Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008460.1 Hibiscus syriacus cultivar Beakdansim tig00111273_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: 2854393
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 15
Found at i:1260 original size:37 final size:36
Alignment explanation
Indices: 1219--1308 Score: 112
Period size: 35 Copynumber: 2.5 Consensus size: 36
1209 TAATTTTCTT
1219 AACTATATATTATATAGTTTTCAAAAAATATTTTAA-A
1 AACTATATATTATATA-TTTTC-AAAAATATTTTAATA
* *
1256 AACTATATAATATATATTTTCAAAAATGTTTTAATA
1 AACTATATATTATATATTTTCAAAAATATTTTAATA
*
1292 TA-TATATATATATATAT
1 AACTATATAT-TATATAT
1309 ATATATATAT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
35 18 0.38
36 14 0.30
37 15 0.32
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (36 bp):
AACTATATATTATATATTTTCAAAAATATTTTAATA
Found at i:1296 original size:2 final size:2
Alignment explanation
Indices: 1289--1324 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1279 AAATGTTTTA
1289 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1325 CGTAGTTTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1298 original size:35 final size:36
Alignment explanation
Indices: 824--1308 Score: 236
Period size: 38 Copynumber: 13.4 Consensus size: 36
814 TATAGTATAC
**
824 ACTATATAATATATA-TTTC-AAAAATATTTTTTAA
1 ACTATATAATATATATTTTCAAAAAATATTTTAAAA
* *
858 ATTATAT-AT-TATATTTT-AAAAAAT-TTTTCAAA
1 ACTATATAATATATATTTTCAAAAAATATTTTAAAA
*
890 ACTATATATTATATAGTTTTC-AAAAATGA-TTTAAAA
1 ACTATATAATATATA-TTTTCAAAAAAT-ATTTTAAAA
* *
926 A-TAT-T-ATATA-AGTTT--AAAAATATTTTTTAAA
1 ACTATATAATATATATTTTCAAAAAATA-TTTTAAAA
* * * *
957 ACTATATATTATATAATTTCTCAAAAAGTTTTTTTAAA
1 ACTATATAATATAT-ATTT-TCAAAAAATATTTTAAAA
*
995 ACTATATATTATATAAGTTTTTC--AAAATACTTTCT-AAA
1 ACTATATAATATAT-A--TTTTCAAAAAATA-TTT-TAAAA
* *
1033 ACTATATATTATATATATTTTTTTCAAAATGATTTTTTAAAA
1 ACTATATA--ATATATA---TTTTCAAAA-AATATTTTAAAA
* *
1075 ACCT-TATAATATATATATTTTCAAAATGATTTTTTAAAA
1 A-CTATAT-A-ATATATATTTTCAAAA-AATATTTTAAAA
* *
1114 ACTATATAATATATATTTTCAAAATGAGTTTTTTAAAA
1 ACTATATAATATATATTTTCAAAA--AATATTTTAAAA
*** * *
1152 ACTATATAATATATATATATGATTTCAAAATGTTTTCAAA
1 ACTATATAATATATAT-T-T--TCAAAAAATATTTTAAAA
* * *
1192 AC--TAT-ATATATA--TT-ATATAAT-TTTCT--TA
1 ACTATATAATATATATTTTCAAAAAATATTT-TAAAA
*
1220 ACTATATATTATATAGTTTTCAAAAAATATTTTAAAA
1 ACTATATAATATATA-TTTTCAAAAAATATTTTAAAA
* *
1257 ACTATATAATATATATTTTC-AAAAATGTTTTAATAT
1 ACTATATAATATATATTTTCAAAAAATATTTTAA-AA
1293 A-TATATATATATATAT
1 ACTATATA-ATATATAT
1309 ATATATATAT
Statistics
Matches: 362, Mismatches: 39, Indels: 98
0.73 0.08 0.20
Matches are distributed among these distances:
28 3 0.01
29 4 0.01
30 14 0.04
31 17 0.05
32 20 0.06
33 18 0.05
34 17 0.05
35 37 0.10
36 28 0.08
37 43 0.12
38 70 0.19
39 36 0.10
40 26 0.07
41 1 0.00
42 23 0.06
43 5 0.01
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.47
Consensus pattern (36 bp):
ACTATATAATATATATTTTCAAAAAATATTTTAAAA
Found at i:2860 original size:33 final size:33
Alignment explanation
Indices: 2789--2861 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
2779 CGCTCGGCTT
* *
2789 CCCTCGGATTCCCATGCATAGCTCGCTCAGTTG
1 CCCTCGGATGCCCATGCATAGCTCGCTCAGATG
* *
2822 CCCTCGGATGCCC-TCGCATAGCTCGTTCGGATG
1 CCCTCGGATGCCCAT-GCATAGCTCGCTCAGATG
*
2855 GCCTCGG
1 CCCTCGG
2862 TCGGATGGCC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
32 1 0.03
33 33 0.97
ACGTcount: A:0.12, C:0.37, G:0.26, T:0.25
Consensus pattern (33 bp):
CCCTCGGATGCCCATGCATAGCTCGCTCAGATG
Found at i:2865 original size:14 final size:14
Alignment explanation
Indices: 2843--2875 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
2833 CCTCGCATAG
*
2843 CTCGTTCGGATGGC
1 CTCGGTCGGATGGC
2857 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
2871 CTCGG
1 CTCGG
2876 ATGCCCAGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.30, G:0.39, T:0.24
Consensus pattern (14 bp):
CTCGGTCGGATGGC
Found at i:3330 original size:29 final size:29
Alignment explanation
Indices: 3297--3352 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
3287 TCCCAACACA
*
3297 TAGGTCACCATGCCCTCCGGGCGACCTTG
1 TAGGTCACCATGCACTCCGGGCGACCTTG
*
3326 TAGGTCGCCATGCACTCCGGGCGACCT
1 TAGGTCACCATGCACTCCGGGCGACCT
3353 ACCCTCGCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.14, C:0.38, G:0.29, T:0.20
Consensus pattern (29 bp):
TAGGTCACCATGCACTCCGGGCGACCTTG
Found at i:3375 original size:10 final size:10
Alignment explanation
Indices: 3360--3446 Score: 57
Period size: 10 Copynumber: 8.1 Consensus size: 10
3350 CCTACCCTCG
3360 CTCGGATGCC
1 CTCGGATGCC
*
3370 CTCGGATTCC
1 CTCGGATGCC
* *
3380 CTCGCATAGCTTG
1 CTCGGAT-GC--C
*
3393 CTCGGCTGCC
1 CTCGGATGCC
3403 CTCGGATGCC
1 CTCGGATGCC
*
3413 CTCGCATAGCTC
1 CTCGGAT-GC-C
* *
3425 GTTCGGATGGC
1 -CTCGGATGCC
3436 CTCGGATGCC
1 CTCGGATGCC
3446 C
1 C
3447 AGCGTGTTGG
Statistics
Matches: 57, Mismatches: 14, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
10 39 0.68
11 4 0.07
12 4 0.07
13 10 0.18
ACGTcount: A:0.10, C:0.38, G:0.28, T:0.24
Consensus pattern (10 bp):
CTCGGATGCC
Found at i:3403 original size:33 final size:33
Alignment explanation
Indices: 3356--3446 Score: 137
Period size: 33 Copynumber: 2.8 Consensus size: 33
3346 GCGACCTACC
*
3356 CTCGCTCGGATGCCCTCGGATTCCCTCGCATAG
1 CTCGCTCGGATGCCCTCGGATGCCCTCGCATAG
* *
3389 CTTGCTCGGCTGCCCTCGGATGCCCTCGCATAG
1 CTCGCTCGGATGCCCTCGGATGCCCTCGCATAG
* *
3422 CTCGTTCGGATGGCCTCGGATGCCC
1 CTCGCTCGGATGCCCTCGGATGCCC
3447 AGCGTGTTGG
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.10, C:0.38, G:0.27, T:0.24
Consensus pattern (33 bp):
CTCGCTCGGATGCCCTCGGATGCCCTCGCATAG
Found at i:3641 original size:31 final size:30
Alignment explanation
Indices: 3586--3646 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
3576 CTAGGGAATG
* * *
3586 CATTATCTCGTAAATTAATTTTTTTCAAAA
1 CATTATCTCGAAAATTAATCTTTTTAAAAA
*
3616 CATTATCTCGAAAAATTTATCTTTTTAAAAA
1 CATTATCTCG-AAAATTAATCTTTTTAAAAA
3647 ACGGTTGAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 10 0.38
31 16 0.62
ACGTcount: A:0.39, C:0.13, G:0.03, T:0.44
Consensus pattern (30 bp):
CATTATCTCGAAAATTAATCTTTTTAAAAA
Found at i:3648 original size:32 final size:30
Alignment explanation
Indices: 3586--3648 Score: 72
Period size: 30 Copynumber: 2.0 Consensus size: 30
3576 CTAGGGAATG
* **
3586 CATTATCTCGTAAATTAATTTTTTTCAAAA
1 CATTATCTCGAAAATTAATTTTTTAAAAAA
*
3616 CATTATCTCGAAAAATTTATCTTTTTAAAAAA
1 CATTATCTCG-AAAATTAAT-TTTTTAAAAAA
3648 C
1 C
3649 GGTTGAATGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 10 0.37
31 7 0.26
32 10 0.37
ACGTcount: A:0.40, C:0.14, G:0.03, T:0.43
Consensus pattern (30 bp):
CATTATCTCGAAAATTAATTTTTTAAAAAA
Found at i:12063 original size:22 final size:23
Alignment explanation
Indices: 12013--12076 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
12003 TCAGTTCCCT
12013 AAAGTGGGGAATCGATTCCCATTC
1 AAAG-GGGGAATCGATTCCCATTC
*
12037 AAAGGGGGAATCGATTCCCCTTC
1 AAAGGGGGAATCGATTCCCATTC
*
12060 -AAGGGGGTATCGATTCC
1 AAAGGGGGAATCGATTCC
12077 TCATGCACTA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 16 0.42
23 18 0.47
