.05
Matches are distributed among these distances:
57 37 0.40
58 13 0.14
59 3 0.03
60 40 0.43
ACGTcount: A:0.45, C:0.04, G:0.19, T:0.33
Consensus pattern (58 bp):
TTAGGGATGAAATTAGAATATTTAAAAGTTTAAAGACTAATTTAAAATGAGTCATAAT
Found at i:23076 original size:28 final size:28
Alignment explanation
Indices: 23044--23098 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
23034 CTGTTCGCTT
* *
23044 ATATTATGTCGTCGAGCCAGTGTTTGAA
1 ATATTATGTCATAGAGCCAGTGTTTGAA
*
23072 ATATTATGTCATAGAGCTAGTGTTTGA
1 ATATTATGTCATAGAGCCAGTGTTTGA
23099 TGCAATAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.27, C:0.11, G:0.24, T:0.38
Consensus pattern (28 bp):
ATATTATGTCATAGAGCCAGTGTTTGAA
Found at i:30168 original size:18 final size:18
Alignment explanation
Indices: 30139--30182 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
30129 GTTTCTAACT
*
30139 TCCTTCAGCCCAGATGTCC
1 TCCTT-AGCCCAGATATCC
*
30158 TCCTTAGCCCAGTTATCC
1 TCCTTAGCCCAGATATCC
30176 TCCTTAG
1 TCCTTAG
30183 TCCAATTGCC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 18 0.78
19 5 0.22
ACGTcount: A:0.16, C:0.39, G:0.14, T:0.32
Consensus pattern (18 bp):
TCCTTAGCCCAGATATCC
Found at i:30730 original size:3 final size:3
Alignment explanation
Indices: 30722--30773 Score: 79
Period size: 3 Copynumber: 17.3 Consensus size: 3
30712 TTAATTTTAA
*
30722 TAT TAT TAT TAT TAT TAT TAT TAAC TA- TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT
30767 TAT TAT T
1 TAT TAT T
30774 TAATATATGT
Statistics
Matches: 46, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
2 2 0.04
3 42 0.91
4 2 0.04
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:34604 original size:31 final size:32
Alignment explanation
Indices: 34569--34630 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
34559 TATTTACATG
34569 TACTAACTTATTT-TTCTCTTTTGTTTGTGTA
1 TACTAACTTATTTCTTCTCTTTTGTTTGTGTA
34600 TACTAACTTATTTCTTCTCTTTTGTTTGTGT
1 TACTAACTTATTTCTTCTCTTTTGTTTGTGT
34631 CAGTTTGTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.15, C:0.15, G:0.10, T:0.61
Consensus pattern (32 bp):
TACTAACTTATTTCTTCTCTTTTGTTTGTGTA
Found at i:36077 original size:26 final size:25
Alignment explanation
Indices: 36048--36125 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 25
36038 AATTTTTGAC
36048 ATTCTATCTCTTTGAGACCTTGAAAT
1 ATTCT-TCTCTTTGAGACCTTGAAAT
* *
36074 A---TTCT-TTT-CGACCTTGAAAC
1 ATTCTTCTCTTTGAGACCTTGAAAT
*
36094 ATTCCCTCTCTTTGAGACCTTGAAAT
1 ATT-CTTCTCTTTGAGACCTTGAAAT
36120 ATTCTT
1 ATTCTT
36126 TCCACCTTGA
Statistics
Matches: 40, Mismatches: 6, Indels: 13
0.68 0.10 0.22
Matches are distributed among these distances:
20 11 0.28
21 3 0.08
22 3 0.08
23 1 0.03
24 3 0.08
25 5 0.12
26 14 0.35
ACGTcount: A:0.24, C:0.23, G:0.10, T:0.42
Consensus pattern (25 bp):
ATTCTTCTCTTTGAGACCTTGAAAT
Found at i:36086 original size:20 final size:20
Alignment explanation
Indices: 36063--36137 Score: 62
Period size: 20 Copynumber: 3.5 Consensus size: 20
36053 ATCTCTTTGA
36063 GACCTTGAAATATTCTTTTC
1 GACCTTGAAATATTCTTTTC
* *
36083 GACCTTGAAACATTCCCTCTCTTTGA
1 GACCTTGAAATA-T---TCT-TTT-C
36109 GACCTTGAAATATTC-TTTC
1 GACCTTGAAATATTCTTTTC
*
36128 CACCTTGAAA
1 GACCTTGAAA
36138 CACTGTATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
19 9 0.20
20 14 0.32
21 1 0.02
22 2 0.05
24 3 0.07
25 4 0.09
26 11 0.25
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.37
Consensus pattern (20 bp):
GACCTTGAAATATTCTTTTC
Found at i:36773 original size:11 final size:11
Alignment explanation
Indices: 36745--36782 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
36735 AAGAGCAAAG
36745 AGAAAAATCAA
1 AGAAAAATCAA
36756 AGCAAAAATCAA
1 AG-AAAAATCAA
*
36768 AGAAAAAGCAA
1 AGAAAAATCAA
36779 AGAA
1 AGAA
36783 TAAAAGAGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.71, C:0.11, G:0.13, T:0.05
Consensus pattern (11 bp):
AGAAAAATCAA
Found at i:36775 original size:18 final size:19
Alignment explanation
Indices: 36754--36789 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
36744 GAGAAAAATC
*
36754 AAAGCAAA-AATCAAAGAA
1 AAAGCAAAGAATAAAAGAA
36772 AAAGCAAAGAATAAAAGA
1 AAAGCAAAGAATAAAAGA
36790 GGACAAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.72, C:0.08, G:0.14, T:0.06
Consensus pattern (19 bp):
AAAGCAAAGAATAAAAGAA
Found at i:37966 original size:4 final size:4
Alignment explanation
Indices: 37957--37998 Score: 70
Period size: 4 Copynumber: 11.0 Consensus size: 4
37947 AAAAGTATAC
37957 ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC-- ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
37999 GATACATAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.06
4 34 0.94
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:38677 original size:101 final size:101
Alignment explanation
Indices: 38473--38702 Score: 267
Period size: 101 Copynumber: 2.3 Consensus size: 101
38463 TGAGAATTTT
* * *
38473 AAAACAAATTGCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGATTCACT
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACT
*
38538 AAAAACAAAATCTCACCTTAGATTGTTGTTTCTTTC-
66 AAAAACAAAATCTCACCTTAGATCGTTGTTTC-TTCA
* * *
38574 AAAACAAATTTCGTCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATTTCGAATTTGTTTCAC-
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACT
*
38638 ATTAAACAAAGTTGATCTCA-CTTGAGATCG-T-TTTC-TCA
66 A-AAAACAAA----ATCTCACCTT-AGATCGTTGTTTCTTCA
38676 AAAACAAACTTT-GTCTCGCTTGAGACA
1 AAAACAAA-TTTCGTCTCGCTTGAGACA
38703 ATTGCTCTAA
Statistics
Matches: 112, Mismatches: 9, Indels: 15
0.82 0.07 0.11
Matches are distributed among these distances:
100 1 0.01
101 67 0.60
102 22 0.20
103 7 0.06
104 4 0.04
105 11 0.10
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.37
Consensus pattern (101 bp):
AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACT
AAAAACAAAATCTCACCTTAGATCGTTGTTTCTTCA
Found at i:38698 original size:36 final size:36
Alignment explanation
Indices: 38653--38729 Score: 93
Period size: 36 Copynumber: 2.1 Consensus size: 36
38643 ACAAAGTTGA
** *
38653 TCTCACTTGAGATCGTTTTCTC-AAAAACAAACTTTG
1 TCTCACTTGAGA-CAATTGCTCTAAAAACAAACTTTG
* *