24 4 0.11
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.23
Consensus pattern (23 bp):
AAAGGGGGAATCGATTCCCATTC
Found at i:17653 original size:23 final size:23
Alignment explanation
Indices: 17623--17672 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
17613 TATATGGAAC
17623 TGCAATTCTACGTGGCACTTCAG
1 TGCAATTCTACGTGGCACTTCAG
17646 TGCAATTCTACGTGGCACTTCAG
1 TGCAATTCTACGTGGCACTTCAG
17669 TGCA
1 TGCA
17673 TTTATACGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.30
Consensus pattern (23 bp):
TGCAATTCTACGTGGCACTTCAG
Found at i:17680 original size:23 final size:23
Alignment explanation
Indices: 17623--17680 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
17613 TATATGGAAC
*
17623 TGCAATTCTACGTGGCACTTCAG
1 TGCAATTATACGTGGCACTTCAG
*
17646 TGCAATTCTACGTGGCACTTCAG
1 TGCAATTATACGTGGCACTTCAG
*
17669 TGCATTTATACG
1 TGCAATTATACG
17681 AGCTATAGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (23 bp):
TGCAATTATACGTGGCACTTCAG
Found at i:21199 original size:20 final size:20
Alignment explanation
Indices: 21174--21211 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
21164 CACATGTTAA
21174 AGAATGTATCGATGCACTGT
1 AGAATGTATCGATGCACTGT
21194 AGAATGTATCGATGCACT
1 AGAATGTATCGATGCACT
21212 TCAAGGGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.29
Consensus pattern (20 bp):
AGAATGTATCGATGCACTGT
Found at i:22814 original size:23 final size:23
Alignment explanation
Indices: 22769--22814 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
22759 ACATTTTATA
* * *
22769 TGGCACTTTGGTGTAATTCTACG
1 TGGCACTTCGGTGCAATTATACG
*
22792 TGGCACTTCGGTGCATTTATACG
1 TGGCACTTCGGTGCAATTATACG
22815 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.37
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTATACG
Found at i:24733 original size:23 final size:23
Alignment explanation
Indices: 24707--24753 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
24697 GAGCCAAAAC
* *
24707 CTTTTAGGGGGTATCGGTTCCCT
1 CTTTTAGGGGGAATCGGTACCCT
*
24730 C-TTTGGGGGGAATCGGTACCCT
1 CTTTTAGGGGGAATCGGTACCCT
24752 CT
1 CT
24754 GGACAATCTG
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.11, C:0.23, G:0.32, T:0.34
Consensus pattern (23 bp):
CTTTTAGGGGGAATCGGTACCCT
Found at i:31757 original size:57 final size:56
Alignment explanation
Indices: 31669--31778 Score: 166
Period size: 57 Copynumber: 1.9 Consensus size: 56
31659 TCTTTCTTGG
* * *
31669 CTTTATACCTTTAGCACCAAGCATGCTTAATTTTTTGGTTCATGTACTTGAAGAACT
1 CTTTATACCTTTAGCACCAAGCATGCTTAA-TTGTAGGTGCATGTACTTGAAGAACT
* *
31726 CTTTATACCTTTAGCACCGAGCTTGCTTAATTGTAGGTGCATGTACTTGAAGA
1 CTTTATACCTTTAGCACCAAGCATGCTTAATTGTAGGTGCATGTACTTGAAGA
31779 GTTGGCTTTA
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
56 20 0.42
57 28 0.58
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.38
Consensus pattern (56 bp):
CTTTATACCTTTAGCACCAAGCATGCTTAATTGTAGGTGCATGTACTTGAAGAACT
Found at i:33492 original size:37 final size:37
Alignment explanation
Indices: 33442--33516 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
33432 ACAATTATAC
33442 ATAAAATAAGGATGTTTTAAATCTTAATGTTGGAACT
1 ATAAAATAAGGATGTTTTAAATCTTAATGTTGGAACT
* *
33479 ATAAAATACGGATGTTTTAAATCTTAATGTTTGAACT
1 ATAAAATAAGGATGTTTTAAATCTTAATGTTGGAACT
33516 A
1 A
33517 ATGGACAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.39
Consensus pattern (37 bp):
ATAAAATAAGGATGTTTTAAATCTTAATGTTGGAACT
Found at i:35487 original size:64 final size:65
Alignment explanation
Indices: 35386--35516 Score: 192
Period size: 64 Copynumber: 2.0 Consensus size: 65
35376 AATACGCATA
* * * * *
35386 GTACACCATCACCAGGTGATTGGTTCAAGTTGTCTTATATTCAT-GTCTCTTTTAGCAATTTGTT
1 GTACACCAGCACCAGGTGATTGGCTCAAGTTGTCTTATAGTCATAATCCCTTTTAGCAATTTGTT
* *
35450 GTACACCAGCACTAGGTGATTTGCTCAAGTTGTCTTATAGTCATAATCCCTTTTAGCAATTTGTT
1 GTACACCAGCACCAGGTGATTGGCTCAAGTTGTCTTATAGTCATAATCCCTTTTAGCAATTTGTT
35515 GT
1 GT
35517 TTTTGGATCT
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
64 39 0.66
65 20 0.34
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.40
Consensus pattern (65 bp):
GTACACCAGCACCAGGTGATTGGCTCAAGTTGTCTTATAGTCATAATCCCTTTTAGCAATTTGTT
Found at i:43628 original size:2 final size:2
Alignment explanation
Indices: 43621--43645 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
43611 GTAGACTGAA
43621 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
43646 GAATGAAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:44023 original size:22 final size:22
Alignment explanation
Indices: 43984--44047 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 22
43974 CCTTTTTAAA
*
43984 TGTAAATTTTTTTATTTTTACT
1 TGTAAATTTTATTATTTTTACT
*
44006 TGTAAATTTTAATT-TTTTTAGT
1 TGTAAATTTT-ATTATTTTTACT
* **
44028 T-TAATTTTTAGCATTTTTAC
1 TGTAAATTTTATTATTTTTAC
44048 AATGTAATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
20 1 0.03
21 13 0.38
22 18 0.53
23 2 0.06
ACGTcount: A:0.25, C:0.05, G:0.06, T:0.64
Consensus pattern (22 bp):
TGTAAATTTTATTATTTTTACT
Found at i:46037 original size:80 final size:80
Alignment explanation
Indices: 45901--46196 Score: 443
Period size: 80 Copynumber: 3.7 Consensus size: 80
45891 CAGCAAAAAG
* * *
45901 GGGAGCCAACCTAAGGATATACCTT-GGATCTACCCAAGGATATCCTTAGATCCGTAGGGTTACC
1 GGGAACCAACCTAAGGATATACCTTGGGACCTACCCAA-GATATCCTTAGGTCCGTAGGGTTACC
*
45965 TTAAGCACACAGCT-AA
65 TTATGCACACAG-TAAA
* * * *
45981 GGGAACCAACCTAAAGATATACCTTGGGGCCTACCGAAGATATCCTTAGGTTCGTAGGGTTACCT
1 GGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
46046 TATGCACACAGTAAA
66 TATGCACACAGTAAA
* *
46061 GGGAACAAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTTCGTAGGGTTACCT
1 GGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
*
46126 TATGCACACAATAAA
66 TATGCACACAGTAAA
* *
46141 GGGAACTAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTCCGTA
1 GGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTA
46197 AGGACTTATA
Statistics
Matches: 198, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
79 1 0.01
80 188 0.95
81 9 0.05
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.23
Consensus pattern (80 bp):
GGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
TATGCACACAGTAAA
Found at i:47868 original size:17 final size:18
Alignment explanation
Indices: 47835--47868 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
47825 TCCATTCTTT
*
47835 CTTATTATTTAATTCCAA
1 CTTATCATTTAATTCCAA
47853 CTTATCATTT-ATTCCA
1 CTTATCATTTAATTCCA
47869 GACCTTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (18 bp):
CTTATCATTTAATTCCAA
Found at i:48325 original size:17 final size:18
Alignment explanation
Indices: 48293--48339 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
48283 AACTAACATT
*
48293 TCTTATGCACATCAATATA
1 TCTTAT-CAGATCAATATA
48312 T-TTATCAGATCAATATA
1 TCTTATCAGATCAATATA
*
48329 TCTTTTCAGAT
1 TCTTATCAGAT
48340 TTATTAATCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 12 0.48
18 12 0.48
19 1 0.04
ACGTcount: A:0.34, C:0.17, G:0.06, T:0.43
Consensus pattern (18 bp):
TCTTATCAGATCAATATA
Found at i:49264 original size:22 final size:23
Alignment explanation
Indices: 49232--49280 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
49222 CCACATTCTA
49232 CAAATATTTAC-CAAACTAACACC
1 CAAATATTTACACAAA-TAACACC
*
49255 CAAAT-TTTACACAAATAGCACC
1 CAAATATTTACACAAATAACACC
49277 CAAA
1 CAAA
49281 CAGAAATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 15 0.62
23 9 0.38
ACGTcount: A:0.49, C:0.29, G:0.02, T:0.20
Consensus pattern (23 bp):
CAAATATTTACACAAATAACACC
Found at i:52043 original size:9 final size:9
Alignment explanation
Indices: 52029--52069 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
52019 TTCACCCCAG
52029 AATTTTATA
1 AATTTTATA
52038 AATTTTAT-
1 AATTTTATA
*
52046 ACTTTCTA-A
1 AATTT-TATA
52055 AATTTTATA
1 AATTTTATA
52064 AATTTT
1 AATTTT
52070 CGCATCTGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
8 6 0.22
9 21 0.78
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (9 bp):
AATTTTATA
Found at i:53448 original size:2 final size:2
Alignment explanation
Indices: 53441--53474 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
53431 ATCTAAGAAG
53441 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53475 GAACTGTGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54371 original size:16 final size:17
Alignment explanation
Indices: 54345--54378 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
54335 TGAATACTCG
54345 ACGAGCGAGCATCATTA
1 ACGAGCGAGCATCATTA
54362 ACGA-CGAGCATCATTA
1 ACGAGCGAGCATCATTA
54378 A
1 A
54379 AGAACACCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.18
Consensus pattern (17 bp):
ACGAGCGAGCATCATTA
Found at i:56071 original size:30 final size:29
Alignment explanation
Indices: 55986--56170 Score: 284
Period size: 29 Copynumber: 6.3 Consensus size: 29
55976 AAAAATTCTT
**
55986 AAAATGTCACCTTTTTCAAAATAATTCTT
1 AAAATGTCACCTTTTTCAAAATAATTCCC
*
56015 AGAATGTCACCTTTTT-AAATATAATTCCC
1 AAAATGTCACCTTTTTCAAA-ATAATTCCC
*
56044 AAAATGTCACATTTTTCAAAAATAATTCCC
1 AAAATGTCACCTTTTTC-AAAATAATTCCC
56074 AAAATGTCACCTTTTTTCAAAATAATTCCC
1 AAAATGTCACC-TTTTTCAAAATAATTCCC
*
56104 AAAATATCACC-TTTTCAAAATAATTCCC
1 AAAATGTCACCTTTTTCAAAATAATTCCC
56132 AAAATGTCACCTTTTTCAAAATAATTCCC
1 AAAATGTCACCTTTTTCAAAATAATTCCC
56161 AAAATGTCAC
1 AAAATGTCAC
56171 TGGGTCGGGT
Statistics
Matches: 143, Mismatches: 8, Indels: 10
0.89 0.05 0.06
Matches are distributed among these distances:
28 30 0.21
29 63 0.44
30 41 0.29
31 9 0.06
ACGTcount: A:0.39, C:0.22, G:0.04, T:0.35
Consensus pattern (29 bp):
AAAATGTCACCTTTTTCAAAATAATTCCC
Found at i:63473 original size:29 final size:29
Alignment explanation
Indices: 63438--63630 Score: 262
Period size: 29 Copynumber: 6.6 Consensus size: 29
63428 CACATTCAAA
63438 AATTCCCAAAATGTCACCTTTTTCAAAAT
1 AATTCCCAAAATGTCACCTTTTTCAAAAT
* * * *
63467 AATTCCCATAATGTCACTTTTTTTAATAT
1 AATTCCCAAAATGTCACCTTTTTCAAAAT
* *
63496 AATTCCCAAAATGTTACATTTTTCAAAAAT
1 AATTCCCAAAATGTCACCTTTTTC-AAAAT
* *
63526 AATTCCCAAAATGTTAACTTTTTTCAAAAT
1 AATTCCCAAAATG-TCACCTTTTTCAAAAT
*
63556 AATTCCCAAAATGTCA-CATTTTCAAAAT
1 AATTCCCAAAATGTCACCTTTTTCAAAAT
63584 AATTCCCAAAATGTCACCTTTTTCAAAAT
1 AATTCCCAAAATGTCACCTTTTTCAAAAT
* *
63613 AATTCCTAAAATATCACC
1 AATTCCCAAAATGTCACC
63631 GGGTCGGGTC
Statistics
Matches: 144, Mismatches: 17, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
28 26 0.18
29 74 0.51
30 35 0.24
31 9 0.06
ACGTcount: A:0.39, C:0.21, G:0.03, T:0.37
Consensus pattern (29 bp):
AATTCCCAAAATGTCACCTTTTTCAAAAT
Found at i:63736 original size:20 final size:19
Alignment explanation
Indices: 63667--63726 Score: 75
Period size: 19 Copynumber: 3.2 Consensus size: 19
63657 CAACGGGTCG
* **
63667 GGTCAGACCGATTTGGACC
1 GGTCAAACCGATTCAGACC
* *
63686 GGTCAAATCAATTCAGACC
1 GGTCAAACCGATTCAGACC
63705 GGTCAAACCGATTCAGACC
1 GGTCAAACCGATTCAGACC
63724 GGT
1 GGT
63727 TTGAACCGAT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.28, C:0.27, G:0.25, T:0.20
Consensus pattern (19 bp):
GGTCAAACCGATTCAGACC
Found at i:64438 original size:10 final size:10
Alignment explanation
Indices: 64423--64447 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
64413 TTTAATTTAG
64423 TCACCAAATT
1 TCACCAAATT
64433 TCACCAAATT
1 TCACCAAATT
64443 TCACC
1 TCACC
64448 GATTTAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.36, G:0.00, T:0.28
Consensus pattern (10 bp):
TCACCAAATT
Found at i:66796 original size:2 final size:2
Alignment explanation
Indices: 66789--66840 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
66779 TCTATTTTAA
66789 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
66831 AT AT AT AT AT
1 AT AT AT AT AT
66841 GAACTACCAC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:67180 original size:60 final size:60
Alignment explanation
Indices: 67094--67381 Score: 389
Period size: 60 Copynumber: 4.8 Consensus size: 60
67084 GCATGTTTTA
* * * * * *
67094 ATCTTCTATATTGGACTCCTATATCTTAGTGGTCTACGATAAGTCCTTATGGATGCATGC
1 ATCTTCCATATTGGACTCCTAGATCTTAGTGGTCTAGGGTAAGTCCTTATGGATACATGT
*
67154 ATCTTCCATATTGGACTCCTAGATCTTAGTGGTCTAGGGTAAGTCCTTATGAATACATGT
1 ATCTTCCATATTGGACTCCTAGATCTTAGTGGTCTAGGGTAAGTCCTTATGGATACATGT
* * * ** *
67214 ATCTTTCATATTGGACTCCAATATCTTAGTGGTCTACTGTAAGTCCTTATGGATGCATGT
1 ATCTTCCATATTGGACTCCTAGATCTTAGTGGTCTAGGGTAAGTCCTTATGGATACATGT
** *
67274 ATCTTCCATATTGGACT-CTAGATCTTAGTTATCTAGGTTAAGTCCTTATGGATACATGT
1 ATCTTCCATATTGGACTCCTAGATCTTAGTGGTCTAGGGTAAGTCCTTATGGATACATGT
* * * *
67333 ATCTTCCAAAATAGACTCCTAGATCTTAGTGGTCAAGGGTAAGTCCTTA
1 ATCTTCCATATTGGACTCCTAGATCTTAGTGGTCTAGGGTAAGTCCTTA
67382 GTGTACGTGT
Statistics
Matches: 197, Mismatches: 30, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
59 48 0.24
60 149 0.76
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.38
Consensus pattern (60 bp):
ATCTTCCATATTGGACTCCTAGATCTTAGTGGTCTAGGGTAAGTCCTTATGGATACATGT
Found at i:67360 original size:119 final size:119
Alignment explanation
Indices: 67107--67381 Score: 399
Period size: 119 Copynumber: 2.3 Consensus size: 119
67097 TTCTATATTG
67107 GACTCCTATATCTTAGTGGTCTACGATAAGTCCTTATGGATGCATGCATCTTCCATATTGGACTC
1 GACTCCTATATCTTAGTGGTCTACG-TAAGTCCTTATGGATGCATGCATCTTCCATATTGGACTC
* * * * *
67172 CTAGATCTTAGTGGTCTAGGGTAAGTCCTTATGAATACATGTATCTTTCATATTG
65 CTAGATCTTAGTGATCTAGGGTAAGTCCTTATGAATACATGTATCTTCCAAAATA
* *
67227 GACTCCAATATCTTAGTGGTCTACTGTAAGTCCTTATGGATGCATGTATCTTCCATATTGGACT-
1 GACTCCTATATCTTAGTGGTCTAC-GTAAGTCCTTATGGATGCATGCATCTTCCATATTGGACTC
* * *
67291 CTAGATCTTAGTTATCTAGGTTAAGTCCTTATGGATACATGTATCTTCCAAAATA
65 CTAGATCTTAGTGATCTAGGGTAAGTCCTTATGAATACATGTATCTTCCAAAATA
* * *
67346 GACTCCTAGATCTTAGTGGTCAAGGGTAAGTCCTTA
1 GACTCCTATATCTTAGTGGTCTA-CGTAAGTCCTTA
67382 GTGTACGTGT
Statistics
Matches: 139, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
119 78 0.56
120 60 0.43
121 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (119 bp):
GACTCCTATATCTTAGTGGTCTACGTAAGTCCTTATGGATGCATGCATCTTCCATATTGGACTCC
TAGATCTTAGTGATCTAGGGTAAGTCCTTATGAATACATGTATCTTCCAAAATA
Found at i:69057 original size:2 final size:2
Alignment explanation
Indices: 69052--69086 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
69042 GTTATATAGT