38689 TCTCGCTTGAGACAATTGCTCTAAAAACAAATTTTG
1 TCTCACTTGAGACAATTGCTCTAAAAACAAACTTTG
38725 TCTCA
1 TCTCA
38730 TTTTAAACTA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
35 6 0.18
36 28 0.82
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.35
Consensus pattern (36 bp):
TCTCACTTGAGACAATTGCTCTAAAAACAAACTTTG
Found at i:39121 original size:29 final size:28
Alignment explanation
Indices: 39015--39179 Score: 210
Period size: 27 Copynumber: 5.8 Consensus size: 28
39005 AAGACAATTT
39015 CTTTTGAGGAAAAAATCTTTGAGTTTGTTC
1 CTTTTGA--AAAAAATCTTTGAGTTTGTTC
*
39045 CTCTTG-AAAAAATCTTTGAGTTTGTTC
1 CTTTTGAAAAAAATCTTTGAGTTTGTTC
*
39072 CTCTTG-AAAAAATCTTTGAGTTTGTTC
1 CTTTTGAAAAAAATCTTTGAGTTTGTTC
*
39099 CTTTTGAATAAAAATCTTGGAGTTTGTTC
1 CTTTTGAA-AAAAATCTTTGAGTTTGTTC
*
39128 CTTTTGAATAAAAATCTTTGAG-TTGTTT
1 CTTTTGAA-AAAAATCTTTGAGTTTGTTC
*
39156 CGTTTGAAAAAAAAATCTTTGAGT
1 CTTTTG--AAAAAAATCTTTGAGT
39180 CTATTTATTT
Statistics
Matches: 124, Mismatches: 6, Indels: 10
0.89 0.04 0.07
Matches are distributed among these distances:
27 53 0.43
28 11 0.09
29 53 0.43
30 7 0.06
ACGTcount: A:0.29, C:0.11, G:0.16, T:0.44
Consensus pattern (28 bp):
CTTTTGAAAAAAATCTTTGAGTTTGTTC
Found at i:39170 original size:58 final size:56
Alignment explanation
Indices: 39023--39179 Score: 205
Period size: 58 Copynumber: 2.8 Consensus size: 56
39013 TTCTTTTGAG
39023 GAAAAAATCTTTGAGTTTGTTCC-TCTTG--AAAAAATCTTTGAGTTTGTTCCTCTT
1 GAAAAAATCTTTGAGTTTGTTCCGT-TTGAAAAAAAATCTTTGAGTTTGTTCCTCTT
* * * *
39077 GAAAAAATCTTTGAGTTTGTTCCTTTTGAATAAAAATCTTGGAGTTTGTTCCTTTT
1 GAAAAAATCTTTGAGTTTGTTCCGTTTGAAAAAAAATCTTTGAGTTTGTTCCTCTT
*
39133 GAATAAAAATCTTTGAG-TTGTTTCGTTTGAAAAAAAAATCTTTGAGT
1 G-A-AAAAATCTTTGAGTTTGTTCCGTTTG-AAAAAAAATCTTTGAGT
39180 CTATTTATTT
Statistics
Matches: 90, Mismatches: 7, Indels: 8
0.86 0.07 0.08
Matches are distributed among these distances:
54 26 0.29
55 1 0.01
56 24 0.27
57 11 0.12
58 28 0.31
ACGTcount: A:0.30, C:0.11, G:0.16, T:0.43
Consensus pattern (56 bp):
GAAAAAATCTTTGAGTTTGTTCCGTTTGAAAAAAAATCTTTGAGTTTGTTCCTCTT
Found at i:39261 original size:29 final size:30
Alignment explanation
Indices: 39228--39491 Score: 123
Period size: 30 Copynumber: 8.1 Consensus size: 30
39218 AATTTTGTGA
*
39228 AAAAATCTTTGAGATTGTTTATTTTGAAAC
1 AAAAATCTTTGAGATTGTTTATTTGGAAAC
* *
39258 AAAAATCTTTGAGTTTGTTTCTTTGGAAAC
1 AAAAATCTTTGAGATTGTTTATTTGGAAAC
* * * * *
39288 AAAATTTTGTCTCTCTTAAGATAGTTTCTTTTGAAAC
1 AAAA------ATCT-TTGAGATTGTTTATTTGGAAAC
* *
39325 AAAAATCTTTGAGTTTGTTTCTTTGGAAAC
1 AAAAATCTTTGAGATTGTTTATTTGGAAAC
* * ** * *
39355 AAAATTTGTCTCTCTTAAGATAATTTCTTTTGAAAC
1 AAAA-----ATCT-TTGAGATTGTTTATTTGGAAAC
* *
39391 AAAAATCTTTGAGTTTGTTTCTTTGGAAAC
1 AAAAATCTTTGAGATTGTTTATTTGGAAAC
* * * * *
39421 AAAATTTTGTCTCTCTTAAGATAGTTTCTTTTGAAAC
1 AAAA------ATCT-TTGAGATTGTTTATTTGGAAAC
* *
39458 AAAAATCTTTGAGTTTGTTTCTTTGGAAAC
1 AAAAATCTTTGAGATTGTTTATTTGGAAAC
39488 AAAA
1 AAAA
39492 TTTTGTCTCT
Statistics
Matches: 179, Mismatches: 35, Indels: 40
0.70 0.14 0.16
Matches are distributed among these distances:
30 96 0.54
31 9 0.05
35 3 0.02
36 27 0.15
37 44 0.25
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.44
Consensus pattern (30 bp):
AAAAATCTTTGAGATTGTTTATTTGGAAAC
Found at i:39266 original size:92 final size:95
Alignment explanation
Indices: 39132--39358 Score: 273
Period size: 92 Copynumber: 2.4 Consensus size: 95
39122 TTGTTCCTTT
* * * *
39132 TGAATAAAAATCTTTGAGTTGTTTCGTTTGAAAAAAAAATCTTTGAGTCTATTTATTTTGAAACA
1 TGAACAAAAATCTTTGAGTTGTTTCTTTTGAAACAAAAATCTTTGAGTCTATTTATTTGGAAACA
* *
39197 AAGTTTTGTCTCTCTTGAGACA-ATT-TTG
66 AAATTTTGTCTCTCTTAAGACAGATTCTTG
* * * *
39225 TG-A-AAAAATCTTTGAGATTGTTTATTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAAC
1 TGAACAAAAATCTTTGAG-TTGTTTCTTTTGAAACAAAAATCTTTGAGTCTATTTATTTGGAAAC
* * *
39288 AAAATTTTGTCTCTCTTAAGATAGTTTCTTT
65 AAAATTTTGTCTCTCTTAAGACAGATTCTTG
*
39319 TGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAA
1 TG-AACAAAAATCTTTGAG-TTGTTTCTTTTGAAACAAAA
39359 TTTGTCTCTC
Statistics
Matches: 113, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
91 13 0.12
92 60 0.53
93 4 0.04
94 4 0.04
96 1 0.01
97 31 0.27
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.43
Consensus pattern (95 bp):
TGAACAAAAATCTTTGAGTTGTTTCTTTTGAAACAAAAATCTTTGAGTCTATTTATTTGGAAACA
AAATTTTGTCTCTCTTAAGACAGATTCTTG
Found at i:39323 original size:67 final size:67
Alignment explanation
Indices: 39249--39746 Score: 874
Period size: 67 Copynumber: 7.5 Consensus size: 67
39239 AGATTGTTTA
*
39249 TTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAGTT
1 TTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATT
39314 TC
66 TC
39316 TTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAA-TTTGTCTCTCTTAAGATAATT
1 TTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATT
39380 TC
66 TC
*
39382 TTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAGTT
1 TTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATT
39447 TC
66 TC
39449 TTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATT
1 TTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATT
39514 TC
66 TC
* * *
39516 TTTTGAAACGAAAATCTTTGAGTATGTTTCTTTGGAAACAAAATTTTGTCTCTTTTAAGATAATT
1 TTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATT
39581 TC
66 TC
* *
39583 TTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTTAGATAATT
1 TTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATT
39648 TC
66 TC
* *
39650 TTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAATAAAATTTTGTCTCTCTTAAGATAATT
1 TTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATT
39715 TC
66 TC
* * *
39717 TTTTGGAA-AAAAATCTTTGAATCTGTTTCT
1 TTTTGAAACAAAAATCTTTGAGTTTGTTTCT
39747 CTTAAAATGA
Statistics
Matches: 416, Mismatches: 14, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
66 86 0.21
67 330 0.79
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.45
Consensus pattern (67 bp):
TTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATT
TC
Found at i:39599 original size:134 final size:134
Alignment explanation
Indices: 39249--39954 Score: 877
Period size: 134 Copynumber: 5.4 Consensus size: 134
39239 AGATTGTTTA
*
39249 TTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAGTT
1 TTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATT
*
39314 TCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAA-TTTGTCTCTCTTAAGATAA
66 TCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
39378 TTTC
131 TTTC
*
39382 TTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAGTT
1 TTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATT
*
39447 TCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
66 TCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
39512 TTTC
131 TTTC
* * *
39516 TTTTGAAACGAAAATCTTTGAGTATGTTTCTTTGGAAACAAAATTTTGTCTCTTTTAAGATAATT
1 TTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATT
*
39581 TCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTTAGATAA
66 TCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
39646 TTTC
131 TTTC
* *
39650 TTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAATAAAATTTTGTCTCTCTTAAGATAATT
1 TTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATT
* * * * * *
39715 TCTTTTGGAA-AAAAATCTTTGAATCTGTTTCTCTT--AAA-ATGAATTTTGTATCTCTTGAGAC
66 TCTTTTGAAACAAAAATCTTTGAGTCTGTTTCT-TTGGAAACA-AAATTTTGTCTCTCTTAAGAT
*
39776 AGTTTC
129 AATTTC
* ** * * * **
39782 TCTTG-AA-GTAAATCTTTGAATATG-TTCATTTTG----AAAATCTTTG--AGT-TT--G----
1 TTTTGAAACAAAAATCTTTGAGTTTGTTTC-TTTGGAAACAAAAT-TTTGTCTCTCTTAAGATAA
* * * * * *
39831 TTTCTCTT-AACA-AAATCATCTTTGAGTCTATTTCTTTTGAAACAAAATTTTATCTCT-TAAAG
64 TTTCTTTTGAA-ACAAA-AATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAG
*
39893 ACAATTTC
127 ATAATTTC
*
39901 TTTTGAAAAAAAAATCTTTGAGTTTGTTTCCTTT-GAAACAAAATTTTGTCTCTC
1 TTTTGAAACAAAAATCTTTGAGTTTGTTT-CTTTGGAAACAAAATTTTGTCTCTC
39955 GAGACAACTT
Statistics
Matches: 509, Mismatches: 43, Indels: 48
0.85 0.07 0.08
Matches are distributed among these distances:
117 1 0.00
118 13 0.03
119 30 0.06
120 15 0.03
121 15 0.03
122 6 0.01
123 1 0.00
124 6 0.01
125 6 0.01
126 6 0.01
127 4 0.01
129 3 0.01
130 17 0.03
131 3 0.01
132 29 0.06
133 131 0.26
134 223 0.44
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (134 bp):
TTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATT
TCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
TTTC
Found at i:39613 original size:30 final size:30
Alignment explanation
Indices: 39579--39692 Score: 88
Period size: 30 Copynumber: 3.6 Consensus size: 30
39569 TTTAAGATAA
*
39579 TTTCTTTTGAAACAAAAATCTTTGAGTCTG
1 TTTCTTTGGAAACAAAAATCTTTGAGTCTG
**
39609 TTTCTTTGGAAAC-AAAAT-TTTGTCTCTCTTTAG
1 TTTCTTTGGAAACAAAAATCTTTG--AGTC--T-G
*
39642 ATAATTTCTTTTGAAACAAAAATCTTTGAGTCTG
1 ----TTTCTTTGGAAACAAAAATCTTTGAGTCTG
*
39676 TTTCTTTGGAAATAAAA
1 TTTCTTTGGAAACAAAA
39693 TTTTGTCTCT
Statistics
Matches: 65, Mismatches: 8, Indels: 22
0.68 0.08 0.23
Matches are distributed among these distances:
28 4 0.06
29 5 0.08
30 29 0.45
32 1 0.02
33 1 0.02
34 1 0.02
35 1 0.02
37 14 0.22
38 5 0.08
39 4 0.06
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (30 bp):
TTTCTTTGGAAACAAAAATCTTTGAGTCTG
Found at i:39819 original size:65 final size:65
Alignment explanation
Indices: 39290--39807 Score: 250
Period size: 67 Copynumber: 7.8 Consensus size: 65
39280 TTGGAAACAA
* * * * * * * *
39290 AATTTTGTCTCTCTTAAGATAGTTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCT-TTGGAAA
1 AATTTTGTATCTCTTAAGACAATTTCTCTTGGAA-AAAAATCTTTGAATATGTTTCTCTT-AAAA
**
39354 CA
64 TG
* * * * * * *
39356 AAATTTGTCTCTCTTAAGATAATTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCT-TTGGAAA
1 AATTTTGTATCTCTTAAGACAATTTCTCTTGGAA-AAAAATCTTTGAATATGTTTCTCTT--AAA
*
39420 CA-A
63 -ATG
* * * * * * *
39423 AATTTTGTCTCTCTTAAGATAGTTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCT-TTGGAAA
1 AATTTTGTATCTCTTAAGACAATTTCTCTTGGAA-AAAAATCTTTGAATATGTTTCTCTT--AAA
*
39487 CA-A
63 -ATG
* * * *
39490 AATTTTGTCTCTCTTAAGATAATTTCT-TTTGAAACGAAAATCTTTGAGTATGTTTCT-TTGGAA
1 AATTTTGTATCTCTTAAGACAATTTCTCTTGGAAA--AAAATCTTTGAATATGTTTCTCTT--AA
*
39553 ACA-A
62 A-ATG
* * * * * * *
39557 AATTTTGTCTCTTTTAAGATAATTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCT-TTGGAAA
1 AATTTTGTATCTCTTAAGACAATTTCTCTTGGAA-AAAAATCTTTGAATATGTTTCTCTT--AAA
*
39621 CA-A
63 -ATG
* * * * * * * *
39624 AATTTTGTCTCTCTTTAGATAATTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCT-TTGGAAA
1 AATTTTGTATCTCTTAAGACAATTTCTCTTGGAA-AAAAATCTTTGAATATGTTTCTCTT-AAAA
*
39688 TAA
64 T-G
* * * *
39691 AATTTTGTCTCTCTTAAGATAATTTCTTTTGGAAAAAAATCTTTGAATCTGTTTCTCTTAAAATG
1 AATTTTGTATCTCTTAAGACAATTTCTCTTGGAAAAAAATCTTTGAATATGTTTCTCTTAAAATG
* * **
39756 AATTTTGTATCTCTTGAGACAGTTTCTCTT-GAAGTAAATCTTTGAATATGTT
1 AATTTTGTATCTCTTAAGACAATTTCTCTTGGAAAAAAATCTTTGAATATGTT
39808 CATTTTGAAA
Statistics
Matches: 414, Mismatches: 29, Indels: 20
0.89 0.06 0.04
Matches are distributed among these distances:
64 19 0.05
65 27 0.07
66 89 0.21
67 273 0.66
68 5 0.01
69 1 0.00
ACGTcount: A:0.30, C:0.12, G:0.13, T:0.45
Consensus pattern (65 bp):
AATTTTGTATCTCTTAAGACAATTTCTCTTGGAAAAAAATCTTTGAATATGTTTCTCTTAAAATG
Found at i:39919 original size:66 final size:65
Alignment explanation
Indices: 39848--39974 Score: 182
Period size: 66 Copynumber: 1.9 Consensus size: 65
39838 TAACAAAATC
* *
39848 ATCTTTGAGTCTATTTCTTTTGAAACAAAATTTTATCTCTTAAAGACAATTTCTTTTGAAAAAAA
1 ATCTTTGAGTCTATTTCCTTTGAAACAAAATTTTATCTC-TAAAGACAACTTCTTTTGAAAAAAA
39913 A
65 A
* * * **
39914 ATCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTCTCGAGACAACTTCTTTTGAAAA
1 ATCTTTGAGTCTATTTCCTTTGAAACAAAATTTTATCTCTAAAGACAACTTCTTTTGAAAA
39975 TACCCACCTT
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
65 19 0.35
66 35 0.65
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (65 bp):
ATCTTTGAGTCTATTTCCTTTGAAACAAAATTTTATCTCTAAAGACAACTTCTTTTGAAAAAAAA
Found at i:40011 original size:40 final size:40
Alignment explanation
Indices: 39956--40035 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
39946 TTGTCTCTCG
39956 AGACAACTTCTTTTGAAAATACCCACCTTTGAGATCGTTT
1 AGACAACTTCTTTTGAAAATACCCACCTTTGAGATCGTTT
39996 AGACAACTTCTTTTGAAAATACCCACCTTTGAGATCGTTT
1 AGACAACTTCTTTTGAAAATACCCACCTTTGAGATCGTTT