69052 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
69087 TTAGCCCATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:71902 original size:122 final size:122
Alignment explanation
Indices: 71685--71931 Score: 494
Period size: 122 Copynumber: 2.0 Consensus size: 122
71675 CAAAATGAGT
71685 TTTGTGGGGTTTATAAGAATTTATGGATTTTTATATCTTTTTTGGTAGATTTGAGTTATATGGGG
1 TTTGTGGGGTTTATAAGAATTTATGGATTTTTATATCTTTTTTGGTAGATTTGAGTTATATGGGG
71750 TGTATTTAATTTGTTTTGAGCATCTAGTTGAGTTAGTAATTTATTTTTTTTATCTTG
66 TGTATTTAATTTGTTTTGAGCATCTAGTTGAGTTAGTAATTTATTTTTTTTATCTTG
71807 TTTGTGGGGTTTATAAGAATTTATGGATTTTTATATCTTTTTTGGTAGATTTGAGTTATATGGGG
1 TTTGTGGGGTTTATAAGAATTTATGGATTTTTATATCTTTTTTGGTAGATTTGAGTTATATGGGG
71872 TGTATTTAATTTGTTTTGAGCATCTAGTTGAGTTAGTAATTTATTTTTTTTATCTTG
66 TGTATTTAATTTGTTTTGAGCATCTAGTTGAGTTAGTAATTTATTTTTTTTATCTTG
71929 TTT
1 TTT
71932 AGTAAAAGAT
Statistics
Matches: 125, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
122 125 1.00
ACGTcount: A:0.21, C:0.03, G:0.21, T:0.55
Consensus pattern (122 bp):
TTTGTGGGGTTTATAAGAATTTATGGATTTTTATATCTTTTTTGGTAGATTTGAGTTATATGGGG
TGTATTTAATTTGTTTTGAGCATCTAGTTGAGTTAGTAATTTATTTTTTTTATCTTG
Found at i:74450 original size:24 final size:25
Alignment explanation
Indices: 74386--74443 Score: 84
Period size: 24 Copynumber: 2.4 Consensus size: 25
74376 AATTTGGATA
*
74386 ATTTATTTCAAA-TAAATTAAAGTT
1 ATTTTTTTCAAATTAAATTAAAGTT
74410 ATTTTTTTCAAATTAAA-TAAAGTT
1 ATTTTTTTCAAATTAAATTAAAGTT
*
74434 TTTTTTTTCA
1 ATTTTTTTCA
74444 TTCTAAACTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
24 27 0.87
25 4 0.13
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.53
Consensus pattern (25 bp):
ATTTTTTTCAAATTAAATTAAAGTT
Found at i:76677 original size:9 final size:9
Alignment explanation
Indices: 76659--76688 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
76649 CAGCGATTCT
*
76659 CGATTGAAC
1 CGATTAAAC
76668 CGATTAAAC
1 CGATTAAAC
76677 CGATTAAAC
1 CGATTAAAC
76686 CGA
1 CGA
76689 CCGATCCGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.20
Consensus pattern (9 bp):
CGATTAAAC
Found at i:77837 original size:487 final size:486
Alignment explanation
Indices: 76920--77889 Score: 1450
Period size: 487 Copynumber: 2.0 Consensus size: 486
76910 GTAATTCAAA
* * ** *
76920 TTTTTATGGGTAAAGTATACAAATTGTCCTTATCATAGATTTATGTTTTATTAAGTTATCTGATT
1 TTTTTATGGGTAAAGTATACAAATTGTCCTTATAATAGATTTATGCTTTATTAAGTTATCAAACT
* * *
76985 ATTAAAAATTATAAATAATTCTTTAATTTTAAGGCGTTGTTTTGTTGAATTTTTTGTCTATTAAA
66 ACTAAAAATTATAAATAATTCTTTAATTTTAAGGCGTTGTTTTGTTGAATTTATTGACTATTAAA
* * * *
77050 ATTTACAAAATTGTCATTTGACTATTCGTATATTTTTTAAACTTGTCTTTTTACGTTAAAAATTT
131 AGTTACAAAATTGTCATTTGAATATTCG-ATATATTTTAAACTCGTCTTTTTACGTTAAAAATTT
* * *
77115 TACAACCATTTGAGCTGCATGTCGAACTAGTGCTTGAAATAATATGTTGTTGAGTCAGTTCTTAA
195 TACAACCATTTGAGCTACATGTCGAACTAGTGCTTGAAATAATATGTCGTTGAGTCAGTTCCTAA
* * * * *
77180 AAGCTATGGTGGTGCCATTAGAAATCATTAAAATATAATTTTACCAAATCCTAATAAATATGTTG
260 AAGCTACGGTGGTGCCACTAGAAATCATTAAAATATAATTTCACCAAATCCTAATAAACATGTTA
* ** * * * * *
77245 ACGTTTAGTTTAGACGACTGTCAATTTTTAGCAAAAAATGACGAGTTTGGTACATATGCAGGTGA
325 ACGTTTAGCTTAGACGACTACCAATTTTTAACAAAAAAAGACAAGTTTAGAACATATGCAGGTGA
* * *
77310 TGATTTTGCAATTTTTAATTGTCGAGTGAGGCAGAAAATGACATCCTATAGTTAGGAGATTATCT
390 TGATTTTGCAATTTTTAATTGTCGAGTGAGGCACAAAATGACATCCTATAATTAGGAGAATATCT
77375 TGTAAATTTTAATAATCGATGAACTTAATAAT
455 TGTAAATTTTAATAATCGATGAACTTAATAAT
77407 TTTTTATGGGTAAAGTATACAAATTGTCCTTGGATAATAGATCTT-TGCTTTATTAAGTTATCAA
1 TTTTTATGGGTAAAGTATACAAATTGTCCTT--ATAATAGAT-TTATGCTTTATTAAGTTATCAA
* *
77471 ACTACTAAAAGTTATAAATAA-TCATTTGATTTTAAGGCGTTGTTTTGTTGAATCTTATT-ACTA
63 ACTACTAAAAATTATAAATAATTC-TTTAATTTTAAGGCGTTGTTTTGTTGAAT-TTATTGACTA
*
77534 TTAAAAGTTACAAAA-TGATCATTTGAATGTTC-ATATATTTTAAACTCGTCTTTTTACGTT-AA
126 TTAAAAGTTACAAAATTG-TCATTTGAATATTCGATATATTTTAAACTCGTCTTTTTACGTTAAA
* *
77596 AATTTTACGACCATTTGAGCTATATGTCGAACTAGTGCTTGAAAATAATATGTCGTTGAGTCAGT
190 AATTTTACAACCATTTGAGCTACATGTCGAACTAGTGCTTG-AAATAATATGTCGTTGAGTCAGT
*
77661 TCCTAAAAGTTACGGTGGTGCCACTAGAAATCATTAAAATATAATTTCACCAAATCCTAATAAAC
254 TCCTAAAAGCTACGGTGGTGCCACTAGAAATCATTAAAATATAATTTCACCAAATCCTAATAAAC
77726 ATGTTAACGTTTAGCTTAGACGACTACCAATTTTTAACAAAAAAAGACAAGTTTAGAACATATGC
319 ATGTTAACGTTTAGCTTAGACGACTACCAATTTTTAACAAAAAAAGACAAGTTTAGAACATATGC
*
77791 AGGT-ACTGATTTTGCAATTTTTAATTGTCGAGTGAGGCACAAAATGACATCTTATAATTAGGAG
384 AGGTGA-TGATTTTGCAATTTTTAATTGTCGAGTGAGGCACAAAATGACATCCTATAATTAGGAG
* *
77855 AATATCTTGTAACTTTTAATAATCGATGGACTTAA
448 AATATCTTGTAAATTTTAATAATCGATGAACTTAA
77890 CAAAGCAATG
Statistics
Matches: 435, Mismatches: 40, Indels: 16
0.89 0.08 0.03
Matches are distributed among these distances:
486 41 0.09
487 285 0.66
488 4 0.01
489 99 0.23
490 6 0.01
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (486 bp):
TTTTTATGGGTAAAGTATACAAATTGTCCTTATAATAGATTTATGCTTTATTAAGTTATCAAACT
ACTAAAAATTATAAATAATTCTTTAATTTTAAGGCGTTGTTTTGTTGAATTTATTGACTATTAAA
AGTTACAAAATTGTCATTTGAATATTCGATATATTTTAAACTCGTCTTTTTACGTTAAAAATTTT
ACAACCATTTGAGCTACATGTCGAACTAGTGCTTGAAATAATATGTCGTTGAGTCAGTTCCTAAA
AGCTACGGTGGTGCCACTAGAAATCATTAAAATATAATTTCACCAAATCCTAATAAACATGTTAA
CGTTTAGCTTAGACGACTACCAATTTTTAACAAAAAAAGACAAGTTTAGAACATATGCAGGTGAT
GATTTTGCAATTTTTAATTGTCGAGTGAGGCACAAAATGACATCCTATAATTAGGAGAATATCTT
GTAAATTTTAATAATCGATGAACTTAATAAT
Found at i:79385 original size:11 final size:12
Alignment explanation
Indices: 79369--79399 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
79359 ATAGACAAAT
79369 ACCTAACTC-TC
1 ACCTAACTCTTC
79380 ACCTAACTCTTC
1 ACCTAACTCTTC
79392 ACCTAACT
1 ACCTAACT
79400 AAATTGATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.29, C:0.42, G:0.00, T:0.29
Consensus pattern (12 bp):
ACCTAACTCTTC
Found at i:83696 original size:19 final size:19
Alignment explanation
Indices: 83672--83717 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
83662 CAAGGTGCTC
83672 CAACTCGGATGACTCGGCT
1 CAACTCGGATGACTCGGCT
83691 CAACTCGGATGACTCGGCT
1 CAACTCGGATGACTCGGCT
83710 CAACTCGG
1 CAACTCGG
83718 TGAGTCAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.22, C:0.33, G:0.26, T:0.20
Consensus pattern (19 bp):
CAACTCGGATGACTCGGCT
Found at i:84117 original size:11 final size:12
Alignment explanation
Indices: 84101--84131 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
84091 ATAGACAAGT
84101 ACCTAACTC-TC
1 ACCTAACTCTTC
84112 ACCTAACTCTTC
1 ACCTAACTCTTC
84124 ACCTAACT
1 ACCTAACT
84132 AAATTGATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.29, C:0.42, G:0.00, T:0.29
Consensus pattern (12 bp):
ACCTAACTCTTC
Found at i:93174 original size:31 final size:31
Alignment explanation
Indices: 93138--93197 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
93128 AACTTAAAAG
*
93138 AGTTTTGCAATACTGAAATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
*
93169 AGTTTTACAATACTTAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTTAAATAATT
93198 CATACAACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.45
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:93686 original size:19 final size:20
Alignment explanation