40036 CTATTAAAAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35
Consensus pattern (40 bp):
AGACAACTTCTTTTGAAAATACCCACCTTTGAGATCGTTT
Found at i:40670 original size:28 final size:28
Alignment explanation
Indices: 40624--40700 Score: 86
Period size: 28 Copynumber: 2.6 Consensus size: 28
40614 GAGACAGTTG
40624 CTTTTGAAACACATTATCTTTGAG-CTTGTT-
1 CTTTTGAAACA-A--ATCTTTGAGTC-TGTTC
*
40654 TTTCTTGAAACAAATCTTTGAGTCTGTTC
1 CTT-TTGAAACAAATCTTTGAGTCTGTTC
40683 CTTTTGAAACAAATCTTT
1 CTTTTGAAACAAATCTTT
40701 CAATCAGTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
28 28 0.67
29 3 0.07
30 3 0.07
31 8 0.19
ACGTcount: A:0.26, C:0.17, G:0.12, T:0.45
Consensus pattern (28 bp):
CTTTTGAAACAAATCTTTGAGTCTGTTC
Found at i:40717 original size:28 final size:28
Alignment explanation
Indices: 40651--40719 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 28
40641 CTTTGAGCTT
* * * *
40651 GTTTTTCTTGAAACAAATCTTTGAGTCT
1 GTTTCTCTTGAAACAAATCTTTCAATCA
* *
40679 GTTCCTTTTGAAACAAATCTTTCAATCA
1 GTTTCTCTTGAAACAAATCTTTCAATCA
40707 GTTTCTCTTGAAA
1 GTTTCTCTTGAAA
40720 TCATAACTCC
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.28, C:0.17, G:0.12, T:0.43
Consensus pattern (28 bp):
GTTTCTCTTGAAACAAATCTTTCAATCA
Found at i:40841 original size:43 final size:41
Alignment explanation
Indices: 40744--40845 Score: 120
Period size: 40 Copynumber: 2.5 Consensus size: 41
40734 GATGGCCAGC
* *
40744 CGTCCTCATCACGTAGGAATCGTGTCATCTCCTGATCAAAT
1 CGTCCTCATCACGTAGGAATCGTGTCATCCCCTGATCAAAA
*
40785 C-TCCTCATCACGTAGGAGTCGTGTCA-CCCCTAGAT-AACTAGA
1 CGTCCTCATCACGTAGGAATCGTGTCATCCCCT-GATCAA--A-A
40827 CGTCCTCATCACGTAGGAA
1 CGTCCTCATCACGTAGGAA
40846 CTATGTTATC
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
39 6 0.12
40 27 0.52
41 2 0.04
42 1 0.02
43 16 0.31
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (41 bp):
CGTCCTCATCACGTAGGAATCGTGTCATCCCCTGATCAAAA
Found at i:41080 original size:135 final size:134
Alignment explanation
Indices: 40727--41223 Score: 698
Period size: 135 Copynumber: 3.7 Consensus size: 134
40717 AAATCATAAC
* * * *
40727 TCCTAAAGATGGCCAG-CCGTCCTCATCACGTA-G-GAATCGTGTCATCTCCT-GATCAAATCTC
1 TCCTAAAGATGGCCAGAAC-TCTTCATCACGTATGAGAA--GTGTCATC-CCTCGACCATATCTC
** * * * *
40788 CTCATCACGTAGGAGTCGTGTCACCCCTAGATAACTAGACGTCCTCATCACGTAGGAA-CTATGT
62 CTCATCACGTAGGAACCGTGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACCGA-GT
*
40852 TATCGCCCT
126 TATCACCCT
* *
40861 TCCTAAAGATGGCCAGAACTCTTCATCACGTATGAGAAGTGTCATCCCCCGACCAGATCTCCTCA
1 TCCTAAAGATGGCCAGAACTCTTCATCACGTATGAGAAGTGTCATCCCTCGACCATATCTCCTCA
**
40926 TTGCGTAGGAACCGTGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACCGAGTTATCA
66 TCACGTAGGAACCGTGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACCGAGTTATCA
40991 CCCT
131 CCCT
* *
40995 TCCTAAAGATGGCCAAGAACTCTTCATCACGTATGAGCAGTGTCATCCCTCGACCATATTTCCTC
1 TCCTAAAGATGGCC-AGAACTCTTCATCACGTATGAGAAGTGTCATCCCTCGACCATATCTCCTC
* *
41060 ATTATGTAGGAACCGTGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACCGAGTTATC
65 ATCACGTAGGAACCGTGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACCGAGTTATC
41125 ACCCT
130 ACCCT
*
41130 TCCTAAAGATGGCCAAGAACTCTTCATCACGTATGAGAAGTGTCATCCCTCGACCATATTTCCTC
1 TCCTAAAGATGGCC-AGAACTCTTCATCACGTATGAGAAGTGTCATCCCTCGACCATATCTCCTC
* *
41195 ATCATGTAGGAACCGTGTCACCCTTAGAT
65 ATCACGTAGGAACCGTGTCACCCCTAGAT
41224 GACCCGAACT
Statistics
Matches: 334, Mismatches: 23, Indels: 11
0.91 0.06 0.03
Matches are distributed among these distances:
133 2 0.01
134 120 0.36
135 209 0.63
136 3 0.01
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (134 bp):
TCCTAAAGATGGCCAGAACTCTTCATCACGTATGAGAAGTGTCATCCCTCGACCATATCTCCTCA
TCACGTAGGAACCGTGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACCGAGTTATCA
CCCT
Found at i:41502 original size:28 final size:28
Alignment explanation
Indices: 41456--41551 Score: 97
Period size: 28 Copynumber: 3.3 Consensus size: 28
41446 GAGACAGTTG
41456 CTTTTGAAACACATTATCTTTGAG-CTTGTTT
1 CTTTTGAAACA-A--ATCTTTGAGTC-TGTTT
41487 -TTCTTGAAACAAATCTTTGAGTCTGTTT
1 CTT-TTGAAACAAATCTTTGAGTCTGTTT
* * *
41515 CTTTTGAAACAAATCTTTCAATCAGTTT
1 CTTTTGAAACAAATCTTTGAGTCTGTTT
*
41543 CTCTTGAAA
1 CTTTTGAAA
41552 TCATAACTCC
Statistics
Matches: 58, Mismatches: 4, Indels: 9
0.82 0.06 0.13
Matches are distributed among these distances:
28 44 0.76
29 3 0.05
30 3 0.05
31 8 0.14
ACGTcount: A:0.27, C:0.17, G:0.11, T:0.45
Consensus pattern (28 bp):
CTTTTGAAACAAATCTTTGAGTCTGTTT
Found at i:41673 original size:43 final size:41
Alignment explanation
Indices: 41576--41677 Score: 120
Period size: 40 Copynumber: 2.5 Consensus size: 41
41566 GATGGCCAGC
* *
41576 CGTCCTCATCACGTAGGAATCGTGTCATCTCCTGATCAAAT
1 CGTCCTCATCACGTAGGAATCGTGTCATCCCCTGATCAAAA
*
41617 C-TCCTCATCACGTAGGAGTCGTGTCA-CCCCTAGAT-AACTAGA
1 CGTCCTCATCACGTAGGAATCGTGTCATCCCCT-GATCAA--A-A
41659 CGTCCTCATCACGTAGGAA
1 CGTCCTCATCACGTAGGAA
41678 CTATGTTATC
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
39 6 0.12
40 27 0.52
41 2 0.04
42 1 0.02
43 16 0.31
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (41 bp):
CGTCCTCATCACGTAGGAATCGTGTCATCCCCTGATCAAAA
Found at i:41913 original size:135 final size:134
Alignment explanation
Indices: 41559--42054 Score: 698
Period size: 134 Copynumber: 3.7 Consensus size: 134
41549 AAATCATAAC
* * * *
41559 TCCTAAAGATGGCCAG-CCGTCCTCATCACGTA-G-GAATCGTGTCATCTCCT-GATCAAATCTC
1 TCCTAAAGATGGCCAGAAC-TCTTCATCACGTATGAGAA--GTGTCATC-CCTCGACCATATCTC
** * * * *
41620 CTCATCACGTAGGAGTCGTGTCACCCCTAGATAACTAGACGTCCTCATCACGTAGGAA-CTATGT
62 CTCATCACGTAGGAACCGTGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACCGA-GT
*
41684 TATCGCCCT
126 TATCACCCT
* *
41693 TCCTAAAGATGGCCAGAACTCTTCATCACGTATGAGAAGTGTCATCCCCCGACCAGATCTCCTCA
1 TCCTAAAGATGGCCAGAACTCTTCATCACGTATGAGAAGTGTCATCCCTCGACCATATCTCCTCA
*
41758 TCGCGTAGGAACCGTGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACCGAGTTATCA
66 TCACGTAGGAACCGTGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACCGAGTTATCA
41823 CCCT
131 CCCT
* *
41827 TCCTAAAGATGGCCAAGAACTCTTCATCACGTATGAGCAGTGTCATCCCTCGACCATATTTCCTC