Indices: 93664--93716 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
93654 TATTTAAACT
93664 TAAATAAAAATAATTAA-AA
1 TAAATAAAAATAATTAATAA
*
93683 TAAATATAAAAT-TTTAATAA
1 TAAATA-AAAATAATTAATAA
*
93703 TATAT-AAAATAATT
1 TAAATAAAAATAATT
93717 TATATGATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 5 0.18
19 12 0.43
20 11 0.39
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
TAAATAAAAATAATTAATAA
Found at i:93718 original size:20 final size:20
Alignment explanation
Indices: 93670--93731 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 20
93660 AACTTAAATA
*
93670 AAAATAATTAAAATAA-ATAT
1 AAAATAATT-TAATAATATAT
93690 AAAAT--TTTAATAATATAT
1 AAAATAATTTAATAATATAT
93708 AAAATAATTT-AT-ATGATAT
1 AAAATAATTTAATAAT-ATAT
93727 AAAAT
1 AAAAT
93732 TAAATATCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
17 5 0.14
18 13 0.35
19 11 0.30
20 8 0.22
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAATAATTTAATAATATAT
Found at i:93796 original size:64 final size:63
Alignment explanation
Indices: 93726--93884 Score: 240
Period size: 63 Copynumber: 2.6 Consensus size: 63
93716 TTATATGATA
*
93726 TAAAATTAAATATCTATAATATAATATTAAAAATTAATATTTATTTTATTTTAAAAAATAATAT
1 TAAAATTAAATATCTATAATATAATATTAAAAATTAATATTTAATTTA-TTTAAAAAATAATAT
*
93790 TAAAATT-AATATCTATAATATAATATTTAAAAAATAATATTTAATTTATTTAAAAAATAATAT
1 TAAAATTAAATATCTATAATATAATA-TTAAAAATTAATATTTAATTTATTTAAAAAATAATAT
93853 TAAAATTAAA-ATC-A-AATATAATA-T-AAAATTAA
1 TAAAATTAAATATCTATAATATAATATTAAAAATTAA
93885 ATATAAAACC
Statistics
Matches: 90, Mismatches: 3, Indels: 10
0.87 0.03 0.10
Matches are distributed among these distances:
58 7 0.08
59 1 0.01
61 9 0.10
62 1 0.01
63 43 0.48
64 29 0.32
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (63 bp):
TAAAATTAAATATCTATAATATAATATTAAAAATTAATATTTAATTTATTTAAAAAATAATAT
Found at i:93815 original size:14 final size:13
Alignment explanation
Indices: 93776--93881 Score: 73
Period size: 12 Copynumber: 8.5 Consensus size: 13
93766 TTATTTTATT
*
93776 TTAAAAAATAATA
1 TTAAAATATAATA
93789 TTAAAAT-TAATA
1 TTAAAATATAATA
*
93801 TCTATAATATAATA
1 T-TAAAATATAATA
*
93815 TTTAAAAAATAATA
1 -TTAAAATATAATA
* *
93829 TT-TAAT-TTAT-
1 TTAAAATATAATA
*
93839 TTAAAAAATAATA
1 TTAAAATATAATA
93852 TTAAAAT-TAA-A
1 TTAAAATATAATA
* *
93863 ATCAAATATAATA
1 TTAAAATATAATA
93876 -TAAAAT
1 TTAAAAT
93882 TAAATATAAA
Statistics
Matches: 71, Mismatches: 14, Indels: 17
0.70 0.14 0.17
Matches are distributed among these distances:
10 2 0.03
11 11 0.15
12 22 0.31
13 20 0.28
14 15 0.21
15 1 0.01
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (13 bp):
TTAAAATATAATA
Found at i:93826 original size:40 final size:37
Alignment explanation
Indices: 93746--93830 Score: 109
Period size: 40 Copynumber: 2.2 Consensus size: 37
93736 TATCTATAAT
* *
93746 ATAATATTAAAAATTAATATTTATTTTATTTTAAAAA
1 ATAATATTAAAAATTAATATTTATATAATTTTAAAAA
93783 ATAATATT-AAAATTAATATCTATAATATAATATTTAAAAA
1 ATAATATTAAAAATTAATAT-T-T-ATATAAT-TTTAAAAA
93823 ATAATATT
1 ATAATATT
93831 TAATTTATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
36 11 0.26
37 9 0.21
38 1 0.02
39 5 0.12
40 16 0.38
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (37 bp):
ATAATATTAAAAATTAATATTTATATAATTTTAAAAA
Found at i:93834 original size:26 final size:27
Alignment explanation
Indices: 93783--93854 Score: 84
Period size: 23 Copynumber: 2.9 Consensus size: 27
93773 ATTTTAAAAA
*
93783 ATAATA-TT-AAAATTAATATCTATAAT
1 ATAATATTTAAAAAATAATAT-TATAAT
93809 ATAATATTTAAAAAATAATATT-TAAT
1 ATAATATTTAAAAAATAATATTATAAT
93835 -T--TATTTAAAAAATAATATTA
1 ATAATATTTAAAAAATAATATTA
93855 AAATTAAAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
23 18 0.43
25 1 0.02
26 10 0.24
27 3 0.07
28 10 0.24
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (27 bp):
ATAATATTTAAAAAATAATATTATAAT
Found at i:99517 original size:20 final size:20
Alignment explanation
Indices: 99492--99530 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
99482 CTATTATTAG
*
99492 TTGCATGACAACTAATAATT
1 TTGCATAACAACTAATAATT
99512 TTGCATAACAACTAATAAT
1 TTGCATAACAACTAATAAT
99531 CTTTCACTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.33
Consensus pattern (20 bp):
TTGCATAACAACTAATAATT
Found at i:103161 original size:23 final size:23
Alignment explanation
Indices: 103135--103178 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
103125 GATTTTATCA
* *
103135 TGTCACTTTTCAACCATTATTAG
1 TGTCACCTATCAACCATTATTAG
*
103158 TGTCACCTATGAACCATTATT
1 TGTCACCTATCAACCATTATT
103179 GTTGTCAACT
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:0.27, C:0.23, G:0.09, T:0.41
Consensus pattern (23 bp):
TGTCACCTATCAACCATTATTAG
Found at i:103261 original size:20 final size:21
Alignment explanation
Indices: 103222--103280 Score: 77
Period size: 20 Copynumber: 2.8 Consensus size: 21
103212 TATGAATTAT
103222 ACAACT-ATAATTAGTTGCATG
1 ACAACTAATAATTA-TTGCATG
103243 ACAACTAATAATT-TTGCATG
1 ACAACTAATAATTATTGCATG
*
103263 ACAATTAATAATATATTG
1 ACAACTAATAAT-TATTG
103281 GGGGAGATCT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
20 18 0.53
21 7 0.21
22 9 0.26
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.36
Consensus pattern (21 bp):
ACAACTAATAATTATTGCATG
Found at i:104597 original size:20 final size:20
Alignment explanation
Indices: 104569--104610 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
104559 GGAATTATTT
*
104569 TAATATTTTAAAATTAATAA
1 TAATATTTTAAAATAAATAA
* *
104589 TAATTTTTTATAATAAATAA
1 TAATATTTTAAAATAAATAA
104609 TA
1 TA
104611 TTAATTATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TAATATTTTAAAATAAATAA
Found at i:104615 original size:26 final size:25
Alignment explanation
Indices: 104579--104652 Score: 64
Period size: 26 Copynumber: 3.0 Consensus size: 25
104569 TAATATTTTA
104579 AAAT-TAA-TAATAATTTTTTATAAT
1 AAATATAATTAATAATTTTTTA-AAT
* *
104603 AAATA-ATATTAATTATTATATTAAAT
1 AAATATA-ATTAATAATT-TTTTAAAT
* *
104629 AAATATAATTAATCATTTTATAAA
1 AAATATAATTAATAATTTTTTAAA
104653 AGTACAATAT
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
24 5 0.12
25 6 0.15
26 24 0.60
27 5 0.12
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (25 bp):
AAATATAATTAATAATTTTTTAAAT
Found at i:104627 original size:22 final size:22
Alignment explanation
Indices: 104596--104639 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
104586 TAATAATTTT
104596 TTATAATAAAT-AATATTAATTA
1 TTATAATAAATAAATA-TAATTA
*
104618 TTATATTAAATAAATATAATTA
1 TTATAATAAATAAATATAATTA
104640 ATCATTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TTATAATAAATAAATATAATTA
Found at i:108177 original size:137 final size:137
Alignment explanation
Indices: 107931--108182 Score: 418
Period size: 137 Copynumber: 1.8 Consensus size: 137
107921 TGTCAGTACC
*
107931 CAAAGTGGTGAAAGCGCGTTCCCGGGGGCATCTTCCATTATTTTGTCAGAGAATATGTTATCATT
1 CAAAGTGGTGAAAGCGCGTTCCCGGGGGCATCTTCCATTATTTTGTCAGAGAATATGTTATAATT
*
107996 GCCCTATTATGTCACTCATGTCCCCCTGAAGAACTATTCATGTCAGTACCTATTATTTCTGAGGG
66 GCCCTATTATGTCACTCATGTCCCCCGGAAGAACTATTCATGTCAGTACCTATTATTTCTGAGGG
108061 GACTTGG
131 GACTTGG