1 TCCTAAAGATGGCC-AGAACTCTTCATCACGTATGAGAAGTGTCATCCCTCGACCATATCTCCTC
* *
41892 ATTATGTAGGAACCGTGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACCGAGTTATC
65 ATCACGTAGGAACCGTGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACCGAGTTATC
41957 ACCCT
130 ACCCT
*
41962 TCCTAAAGATGGCCAAGAACTC-TCATCACGTATGAGAAGTGTCATCCCTCGACCATATTTCCTC
1 TCCTAAAGATGGCC-AGAACTCTTCATCACGTATGAGAAGTGTCATCCCTCGACCATATCTCCTC
* *
42026 ATCATGTAGGAACCGTGTCACCCTTAGAT
65 ATCACGTAGGAACCGTGTCACCCCTAGAT
42055 GACCCGAACT
Statistics
Matches: 333, Mismatches: 23, Indels: 12
0.90 0.06 0.03
Matches are distributed among these distances:
133 2 0.01
134 189 0.57
135 139 0.42
136 3 0.01
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (134 bp):
TCCTAAAGATGGCCAGAACTCTTCATCACGTATGAGAAGTGTCATCCCTCGACCATATCTCCTCA
TCACGTAGGAACCGTGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACCGAGTTATCA
CCCT
Found at i:42332 original size:28 final size:28
Alignment explanation
Indices: 42286--42381 Score: 97
Period size: 28 Copynumber: 3.3 Consensus size: 28
42276 GAGACAGTTG
42286 CTTTTGAAACACATTATCTTTGAG-CTTGTTT
1 CTTTTGAAACA-A--ATCTTTGAGTC-TGTTT
42317 -TTCTTGAAACAAATCTTTGAGTCTGTTT
1 CTT-TTGAAACAAATCTTTGAGTCTGTTT
* * *
42345 CTTTTGAAACAAATCTTTCAATCAGTTT
1 CTTTTGAAACAAATCTTTGAGTCTGTTT
*
42373 CTCTTGAAA
1 CTTTTGAAA
42382 TCATAACTCC
Statistics
Matches: 58, Mismatches: 4, Indels: 9
0.82 0.06 0.13
Matches are distributed among these distances:
28 44 0.76
29 3 0.05
30 3 0.05
31 8 0.14
ACGTcount: A:0.27, C:0.17, G:0.11, T:0.45
Consensus pattern (28 bp):
CTTTTGAAACAAATCTTTGAGTCTGTTT
Found at i:42503 original size:43 final size:40
Alignment explanation
Indices: 42406--42507 Score: 116
Period size: 40 Copynumber: 2.5 Consensus size: 40
42396 GATGGCCAGC
*
42406 CGTCCTCATCACGTAGGAATCGTGTCATCTCCTGATCAAA
1 CGTCCTCATCACGTAGGAATCGTGTCATCCCCTGATCAAA
** * *
42446 TTTCCTCATCACGTAGGAGTCGTGTCA-CCCCTAGATAACTAGA
1 CGTCCTCATCACGTAGGAATCGTGTCATCCCCT-GAT--C-AAA
42489 CGTCCTCATCACGTAGGAA
1 CGTCCTCATCACGTAGGAA
42508 CTATGTTATC
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
39 4 0.08
40 27 0.54
42 1 0.02
43 18 0.36
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.26
Consensus pattern (40 bp):
CGTCCTCATCACGTAGGAATCGTGTCATCCCCTGATCAAA
Found at i:42559 original size:830 final size:832
Alignment explanation
Indices: 40547--43015 Score: 4888
Period size: 832 Copynumber: 3.0 Consensus size: 832
40537 TTTTGTCTCG
40547 CTTGAGACAATTCCCTTTAAACGTCATCTTTTGAGTTGTTTCATTTGAAACGAATTTTGTCTCTT
1 CTTGAGACAATTCCCTTTAAACGTCATCTTTTGAGTTGTTTCATTTGAAACGAATTTTGTCTCTT
40612 TCGAGACAGTTGCTTTTGAAACACATTATCTTTGAGCTTGTTTTTCTTGAAACAAATCTTTGAGT
66 TCGAGACAGTTGCTTTTGAAACACATTATCTTTGAGCTTGTTTTTCTTGAAACAAATCTTTGAGT
*
40677 CTGTTCCTTTTGAAACAAATCTTTCAATCAGTTTCTCTTGAAATCATAACTCCTAAAGATGGCCA
131 CTGTTTCTTTTGAAACAAATCTTTCAATCAGTTTCTCTTGAAATCATAACTCCTAAAGATGGCCA
40742 GCCGTCCTCATCACGTAGGAATCGTGTCATCTCCTGATCAAATCTCCTCATCACGTAGGAGTCGT
196 GCCGTCCTCATCACGTAGGAATCGTGTCATCTCCTGATCAAATCTCCTCATCACGTAGGAGTCGT
40807 GTCACCCCTAGATAACTAGACGTCCTCATCACGTAGGAACTATGTTATCGCCCTTCCTAAAGATG
261 GTCACCCCTAGATAACTAGACGTCCTCATCACGTAGGAACTATGTTATCGCCCTTCCTAAAGATG
*
40872 GCCAGAACTCTTCATCACGTATGAGAAGTGTCATCCCCCGACCAGATCTCCTCATTGCGTAGGAA
326 GCCAGAACTCTTCATCACGTATGAGAAGTGTCATCCCCCGACCAGATCTCCTCATCGCGTAGGAA
40937 CCGTGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACCGAGTTATCACCCTTCCTAAA
391 CCGTGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACCGAGTTATCACCCTTCCTAAA
41002 GATGGCCAAGAACTCTTCATCACGTATGAGCAGTGTCATCCCTCGACCATATTTCCTCATTATGT
456 GATGGCCAAGAACTCTTCATCACGTATGAGCAGTGTCATCCCTCGACCATATTTCCTCATTATGT
41067 AGGAACCGTGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACCGAGTTATCACCCTTC
521 AGGAACCGTGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACCGAGTTATCACCCTTC
41132 CTAAAGATGGCCAAGAACTCTTCATCACGTATGAGAAGTGTCATCCCTCGACCATATTTCCTCAT
586 CTAAAGATGGCCAAGAACTCTTCATCACGTATGAGAAGTGTCATCCCTCGACCATATTTCCTCAT
41197 CATGTAGGAACCGTGTCACCCTTAGATGACCCGAACTCTTCCTCACGTATGAGCAGTGTCGTCCC
651 CATGTAGGAACCGTGTCACCCTTAGATGACCCGAACTCTTCCTCACGTATGAGCAGTGTCGTCCC
41262 CAACAACCAACATTATCCAATTTATAAGTTTAAAAGGGAGAGAACCAGACAAAAACGTGTTGTCT
716 CAACAACCAACATTATCCAATTTATAAGTTTAAAAGGGAGAGAACCAGACAAAAACGTGTTGTCT
41327 TGTCATCTTTGCCCTATTCTTGTTAAACGTCATCTTTCGAGATTGCCCTATT
781 TGTCATCTTTGCCCTATTCTTGTTAAACGTCATCTTTCGAGATTGCCCTATT
41379 CTTGAGACAATTCCCTTTAAACGTCATCTTTTGAGTTGTTTCATTTGAAACGAATTTTGTCTCTT
1 CTTGAGACAATTCCCTTTAAACGTCATCTTTTGAGTTGTTTCATTTGAAACGAATTTTGTCTCTT
41444 TCGAGACAGTTGCTTTTGAAACACATTATCTTTGAGCTTGTTTTTCTTGAAACAAATCTTTGAGT
66 TCGAGACAGTTGCTTTTGAAACACATTATCTTTGAGCTTGTTTTTCTTGAAACAAATCTTTGAGT
41509 CTGTTTCTTTTGAAACAAATCTTTCAATCAGTTTCTCTTGAAATCATAACTCCTAAAGATGGCCA
131 CTGTTTCTTTTGAAACAAATCTTTCAATCAGTTTCTCTTGAAATCATAACTCCTAAAGATGGCCA
41574 GCCGTCCTCATCACGTAGGAATCGTGTCATCTCCTGATCAAATCTCCTCATCACGTAGGAGTCGT
196 GCCGTCCTCATCACGTAGGAATCGTGTCATCTCCTGATCAAATCTCCTCATCACGTAGGAGTCGT
41639 GTCACCCCTAGATAACTAGACGTCCTCATCACGTAGGAACTATGTTATCGCCCTTCCTAAAGATG
261 GTCACCCCTAGATAACTAGACGTCCTCATCACGTAGGAACTATGTTATCGCCCTTCCTAAAGATG
41704 GCCAGAACTCTTCATCACGTATGAGAAGTGTCATCCCCCGACCAGATCTCCTCATCGCGTAGGAA
326 GCCAGAACTCTTCATCACGTATGAGAAGTGTCATCCCCCGACCAGATCTCCTCATCGCGTAGGAA
41769 CCGTGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACCGAGTTATCACCCTTCCTAAA
391 CCGTGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACCGAGTTATCACCCTTCCTAAA
41834 GATGGCCAAGAACTCTTCATCACGTATGAGCAGTGTCATCCCTCGACCATATTTCCTCATTATGT
456 GATGGCCAAGAACTCTTCATCACGTATGAGCAGTGTCATCCCTCGACCATATTTCCTCATTATGT
41899 AGGAACCGTGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACCGAGTTATCACCCTTC
521 AGGAACCGTGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACCGAGTTATCACCCTTC
41964 CTAAAGATGGCCAAGAACTC-TCATCACGTATGAGAAGTGTCATCCCTCGACCATATTTCCTCAT
586 CTAAAGATGGCCAAGAACTCTTCATCACGTATGAGAAGTGTCATCCCTCGACCATATTTCCTCAT
42028 CATGTAGGAACCGTGTCACCCTTAGATGACCCGAACTCTTCCTCACGTATGAGCAGTGTCGT-CC
651 CATGTAGGAACCGTGTCACCCTTAGATGACCCGAACTCTTCCTCACGTATGAGCAGTGTCGTCCC
42092 CAACAACCAACATTATCCAATTTATAAGTTTAAAAGGGAGAGAACCAGACAAAAACGTGTTGTCT
716 CAACAACCAACATTATCCAATTTATAAGTTTAAAAGGGAGAGAACCAGACAAAAACGTGTTGTCT
42157 TGTCATCTTTGCCCTATTCTTGTTAAACGTCATCTTTCGAGATTGCCCTATT
781 TGTCATCTTTGCCCTATTCTTGTTAAACGTCATCTTTCGAGATTGCCCTATT
42209 CTTGAGACAATTCCCTTTAAACGTCATCTTTTGAGTTGTTTCATTTGAAACGAATTTTGTCTCTT
1 CTTGAGACAATTCCCTTTAAACGTCATCTTTTGAGTTGTTTCATTTGAAACGAATTTTGTCTCTT
42274 TCGAGACAGTTGCTTTTGAAACACATTATCTTTGAGCTTGTTTTTCTTGAAACAAATCTTTGAGT
66 TCGAGACAGTTGCTTTTGAAACACATTATCTTTGAGCTTGTTTTTCTTGAAACAAATCTTTGAGT
42339 CTGTTTCTTTTGAAACAAATCTTTCAATCAGTTTCTCTTGAAATCATAACTCCTAAAGATGGCCA
131 CTGTTTCTTTTGAAACAAATCTTTCAATCAGTTTCTCTTGAAATCATAACTCCTAAAGATGGCCA
*
42404 GCCGTCCTCATCACGTAGGAATCGTGTCATCTCCTGATCAAATTTCCTCATCACGTAGGAGTCGT
196 GCCGTCCTCATCACGTAGGAATCGTGTCATCTCCTGATCAAATCTCCTCATCACGTAGGAGTCGT
42469 GTCACCCCTAGATAACTAGACGTCCTCATCACGTAGGAACTATGTTATCGCCCTTCCTAAAGATG
261 GTCACCCCTAGATAACTAGACGTCCTCATCACGTAGGAACTATGTTATCGCCCTTCCTAAAGATG
42534 GCCAGAACTCTTCATCACGTATGAGAAGTGTCATCCCCCGACCAGATCTCCTCATCGCGTAGGAA
326 GCCAGAACTCTTCATCACGTATGAGAAGTGTCATCCCCCGACCAGATCTCCTCATCGCGTAGG-A
42599 ACCGTGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACCGAGTTATCACCCTTCCTAA
390 ACCGTGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACCGAGTTATCACCCTTCCTAA
42664 AGATGGCCAAGAACTCTTCATCACGTATGAGCAGTGTCATCCCTCGACCATATTTCCTCATTATG
455 AGATGGCCAAGAACTCTTCATCACGTATGAGCAGTGTCATCCCTCGACCATATTTCCTCATTATG
42729 TAGGAACCGTGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACCGAGTTATCACCCTT
520 TAGGAACCGTGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACCGAGTTATCACCCTT
42794 CCTAAAGATGGCCAAGAACTCTTCATCACGTATGAGAAGTGTCATCCCTCGACCATATTTCCTCA
585 CCTAAAGATGGCCAAGAACTCTTCATCACGTATGAGAAGTGTCATCCCTCGACCATATTTCCTCA
42859 TCATGTAGGAACCGTGTCACCCTTAGATGACCCGAACTCTTCCTCACGTATGAGCAGTGTCGTCC
650 TCATGTAGGAACCGTGTCACCCTTAGATGACCCGAACTCTTCCTCACGTATGAGCAGTGTCGTCC
42924 CCAACAACCAACATTATCCAATTTATAAGTTTAAAAGGGAGAGAACCAGACAAAAACGTGTTGTC
715 CCAACAACCAACATTATCCAATTTATAAGTTTAAAAGGGAGAGAACCAGACAAAAACGTGTTGTC
42989 TTGTCATCTTTGCCCTATTCTTGTTAA
780 TTGTCATCTTTGCCCTATTCTTGTTAA
43016 CACAAGAATG
Statistics
Matches: 1631, Mismatches: 3, Indels: 5
1.00 0.00 0.00
Matches are distributed among these distances:
830 506 0.31
831 323 0.20
832 709 0.43
833 93 0.06
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.30
Consensus pattern (832 bp):
CTTGAGACAATTCCCTTTAAACGTCATCTTTTGAGTTGTTTCATTTGAAACGAATTTTGTCTCTT
TCGAGACAGTTGCTTTTGAAACACATTATCTTTGAGCTTGTTTTTCTTGAAACAAATCTTTGAGT
CTGTTTCTTTTGAAACAAATCTTTCAATCAGTTTCTCTTGAAATCATAACTCCTAAAGATGGCCA
GCCGTCCTCATCACGTAGGAATCGTGTCATCTCCTGATCAAATCTCCTCATCACGTAGGAGTCGT
GTCACCCCTAGATAACTAGACGTCCTCATCACGTAGGAACTATGTTATCGCCCTTCCTAAAGATG
GCCAGAACTCTTCATCACGTATGAGAAGTGTCATCCCCCGACCAGATCTCCTCATCGCGTAGGAA
CCGTGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACCGAGTTATCACCCTTCCTAAA
GATGGCCAAGAACTCTTCATCACGTATGAGCAGTGTCATCCCTCGACCATATTTCCTCATTATGT
AGGAACCGTGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACCGAGTTATCACCCTTC
CTAAAGATGGCCAAGAACTCTTCATCACGTATGAGAAGTGTCATCCCTCGACCATATTTCCTCAT
CATGTAGGAACCGTGTCACCCTTAGATGACCCGAACTCTTCCTCACGTATGAGCAGTGTCGTCCC
CAACAACCAACATTATCCAATTTATAAGTTTAAAAGGGAGAGAACCAGACAAAAACGTGTTGTCT
TGTCATCTTTGCCCTATTCTTGTTAAACGTCATCTTTCGAGATTGCCCTATT
Found at i:42658 original size:135 final size:135
Alignment explanation
Indices: 42389--42886 Score: 702
Period size: 135 Copynumber: 3.7 Consensus size: 135
42379 AAATCATAAC
* * * * * *
42389 TCCTAAAGATGGCC-AG-CCGTCCTCATCACGTA-G-GAATCGTGTCATCTCCTGATCAAATTTC
1 TCCTAAAGATGGCCAAGAAC-TCTTCATCACGTATGAGAA--GTGTCATCCCCCGACCATATTTC
** * * * *
42450 CTCATCACGTAGGAGTCGTGTCACCCCTAGATAACTAGACGTCCTCATCACGTAGGAA-CTATGT
63 CTCATCACGTAGGAACCGTGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACCGA-GT
*
42514 TATCGCCCT
127 TATCACCCT
* *
42523 TCCTAAAGATGGCC-AGAACTCTTCATCACGTATGAGAAGTGTCATCCCCCGACCAGATCTCCTC
1 TCCTAAAGATGGCCAAGAACTCTTCATCACGTATGAGAAGTGTCATCCCCCGACCATATTTCCTC
*
42587 ATCGCGTAGGAAACCGTGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACCGAGTTAT
66 ATCACGTAGG-AACCGTGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACCGAGTTAT
42652 CACCCT
130 CACCCT
* *
42658 TCCTAAAGATGGCCAAGAACTCTTCATCACGTATGAGCAGTGTCATCCCTCGACCATATTTCCTC
1 TCCTAAAGATGGCCAAGAACTCTTCATCACGTATGAGAAGTGTCATCCCCCGACCATATTTCCTC
* *
42723 ATTATGTAGGAACCGTGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACCGAGTTATC
66 ATCACGTAGGAACCGTGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACCGAGTTATC
42788 ACCCT
131 ACCCT
*
42793 TCCTAAAGATGGCCAAGAACTCTTCATCACGTATGAGAAGTGTCATCCCTCGACCATATTTCCTC
1 TCCTAAAGATGGCCAAGAACTCTTCATCACGTATGAGAAGTGTCATCCCCCGACCATATTTCCTC
* *
42858 ATCATGTAGGAACCGTGTCACCCTTAGAT
66 ATCACGTAGGAACCGTGTCACCCCTAGAT
42887 GACCCGAACT
Statistics
Matches: 333, Mismatches: 25, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
134 58 0.17
135 217 0.65
136 58 0.17
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (135 bp):
TCCTAAAGATGGCCAAGAACTCTTCATCACGTATGAGAAGTGTCATCCCCCGACCATATTTCCTC
ATCACGTAGGAACCGTGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACCGAGTTATC
ACCCT
Found at i:43093 original size:3 final size:3
Alignment explanation
Indices: 43085--43128 Score: 63
Period size: 3 Copynumber: 14.7 Consensus size: 3
43075 TTAATTTTAA
*
43085 TAT TAT TAT TAT TAT TAAC TA- TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TA
43129 ATATATGTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
2 2 0.05
3 34 0.89
4 2 0.05
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:43111 original size:15 final size:14
Alignment explanation
Indices: 43091--43134 Score: 65
Period size: 12 Copynumber: 3.2 Consensus size: 14
43081 TTAATATTAT
43091 TATTATTATTAACTA
1 TATTATTATTAA-TA
43106 TATTATTATT-AT-
1 TATTATTATTAATA
43118 TATTATTATTAATA
1 TATTATTATTAATA
43132 TAT
1 TAT
43135 GTTTGCATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 10 0.37
13 3 0.11
14 4 0.15
15 10 0.37
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (14 bp):
TATTATTATTAATA
Found at i:46283 original size:15 final size:16
Alignment explanation