108068 CAAAGTGGTGAAAGCGCGTT-CCGGGGTG-AGTCTTCCATTATTTTGTCAGAGAATATGTTATAA
1 CAAAGTGGTGAAAGCGCGTTCCCGGGG-GCA-TCTTCCATTATTTTGTCAGAGAATATGTTATAA
* ** *
108131 TTGCCCTATTATGTCACTCATGTCCCTCGGGGGCACTATTCATGTCAGTACC
64 TTGCCCTATTATGTCACTCATGTCCCCCGGAAGAACTATTCATGTCAGTACC
108183 CAAAGTGGTG
Statistics
Matches: 107, Mismatches: 6, Indels: 4
0.91 0.05 0.03
Matches are distributed among these distances:
136 7 0.07
137 100 0.93
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.33
Consensus pattern (137 bp):
CAAAGTGGTGAAAGCGCGTTCCCGGGGGCATCTTCCATTATTTTGTCAGAGAATATGTTATAATT
GCCCTATTATGTCACTCATGTCCCCCGGAAGAACTATTCATGTCAGTACCTATTATTTCTGAGGG
GACTTGG
Found at i:108244 original size:116 final size:114
Alignment explanation
Indices: 108068--108398 Score: 446
Period size: 125 Copynumber: 2.8 Consensus size: 114
108058 GGGGACTTGG
* *
108068 CAAAGTGGTGAAAGCGCGTTCCGGGGTGAGTCTTCCATTATTTTGTCAGAGAATATGTTATAATT
1 CAAAGTGGTGAAAGCGCGTTCCGGGG-GAGCCTTCCATTATTTTGTCAGAGAATATGTTATCATT
108133 GCCCTATTATGTCACTCATGTCCCTCGGGGGCACTATTCATGTCAGTACC
65 GCCCTATTATGTCACTCATGTCCCTCGGGGGCACTATTCATGTCAGTACC
* *
108183 CAAAGTGGTGAAAGCGCGTTCTCAGGGGGCGCCTTCCATTATTTTGTCAGAGAATAGGTTATCAT
1 CAAAGTGGTGAAAGCGCGTTC-C-GGGGGAGCCTTCCATTATTTTGTCAGAGAATATGTTATCAT
*
108248 TGCTCTATTATGTCACTTATGTCACTCATGTCCCTCGGGGGCACTATTCATGTCAGTACC
64 TGC-C------CT-A-TTATGTCACTCATGTCCCTCGGGGGCACTATTCATGTCAGTACC
* * *
108308 CAAAGTGGTGAAAGCGCGTTCCCGGGGGGATGCATTCCATTTTTTTGTCAGAGAATATATTATCA
1 CAAAGTGGTGAAAGCGCGTT-CC-GGGGGA-GCCTTCCATTATTTTGTCAGAGAATATGTTATCA
*
108373 TTGCCCTATTATGTCACTCGTGTCCC
63 TTGCCCTATTATGTCACTCATGTCCC
108399 CCCGAAGAAC
Statistics
Matches: 190, Mismatches: 13, Indels: 24
0.84 0.06 0.11
Matches are distributed among these distances:
115 21 0.11
116 37 0.19
117 22 0.12
118 1 0.01
119 1 0.01
123 1 0.01
124 1 0.01
125 71 0.37
126 35 0.18
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.32
Consensus pattern (114 bp):
CAAAGTGGTGAAAGCGCGTTCCGGGGGAGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTG
CCCTATTATGTCACTCATGTCCCTCGGGGGCACTATTCATGTCAGTACC
Found at i:108558 original size:139 final size:138
Alignment explanation
Indices: 108308--108563 Score: 388
Period size: 139 Copynumber: 1.8 Consensus size: 138
108298 TGTCAGTACC
* *
108308 CAAAGTGGTGAAAGCGCGTTCCCGGGGGGATGCATTCCATTTTTTTGTCAGAGAATATATTATCA
1 CAAAGTGGTGAAAGCGCGTTCCC-GGGGGATGCATTCCATTATTTTGTCAGAGAATATATTATAA
*
108373 TTGCCCTATTATGTCACTCGTGTCCCCCCGAAGAACTATTCATATCAGTACCTATTATTTTTTAG
65 TTGCCCTATTATGTCACTCATGTCCCCCCGAAGAACTATTCATATCAGTACCTATTATTTTTTAG
108438 GGGACTTGG
130 GGGACTTGG
* *
108447 CAAAGTGGTGAAAGCGCGTTCCC-GGGGATGCGTCTTCCATTATTTTGTCAGAGAATATGTTATA
1 CAAAGTGGTGAAAGCGCGTTCCCGGGGGATGC--ATTCCATTATTTTGTCAGAGAATATATTATA
* * ** *
108511 ATTGCCCTATTATGTCACTCATGTCCCTCGGGGGCACTATTCATATCAGTACC
64 ATTGCCCTATTATGTCACTCATGTCCCCCCGAAGAACTATTCATATCAGTACC
108564 CAAAGTGGTG
Statistics
Matches: 105, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
137 8 0.08
139 97 0.92
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.33
Consensus pattern (138 bp):
CAAAGTGGTGAAAGCGCGTTCCCGGGGGATGCATTCCATTATTTTGTCAGAGAATATATTATAAT
TGCCCTATTATGTCACTCATGTCCCCCCGAAGAACTATTCATATCAGTACCTATTATTTTTTAGG
GGACTTGG
Found at i:108722 original size:23 final size:23
Alignment explanation
Indices: 108696--108758 Score: 108
Period size: 23 Copynumber: 2.7 Consensus size: 23
108686 ATGTGAAGTT
108696 TGAATAAATTGGATAAAATGTTA
1 TGAATAAATTGGATAAAATGTTA
108719 TGAATAAATTGGATAAAATGTTA
1 TGAATAAATTGGATAAAATGTTA
* *
108742 TGGATAAATTGAATAAA
1 TGAATAAATTGGATAAA
108759 TGTGAAGTGA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.49, C:0.00, G:0.17, T:0.33
Consensus pattern (23 bp):
TGAATAAATTGGATAAAATGTTA
Found at i:108815 original size:23 final size:23
Alignment explanation
Indices: 108699--108815 Score: 104
Period size: 23 Copynumber: 5.3 Consensus size: 23
108689 TGAAGTTTGA
*
108699 ATAAATTGGATAAAATGTTATGA
1 ATAAATTGGATAAAATGTTATGG
108722 ATAAATTGGATAAAATGTTATGG
1 ATAAATTGGATAAAATGTTATGG
* * *
108745 ATAAATTGAAT-AAATGTGAAGTG
1 ATAAATTGGATAAAATGTTATG-G
* * *
108768 ATCAGTTGG-T----TGTT-TGA
1 ATAAATTGGATAAAATGTTATGG
*
108785 ATATATTGGATAAAATGTTATGG
1 ATAAATTGGATAAAATGTTATGG
108808 ATAAATTG
1 ATAAATTG
108816 AACAAATATG
Statistics
Matches: 72, Mismatches: 15, Indels: 14
0.71 0.15 0.14
Matches are distributed among these distances:
17 6 0.08
18 2 0.03
19 3 0.04
22 13 0.18
23 48 0.67
ACGTcount: A:0.41, C:0.01, G:0.21, T:0.37
Consensus pattern (23 bp):
ATAAATTGGATAAAATGTTATGG
Found at i:108828 original size:63 final size:64
Alignment explanation
Indices: 108714--108843 Score: 208
Period size: 63 Copynumber: 2.0 Consensus size: 64
108704 TTGGATAAAA
* * * *
108714 TGTTATGAATAAATTGGATAAAATGTTATGGATAAATTGAATAAATGTGAAGTGATCAGTTGGT
1 TGTTATGAATAAATTGGATAAAATGTTATGGATAAATTGAACAAATATGAAGTGATAAGTTAGT
*
108778 TGTT-TGAATATATTGGATAAAATGTTATGGATAAATTGAACAAATATGAAGTGATAAGTTAGT
1 TGTTATGAATAAATTGGATAAAATGTTATGGATAAATTGAACAAATATGAAGTGATAAGTTAGT
108841 TGT
1 TGT
108844 GAGCATGAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
63 57 0.93
64 4 0.07
ACGTcount: A:0.39, C:0.02, G:0.22, T:0.37
Consensus pattern (64 bp):
TGTTATGAATAAATTGGATAAAATGTTATGGATAAATTGAACAAATATGAAGTGATAAGTTAGT
Found at i:108928 original size:14 final size:14
Alignment explanation
Indices: 108909--108939 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
108899 TGATAAGTTG
108909 GTTTTAATGTATAT
1 GTTTTAATGTATAT
108923 GTTTTAATGTATAT
1 GTTTTAATGTATAT
108937 GTT
1 GTT
108940 AAGGATAAAA
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:0.00, G:0.16, T:0.58
Consensus pattern (14 bp):
GTTTTAATGTATAT
Found at i:109645 original size:21 final size:21
Alignment explanation
Indices: 109594--109645 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
109584 GGTGTCATAA
*
109594 AACCCTGCGGGCTAAGCATGT
1 AACCCTGCGGGCTAAGAATGT
*
109615 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAAGAATGT
109636 AACCCTGCGG
1 AACCCTGCGG
109646 AGATTTCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 3 0.11
21 21 0.78
22 3 0.11
ACGTcount: A:0.23, C:0.27, G:0.33, T:0.17
Consensus pattern (21 bp):
AACCCTGCGGGCTAAGAATGT
Found at i:110297 original size:18 final size:19
Alignment explanation
Indices: 110249--110318 Score: 67
Period size: 18 Copynumber: 3.8 Consensus size: 19
110239 ACTGAAATTG
110249 AAATATAAATATACA-ATTC-
1 AAATAT-AATATA-ATATTCT
110268 AAATA-AATATAATATTCT
1 AAATATAATATAATATTCT
* * *
110286 AATTAT-ATATAACATTTT
1 AAATATAATATAATATTCT
110304 AAATATAATATAATA
1 AAATATAATATAATA
110319 GTCATATTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
16 1 0.02
17 10 0.24
18 19 0.45
19 12 0.29
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (19 bp):
AAATATAATATAATATTCT
Found at i:110554 original size:36 final size:35
Alignment explanation
Indices: 110503--110871 Score: 151
Period size: 36 Copynumber: 10.4 Consensus size: 35
110493 TTTTTATCAT
*
110503 ATATATATAGTATATAGTTTGAAAACATTTTTAAAAA
1 ATATATATA--ATATAGTTTAAAAACATTTTTAAAAA
* *
110540 CATATATATAATATATAGTTTTGAAAACATGTTTGAAAACA