Indices: 46265--46298 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
46255 TGTATATTGA
46265 GGTTTTGTGG-TCTGT
1 GGTTTTGTGGTTCTGT
*
46280 GGTTTTTTGGTTCTGT
1 GGTTTTGTGGTTCTGT
46296 GGT
1 GGT
46299 AATTGTAGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.00, C:0.06, G:0.38, T:0.56
Consensus pattern (16 bp):
GGTTTTGTGGTTCTGT
Found at i:46473 original size:91 final size:91
Alignment explanation
Indices: 46318--46500 Score: 294
Period size: 91 Copynumber: 2.0 Consensus size: 91
46308 ATTTTTTATT
* * * * *
46318 GTCGATTGCTGCTTTGGAGTAAGCAAAGCTGAGGTGGGTTGATTTATTGGGGAATAGCGGATCAT
1 GTCGATTGCTGCTATGGAGTAAGCAAAGCTGAAGCGGGTGGATTTATTGGGGAATAACGGATCAT
46383 GTAGCCATTGCTGAAGCTGGTTTTGG
66 GTAGCCATTGCTGAAGCTGGTTTTGG
* *
46409 GTCGATTGCTGCTATGGAGTAAGCAAAGCTGAAGCGGGTGGATTTATTGGGGATTAATGGATCAT
1 GTCGATTGCTGCTATGGAGTAAGCAAAGCTGAAGCGGGTGGATTTATTGGGGAATAACGGATCAT
*
46474 GTAGCCATTGTTGAAGCTGGTTTTGG
66 GTAGCCATTGCTGAAGCTGGTTTTGG
46500 G
1 G
46501 GGTTTGAGGA
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
91 84 1.00
ACGTcount: A:0.22, C:0.11, G:0.35, T:0.32
Consensus pattern (91 bp):
GTCGATTGCTGCTATGGAGTAAGCAAAGCTGAAGCGGGTGGATTTATTGGGGAATAACGGATCAT
GTAGCCATTGCTGAAGCTGGTTTTGG
Found at i:48871 original size:22 final size:22
Alignment explanation
Indices: 48846--48895 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
48836 AATTATGAAC
*
48846 AATATTATTTTTTTAATAATTA
1 AATATTATTATTTTAATAATTA
* *
48868 AATAGTATTATTTTAATAATTC
1 AATATTATTATTTTAATAATTA
48890 AATATT
1 AATATT
48896 TAAACATTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (22 bp):
AATATTATTATTTTAATAATTA
Found at i:55604 original size:20 final size:20
Alignment explanation
Indices: 55581--55619 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
55571 AGTTTTCAAA
*
55581 TTCGCAACGCGAATTTCGTT
1 TTCGCAACGCAAATTTCGTT
*
55601 TTCGCAACTCAAATTTCGT
1 TTCGCAACGCAAATTTCGT
55620 AACGCTAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.26, G:0.15, T:0.36
Consensus pattern (20 bp):
TTCGCAACGCAAATTTCGTT
Found at i:55908 original size:21 final size:21
Alignment explanation
Indices: 55865--55941 Score: 120
Period size: 21 Copynumber: 3.7 Consensus size: 21
55855 ATCAGAAATT
*
55865 CGCGTTGCGAATTT-GAAAAC
1 CGCGTTGCGAATTTGGAGAAC
55885 CGCGTTGCGAATTTGGAGAAC
1 CGCGTTGCGAATTTGGAGAAC
*
55906 CGCGTTGCGAATTTGGAGAAT
1 CGCGTTGCGAATTTGGAGAAC
*
55927 CGCGTTGTGAATTTG
1 CGCGTTGCGAATTTG
55942 AAAACTGTGT
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
20 14 0.26
21 39 0.74
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.29
Consensus pattern (21 bp):
CGCGTTGCGAATTTGGAGAAC
Found at i:55954 original size:41 final size:41
Alignment explanation
Indices: 55865--55957 Score: 116
Period size: 41 Copynumber: 2.3 Consensus size: 41
55855 ATCAGAAATT
*
55865 CGCGTTGCGAATTTGAAAACCGCGTTGCGAATTTGGAGAAC
1 CGCGTTGCGAATTTGAAAACCGCGTTGCGAATTTGGAAAAC
* * *
55906 CGCGTTGCGAATTTGGAGAATCGCGTTGTGAATTT-GAAAAC
1 CGCGTTGCGAATTT-GAAAACCGCGTTGCGAATTTGGAAAAC
* *
55947 TGTGTTGCGAA
1 CGCGTTGCGAA
55958 ACTGGTGTTC
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
41 28 0.62
42 17 0.38
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.28
Consensus pattern (41 bp):
CGCGTTGCGAATTTGAAAACCGCGTTGCGAATTTGGAAAAC
Found at i:59483 original size:21 final size:21
Alignment explanation
Indices: 59457--59516 Score: 102
Period size: 21 Copynumber: 2.9 Consensus size: 21
59447 CAATACAGTT
59457 TCCAAAATCGCAACGCGATTC
1 TCCAAAATCGCAACGCGATTC
* *
59478 TCCAAAATCACAACGTGATTC
1 TCCAAAATCGCAACGCGATTC
59499 TCCAAAATCGCAACGCGA
1 TCCAAAATCGCAACGCGA
59517 ATTTTGTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.32, G:0.13, T:0.18
Consensus pattern (21 bp):
TCCAAAATCGCAACGCGATTC
Found at i:59642 original size:14 final size:14
Alignment explanation
Indices: 59623--59653 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
59613 CGAATTTCGT
59623 TTTCGCAACTCGAA
1 TTTCGCAACTCGAA
59637 TTTCGCAACTCGAA
1 TTTCGCAACTCGAA
59651 TTT
1 TTT
59654 TTCCACGCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.35
Consensus pattern (14 bp):
TTTCGCAACTCGAA
Found at i:59761 original size:38 final size:37
Alignment explanation
Indices: 59706--59783 Score: 120
Period size: 38 Copynumber: 2.1 Consensus size: 37
59696 ACTCAGTTTT
*
59706 CAAATTCGCAACGCGATTATCTAAATTCGCGTTTTCTC
1 CAAATTCGCAACACGATTATCTAAATTCGCG-TTTCTC
* *
59744 CAAATTCGTAACACGATTCTCTAAATTCGCGTTTCTC
1 CAAATTCGCAACACGATTATCTAAATTCGCGTTTCTC
59781 CAA
1 CAA
59784 TTTTACCAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
37 9 0.24
38 28 0.76
ACGTcount: A:0.28, C:0.27, G:0.12, T:0.33
Consensus pattern (37 bp):
CAAATTCGCAACACGATTATCTAAATTCGCGTTTCTC
Found at i:67174 original size:27 final size:24
Alignment explanation
Indices: 67128--67176 Score: 71
Period size: 27 Copynumber: 1.9 Consensus size: 24
67118 ACTTTTTATC
67128 TTTTCCATCTCTATTTTCTCTTTA
1 TTTTCCATCTCTATTTTCTCTTTA
67152 TTTTCCTATCTTCTCATTTTCTCTT
1 TTTTCC-ATC-TCT-ATTTTCTCTT
67177 CCTCCCTCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 6 0.27
25 3 0.14
26 3 0.14
27 10 0.45
ACGTcount: A:0.10, C:0.27, G:0.00, T:0.63
Consensus pattern (24 bp):
TTTTCCATCTCTATTTTCTCTTTA
Found at i:68836 original size:32 final size:32
Alignment explanation
Indices: 68793--68864 Score: 108
Period size: 32 Copynumber: 2.2 Consensus size: 32
68783 ATCAGTATTG
* *
68793 CATTCAAATAATGCATACCAGAGTTAATCTTG
1 CATTCAGATAATGCATACCAGAGTTAATCTTA
* *
68825 TATTCAGATAATGCATATCAGAGTTAATCTTA
1 CATTCAGATAATGCATACCAGAGTTAATCTTA
68857 CATTCAGA
1 CATTCAGA
68865 CAATATACAG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (32 bp):
CATTCAGATAATGCATACCAGAGTTAATCTTA
Found at i:70949 original size:21 final size:21
Alignment explanation
Indices: 70912--70952 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
70902 CCCTAACATG
*
70912 GGGTATCGGTATCCCTTCATA
1 GGGTATCGATATCCCTTCATA
70933 GGGTATCGATA-CACCTTCAT
1 GGGTATCGATATC-CCTTCAT
70953 TAAATTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.32
Consensus pattern (21 bp):
GGGTATCGATATCCCTTCATA
Found at i:71036 original size:16 final size:18
Alignment explanation