1 -ATATATAT-A-ATATAG-TTTAAAAACAT-TTTTAAAA-A
* * * *
110581 TTTATATATTATATAGTTTTTAAAACATTTTGAAAATA
1 -ATATATATAATATAG-TTTAAAAACATTTTTAAAA-A
* * *
110619 A-ATATA-ATATATAGTTTTTAAAATATTTTT-GAAA
1 ATATATATA-ATATAG-TTTAAAAACATTTTTAAAAA
* * * *
110653 ATATATATTATATAATTTTTAAAACA-TTTT-GAAA
1 ATATATATAATAT-AGTTTAAAAACATTTTTAAAAA
* * * *
110687 ATATATGTAGT-T--TTTAAAAATATTTTGAAAACA
1 ATATATATAATATAGTTTAAAAACATTTTTAAAA-A
* * * ** *
110720 TATATATATTATATAATTTTGAATTCATTTTGAAAAA
1 -ATATATATAATAT-AGTTTAAAAACATTTTTAAAAA
* * *
110757 TTATATAGT-ATATAGTTTTAAAAATATTTTT-GAAA
1 ATATATA-TAATATAG-TTTAAAAACATTTTTAAAAA
*
110792 A-CTATAT-A-AT--TTTAAAAACATTTTTTAAAAA
1 ATATATATAATATAGTTTAAAAACA-TTTTTAAAAA
* *
110823 ATATATA-ATATATAATTTAAAAATATTTTT-AAAA
1 ATATATATA-ATATAGTTTAAAAACATTTTTAAAAA
*
110857 ATATATATTATATAG
1 ATATATATAATATAG
110872 GTTTTTGAAT
Statistics
Matches: 260, Mismatches: 44, Indels: 58
0.72 0.12 0.16
Matches are distributed among these distances:
29 9 0.03
30 13 0.05
31 7 0.03
32 8 0.03
33 5 0.02
34 48 0.18
35 30 0.12
36 55 0.21
37 2 0.01
38 39 0.15
39 29 0.11
40 7 0.03
41 8 0.03
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.45
Consensus pattern (35 bp):
ATATATATAATATAGTTTAAAAACATTTTTAAAAA
Found at i:110714 original size:30 final size:29
Alignment explanation
Indices: 110625--110725 Score: 103
Period size: 30 Copynumber: 3.2 Consensus size: 29
110615 AATAAATATA
110625 ATATATAGTTTTTAAAATATTTTTGAAAATATAT
1 ATATATAGTTTTTAAAATA-TTTTG--AA-A-AT
* *
110659 ATTATATAATTTTTAAAACATTTTGAAAAT
1 A-TATATAGTTTTTAAAATATTTTGAAAAT
* *
110689 ATATGTAGTTTTTAAAAATATTTTGAAAAC
1 ATATATAGTTTTT-AAAATATTTTGAAAAT
110719 ATATATA
1 ATATATA
110726 TATTATATAA
Statistics
Matches: 58, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
29 10 0.17
30 23 0.40
31 1 0.02
32 2 0.03
34 6 0.10
35 16 0.28
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.47
Consensus pattern (29 bp):
ATATATAGTTTTTAAAATATTTTGAAAAT
Found at i:110752 original size:68 final size:71
Alignment explanation
Indices: 110571--110799 Score: 242
Period size: 71 Copynumber: 3.2 Consensus size: 71
110561 TGAAAACATG
* * * *
110571 TTTGAAAACATTTATATATTATATAGTTTTTAAAACATTTTGAAAATAAATATAATATATAGTTT
1 TTTGAAAACATATATATATTATATAATTTTGAAAACATTTTG--AA-AAAT-T-ATATGTAGTTT
110636 TT-AAAATATT
61 TTAAAAATATT
*
110646 TTTG--AA-A-ATATATATTATATAATTTTTAAAACATTTTG-AAAA-TATATGTAGTTTTTAAA
1 TTTGAAAACATATATATATTATATAATTTTGAAAACATTTTGAAAAATTATATGTAGTTTTTAAA
110705 AATA-T
66 AATATT
** *
110710 TTTGAAAACATATATATATTATATAATTTTGAATTCATTTTGAAAAATTATATAGTATATAGTTT
1 TTTGAAAACATATATATATTATATAATTTTGAAAACATTTTGAAAAATTATAT-GTA-GT--TTT
110775 TAAAAATATT
62 TAAAAATATT
110785 TTTGAAAAC-TATATA
1 TTTGAAAACATATATA
110800 ATTTTAAAAA
Statistics
Matches: 135, Mismatches: 7, Indels: 25
0.81 0.04 0.15
Matches are distributed among these distances:
64 17 0.13
65 7 0.05
66 2 0.01
67 4 0.03
68 29 0.21
69 4 0.03
70 5 0.04
71 32 0.24
72 2 0.01
73 2 0.01
74 17 0.13
75 14 0.10
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (71 bp):
TTTGAAAACATATATATATTATATAATTTTGAAAACATTTTGAAAAATTATATGTAGTTTTTAAA
AATATT
Found at i:110807 original size:29 final size:30
Alignment explanation
Indices: 110765--110831 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 30
110755 AATTATATAG
* * * *
110765 TATATAGTTTTAAAAATA-TTTTTGAAAAC
1 TATATAATTTTAAAAACATTTTTTAAAAAA
110794 TATATAATTTTAAAAACATTTTTTAAAAAA
1 TATATAATTTTAAAAACATTTTTTAAAAAA
110824 TATATAAT
1 TATATAAT
110832 ATATAATTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (30 bp):
TATATAATTTTAAAAACATTTTTTAAAAAA
Found at i:110814 original size:65 final size:64
Alignment explanation
Indices: 110729--110863 Score: 173
Period size: 65 Copynumber: 2.1 Consensus size: 64
110719 ATATATATAT
* ** * * *
110729 TATATAATTTTGAATTCA-TTTTGAAAAATTATATAGTATATAGTTTTAAAAATATTTTTGAAAA
1 TATATAATTTTAAAAACATTTTTGAAAAAATATATAATATATA-ATTTAAAAATATTTTT-AAAA
*
110793 C
64 A
*
110794 TATATAATTTTAAAAACATTTTTTAAAAAATATATAATATATAATTTAAAAATATTTTTAAAAA
1 TATATAATTTTAAAAACATTTTTGAAAAAATATATAATATATAATTTAAAAATATTTTTAAAAA
110858 TATATA
1 TATATA
110864 TTATATAGGT
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
64 10 0.16
65 30 0.49
66 21 0.34
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (64 bp):
TATATAATTTTAAAAACATTTTTGAAAAAATATATAATATATAATTTAAAAATATTTTTAAAAA
Found at i:110842 original size:139 final size:142
Alignment explanation
Indices: 110505--110864 Score: 368
Period size: 139 Copynumber: 2.6 Consensus size: 142
110495 TTTATCATAT
* * * * * *
110505 ATATATAGTATAT-AGTTTGAAAACATTTTTAAAAACATATATATAATATATAGTTTTGAAAACA
1 ATATATACTATATAATTTTAAAAACATTTTTTAAAA-A-ATATATAATATATA--TTTAAAAATA
* * *
110569 TGTTTGAAAACATTTATATATTATATAGTTTTTAAAACATTTTGAAAATAAATATAATATATAGT
62 T-TTTGAAAACATATATATATTATATAATTTTGAAAACATTTTGAAAATAAATATAATATATAGT
*
110634 TTTTAAAATATTTTTGAAA
126 TTTAAAAATATTTTTG--A
* * * *
110653 ATATATATTATATAATTTTTAAAACA--TTTT-GAAAATATAT-GTAGT-T-TTTAAAAATATTT
1 ATATATACTATATAATTTTAAAAACATTTTTTAAAAAATATATAATA-TATATTTAAAAATATTT
** * *
110712 TGAAAACATATATATATTATATAATTTTGAATTCATTTTGAAAA-ATTATATAGTATATAGTTTT
65 TGAAAACATATATATATTATATAATTTTGAAAACATTTTGAAAATA-AATATAATATATAGTTTT
110776 AAAAATATTTTTG-
129 AAAAATATTTTTGA
110789 A-A-A-ACTATATAATTTTAAAAACATTTTTTAAAAAATATATAATATATAATTTAAAAATATTT
1 ATATATACTATATAATTTTAAAAACATTTTTTAAAAAATATATAATATAT-ATTTAAAAATATTT
*
110851 TTAAAA-ATATATAT
65 TGAAAACATATATAT
110865 TATATAGGTT
Statistics
Matches: 181, Mismatches: 21, Indels: 30
0.78 0.09 0.13
Matches are distributed among these distances:
133 18 0.10
134 1 0.01
135 5 0.03
136 11 0.06
137 3 0.02
138 9 0.05
139 87 0.48
140 9 0.05
143 3 0.02
144 7 0.04
145 1 0.01
146 2 0.01
147 3 0.02
148 12 0.07
149 10 0.06
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.45
Consensus pattern (142 bp):
ATATATACTATATAATTTTAAAAACATTTTTTAAAAAATATATAATATATATTTAAAAATATTTT
GAAAACATATATATATTATATAATTTTGAAAACATTTTGAAAATAAATATAATATATAGTTTTAA
AAATATTTTTGA
Found at i:112157 original size:17 final size:16
Alignment explanation
Indices: 112137--112239 Score: 59
Period size: 17 Copynumber: 6.1 Consensus size: 16
112127 TTTTTTAACC
*
112137 TTTTGTTTTTTACTTTA
1 TTTTGTTATTTA-TTTA
112154 TTTTGTTATTTATTTA
1 TTTTGTTATTTATTTA
*
112170 TTTAT-TTATTGTTTTTA
1 TTT-TGTTATT-TATTTA
* *
112187 TTATTTTTATTTTTATTA
1 TT-TTGTTATTTAT-TTA
*
112205 TTATT-TTCATTTTTATTA
1 TT-TTGTT-ATTTAT-TTA
112223 TTTT-TATATTTATTTA
1 TTTTGT-TATTTATTTA
112239 T
1 T
112240 CCATGTTCTT
Statistics
Matches: 76, Mismatches: 3, Indels: 15
0.81 0.03 0.16
Matches are distributed among these distances:
16 16 0.21
17 33 0.43
18 27 0.36
ACGTcount: A:0.19, C:0.02, G:0.03, T:0.76
Consensus pattern (16 bp):
TTTTGTTATTTATTTA
Found at i:112165 original size:12 final size:11
Alignment explanation
Indices: 112142--112237 Score: 67
Period size: 12 Copynumber: 8.3 Consensus size: 11
112132 TAACCTTTTG
112142 TTTTTTACTTTA
1 TTTTTTA-TTTA
112154 TTTTGTTATTTA
1 TTTT-TTATTTA
112166 TTTATTTATTTA
1 TTT-TTTATTTA
112178 TTGTTTT-TATTA
1 TT-TTTTAT-TTA
112190 -TTTTTATTT-
1 TTTTTTATTTA
112199 TTATTATTATTT-