Indices: 71015--71066 Score: 56
Period size: 20 Copynumber: 2.9 Consensus size: 18
71005 TATACTACAG
71015 AGTGTATCGGTACA-T-C
1 AGTGTATCGGTACACTGC
71031 AGTGTAT-GGATACACTGC
1 AGTGTATCGG-TACACTGC
71049 AGGGTGTATCGGTACACT
1 A--GTGTATCGGTACACT
71067 AATTACATTC
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
15 2 0.07
16 11 0.37
17 1 0.03
18 2 0.07
20 12 0.40
21 2 0.07
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (18 bp):
AGTGTATCGGTACACTGC
Found at i:71056 original size:36 final size:36
Alignment explanation
Indices: 70996--71064 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
70986 TGCAGCCAAG
*
70996 GTGTATAGATATACTACAGAGTGTATCGGTACATCA
1 GTGTATAGATACACTACAGAGTGTATCGGTACATCA
* * *
71032 GTGTATGGATACACTGCAGGGTGTATCGGTACA
1 GTGTATAGATACACTACAGAGTGTATCGGTACA
71065 CTAATTACAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (36 bp):
GTGTATAGATACACTACAGAGTGTATCGGTACATCA
Found at i:71427 original size:18 final size:20
Alignment explanation
Indices: 71379--71434 Score: 71
Period size: 18 Copynumber: 2.9 Consensus size: 20
71369 TGTTTAATGA
*
71379 AAAAGATATCAATTGTTAAC
1 AAAAGATACCAATTGTTAAC
71399 AAAAGGATACCAATTGTT-A-
1 AAAA-GATACCAATTGTTAAC
*
71418 AGAAGATACCAATTGTT
1 AAAAGATACCAATTGTT
71435 GGAAAATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 13 0.39
19 3 0.09
20 5 0.15
21 12 0.36
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.29
Consensus pattern (20 bp):
AAAAGATACCAATTGTTAAC
Found at i:74444 original size:21 final size:21
Alignment explanation
Indices: 74418--74458 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
74408 CCATAACATG
*
74418 GGGTATC-GATACCCCTTCATA
1 GGGTATCAG-TACACCTTCATA
74439 GGGTATCAGTACACCTTCAT
1 GGGTATCAGTACACCTTCAT
74459 TAAATTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (21 bp):
GGGTATCAGTACACCTTCATA
Found at i:74560 original size:16 final size:17
Alignment explanation
Indices: 74541--74591 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 17
74531 TATACTGCAG
74541 AGTGTATCGGTACAC-C
1 AGTGTATCGGTACACGC
74557 AGTGTAT-GGATACACTGC
1 AGTGTATCGG-TACAC-GC
74575 AGGGTGTATCGGTACAC
1 A--GTGTATCGGTACAC
74592 TAATTACATT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
15 2 0.07
16 12 0.41
18 2 0.07
20 11 0.38
21 2 0.07
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.25
Consensus pattern (17 bp):
AGTGTATCGGTACACGC
Found at i:74563 original size:36 final size:36
Alignment explanation
Indices: 74522--74591 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
74512 ACATTACAGG
* *
74522 GTGTATGTATATACTGCAGAGTGTATCGGTACACCA
1 GTGTATGGATACACTGCAGAGTGTATCGGTACACCA
*
74558 GTGTATGGATACACTGCAGGGTGTATCGGTACAC
1 GTGTATGGATACACTGCAGAGTGTATCGGTACAC
74592 TAATTACATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.29
Consensus pattern (36 bp):
GTGTATGGATACACTGCAGAGTGTATCGGTACACCA
Found at i:74583 original size:20 final size:20
Alignment explanation
Indices: 74499--74592 Score: 83
Period size: 20 Copynumber: 4.9 Consensus size: 20
74489 CGTTGCACCT
* *
74499 AGGGTGTATGGATACATTAC
1 AGGGTGTATGGATACACTGC
* *
74519 AGGGTGTATGTATATACTGC
1 AGGGTGTATGGATACACTGC
*
74539 AGAGTGTATCGG-TACAC--C
1 AGGGTGTAT-GGATACACTGC
74557 A--GTGTATGGATACACTGC
1 AGGGTGTATGGATACACTGC
74575 AGGGTGTATCGG-TACACT
1 AGGGTGTAT-GGATACACT
74593 AATTACATTC
Statistics
Matches: 60, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
15 2 0.03
16 11 0.18
18 4 0.07
20 40 0.67
21 3 0.05
ACGTcount: A:0.27, C:0.15, G:0.30, T:0.29
Consensus pattern (20 bp):
AGGGTGTATGGATACACTGC
Found at i:74647 original size:20 final size:20
Alignment explanation
Indices: 74622--74683 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
74612 ATAGTCATAT
74622 GTGTATGGATACACTGCAGG
1 GTGTATGGATACACTGCAGG
74642 GTGTATTGG-TACAC--CA--
1 GTGTA-TGGATACACTGCAGG
*
74658 GTGTATGGATACACTGTAGG
1 GTGTATGGATACACTGCAGG
74678 GTGTAT
1 GTGTAT
74684 CCATACACTT
Statistics
Matches: 35, Mismatches: 1, Indels: 12
0.73 0.02 0.25
Matches are distributed among these distances:
15 3 0.09
16 10 0.29
18 3 0.09
20 16 0.46
21 3 0.09
ACGTcount: A:0.24, C:0.13, G:0.32, T:0.31
Consensus pattern (20 bp):
GTGTATGGATACACTGCAGG
Found at i:74670 original size:16 final size:18
Alignment explanation
Indices: 74622--74671 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 18
74612 ATAGTCATAT
74622 GTGTATGGATACACTGCAGG
1 GTGTATGGATACAC-GCA-G
74642 GTGTATTGG-TACAC-CA-
1 GTGTA-TGGATACACGCAG
74658 GTGTATGGATACAC
1 GTGTATGGATACAC
74672 TGTAGGGTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
15 3 0.11
16 10 0.36
18 2 0.07
20 10 0.36
21 3 0.11
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.28
Consensus pattern (18 bp):
GTGTATGGATACACGCAG
Found at i:74691 original size:36 final size:36
Alignment explanation
Indices: 74622--74691 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
74612 ATAGTCATAT
***
74622 GTGTATGGATACACTGCAGGGTGTATTGGTACACCA
1 GTGTATGGATACACTGCAGGGTGTATCCATACACCA
*
74658 GTGTATGGATACACTGTAGGGTGTATCCATACAC
1 GTGTATGGATACACTGCAGGGTGTATCCATACAC
74692 TTTAGCATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.29
Consensus pattern (36 bp):
GTGTATGGATACACTGCAGGGTGTATCCATACACCA
Found at i:78270 original size:2 final size:2
Alignment explanation
Indices: 78263--78290 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
78253 ATAAGATCAA
78263 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
78291 TATCATATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:80045 original size:60 final size:60
Alignment explanation
Indices: 79972--80092 Score: 206
Period size: 60 Copynumber: 2.0 Consensus size: 60
79962 GAGACTAAAA
* * *
79972 TTCTTCCTTGGGATTGAGGTTGCTCACTCTAAGAAGGAAGTTTTCAGTTCTCAACAAAGT
1 TTCTTCCTTGGGATTGAGGCTGCTCAATCCAAGAAGGAAGTTTTCAGTTCTCAACAAAGT
*
80032 TTCTTCCTTGGGATTGAGGCTGCTCAATCCAAGAAGGAAGTTTTCATTTCTCAACAAAGT
1 TTCTTCCTTGGGATTGAGGCTGCTCAATCCAAGAAGGAAGTTTTCAGTTCTCAACAAAGT
80092 T
1 T
80093 ATGTACTCGA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.35
Consensus pattern (60 bp):
TTCTTCCTTGGGATTGAGGCTGCTCAATCCAAGAAGGAAGTTTTCAGTTCTCAACAAAGT
Done.