1 TT-TT-TTATTTA
112211 TCATTTTTA-TTA
1 T--TTTTTATTTA
112223 TTTTTATATTTA
1 TTTTT-TATTTA
112235 TTT
1 TTT
112238 ATCCATGTTC
Statistics
Matches: 71, Mismatches: 0, Indels: 26
0.73 0.00 0.27
Matches are distributed among these distances:
10 11 0.15
11 9 0.13
12 43 0.61
13 7 0.10
14 1 0.01
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (11 bp):
TTTTTTATTTA
Found at i:112190 original size:24 final size:24
Alignment explanation
Indices: 112145--112239 Score: 80
Period size: 21 Copynumber: 4.2 Consensus size: 24
112135 CCTTTTGTTT
*
112145 TTTACTTTATT-TTGTTATTTATTTA
1 TTTA-TTTATTATTTTTA-TTATTTA
*
112170 TTTATTTATTGTTTTTATTA-TT-
1 TTTATTTATTATTTTTATTATTTA
* *
112192 TTTATTT-TTATTATTATT-TTCA
1 TTTATTTATTATTTTTATTATTTA
112214 -TT-TTTATTATTTTTA-TATTTA
1 TTTATTTATTATTTTTATTATTTA
112235 TTTAT
1 TTTAT
112240 CCATGTTCTT
Statistics
Matches: 57, Mismatches: 6, Indels: 16
0.72 0.08 0.20
Matches are distributed among these distances:
20 4 0.07
21 23 0.40
22 9 0.16
23 3 0.05
24 9 0.16
25 9 0.16
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.75
Consensus pattern (24 bp):
TTTATTTATTATTTTTATTATTTA
Found at i:112197 original size:18 final size:17
Alignment explanation
Indices: 112150--112239 Score: 80
Period size: 18 Copynumber: 5.3 Consensus size: 17
112140 TGTTTTTTAC
* *
112150 TTTATT-TTGTTATTTA
1 TTTATTATTTTTATTTT
*
112166 TTTATT-TATTTATTGTT
1 TTTATTATTTTTATT-TT
112183 TTTATTATTTTTATTTT
1 TTTATTATTTTTATTTT
*
112200 TATTATTATTTTCA--TT
1 T-TTATTATTTTTATTTT
112216 TTTATTATTTTTATATTT
1 TTTATTATTTTTAT-TTT
112234 ATTTAT
1 -TTTAT
112240 CCATGTTCTT
Statistics
Matches: 61, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
15 11 0.18
16 15 0.25
17 10 0.16
18 20 0.33
19 5 0.08
ACGTcount: A:0.21, C:0.01, G:0.02, T:0.76
Consensus pattern (17 bp):
TTTATTATTTTTATTTT
Found at i:112198 original size:6 final size:6
Alignment explanation
Indices: 112174--112237 Score: 55
Period size: 6 Copynumber: 11.2 Consensus size: 6
112164 TATTTATTTA
* * *
112174 TTTATT GTTT-TT ATTATT TTTATT TTTATT ATTATT TTCATT TTTA--
1 TTTATT -TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
*
112220 -TTATT TTTATA TTTATT T
1 TTTATT TTTATT TTTATT T
112238 ATCCATGTTC
Statistics
Matches: 45, Mismatches: 8, Indels: 9
0.73 0.13 0.15
Matches are distributed among these distances:
3 3 0.07
5 2 0.04
6 37 0.82
7 3 0.07
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.77
Consensus pattern (6 bp):
TTTATT
Found at i:112201 original size:15 final size:15
Alignment explanation
Indices: 112162--112236 Score: 80
Period size: 15 Copynumber: 4.8 Consensus size: 15
112152 TATTTTGTTA
*
112162 TTTATTTAT-TTATT
1 TTTATTTTTATTATT
*
112176 TATTGTTTTTATTATT
1 T-TTATTTTTATTATT
112192 TTTATTTTTATTATTAT
1 TTTATTTTTATTA-T-T
112209 TTTCATTTTTATTATT
1 TTT-ATTTTTATTATT
*
112225 TTTATATTTATT
1 TTTATTTTTATT
112237 TATCCATGTT
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
14 1 0.02
15 25 0.48
16 11 0.21
17 5 0.10
18 10 0.19
ACGTcount: A:0.21, C:0.01, G:0.01, T:0.76
Consensus pattern (15 bp):
TTTATTTTTATTATT
Found at i:112205 original size:27 final size:26
Alignment explanation
Indices: 112161--112260 Score: 78
Period size: 27 Copynumber: 3.7 Consensus size: 26
112151 TTATTTTGTT
* * * *
112161 ATTTATTTATTTAT-TTATTGTTTTT
1 ATTTTTTTATTTTTATTATTATTTTC
112186 ATTATTTTTATTTTTATTATTATTTTC
1 ATT-TTTTTATTTTTATTATTATTTTC
112213 ATTTTTATTATTTTTA-TATTTATTTATCC
1 ATTTTT-TTATTTTTATTA-TTATTT-T-C
* *
112242 ATGTTCTTTATTATTATTA
1 AT-TTTTTTATTTTTATTA
112261 ATATATTAAC
Statistics
Matches: 61, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
25 3 0.05
26 14 0.23
27 27 0.44
28 1 0.02
29 11 0.18
30 5 0.08
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.71
Consensus pattern (26 bp):
ATTTTTTTATTTTTATTATTATTTTC
Found at i:112225 original size:9 final size:9
Alignment explanation
Indices: 112174--112233 Score: 58
Period size: 9 Copynumber: 7.1 Consensus size: 9
112164 TATTTATTTA
*
112174 TTTATTGTT
1 TTTATTATT
112183 TTTATTA--
1 TTTATTATT
112190 TTT-TTATT
1 TTTATTATT
112198 TTTATTATT
1 TTTATTATT
*
112207 ATTT-TCATT
1 -TTTATTATT
112216 TTTATTATT
1 TTTATTATT
112225 TTTA-TATT
1 TTTATTATT
112233 T
1 T
112234 ATTTATCCAT
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
6 3 0.07
7 3 0.07
8 11 0.26
9 23 0.53
10 3 0.07
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.77
Consensus pattern (9 bp):
TTTATTATT
Found at i:113333 original size:15 final size:15
Alignment explanation
Indices: 113313--113342 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
113303 ACTAACTCTT
113313 TTTTATTTTGTTTTC
1 TTTTATTTTGTTTTC
*
113328 TTTTATTTTTTTTTC
1 TTTTATTTTGTTTTC
113343 ATCATTTGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.07, G:0.03, T:0.83
Consensus pattern (15 bp):
TTTTATTTTGTTTTC
Found at i:117789 original size:165 final size:163
Alignment explanation
Indices: 117355--118199 Score: 1113
Period size: 165 Copynumber: 5.1 Consensus size: 163
117345 GCTTAAGTCA
* * * * *
117355 AGAAGGGATATATGTCACCAAAAGACCTTCGAGTTTGACTACGCTCAGCTCCGAGGCATATCATT
1 AGAAGGGTTATCTGTCACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* *
117420 TGCAGAATAGCTTAAGTCGAGAAGGGTTATCT-ACCAAAGATCCCCGAGTTCGATTACACTCAGC
65 TGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGA-CAAAGA-CCTCGAGTTCGATTACACTCAGC
*
117484 TTCGAGGGCACATCATTTACATCATAACTCAAGGCT
128 TTCGAGGGCACATCATTTACAGCATAACTCAAGGCT
* *
117520 AGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAATGTACATCATTT
1 AGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
* *
117585 GCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACCTTCAAGTTCGATTACACTCAGCTT
66 GCAGCATAGCTTAAGTCGAGAAGGGTTATCTGACAAAGACC-TCGAGTTCGATTACACTCAGCTT
* * * *
117650 CGAGGGCACATCATTTGCAGCATAACTTAAGTCG
130 CGAGGGCACATCATTTACAGCATAACTCAAGGCT
* * *
117684 AGAAGGGTTATCT-TCCAACCAAAGACCTTCGAGTTCGACTAAGCCCAGCTCCAAGGCGCATCAT
1 AGAAGGGTTATCTGT-C-ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCAT
* *
117748 TTACAGCATAGCTTAAGTCGAGAAGGGCTATCTGACAAAGACCCTCGAGTTCGATTACACTCAGC
64 TTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGACAAAGA-CCTCGAGTTCGATTACACTCAGC
*
117813 TTCGAGGGCACATCATTTACAGCATAACACAAGGCT
128 TTCGAGGGCACATCATTTACAGCATAACTCAAGGCT
* * *
117849 AGAAGGGTTATCTGTCACCAAAACACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCATATCATT
1 AGAAGGGTTATCTGTCACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* * * * *
117914 TGCAGCATAGCTTAAGTCGAGAAAGGCTATCTGCCAAAGACACTCAAGTTCGATTATACTCAGCT
65 TGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGACAAAGAC-CTCGAGTTCGATTACACTCAGCT
* *
117979 TCGAGGACACATCATTTACAGCATAACTGAAGGCT
129 TCGAGGGCACATCATTTACAGCATAACTCAAGGCT
* * * *
118014 ATAAGGGTTATCTGTCACCAAAGACCATCGAGTTCGACTACTCTCAGCTCAAAGGCACATCATTT
1 AGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
*
118079 GCAGCATAGCTTAAGTCGAGAAGGGTTATCTGGCTACCAAAGACCTTTGAGTTCGATTACACTCA
66 GCAGCATAGCTTAAGTCGAGAAGGGTTATCT-G--A-CAAAGACC-TCGAGTTCGATTACACTCA
* * * * *
118144 GC-TC-ATAGGCAAACCAAATTTACAGAATAACTCAAGGCA
126 GCTTCGA-GGGCACATC--ATTTACAGCATAACTCAAGGCT
* *
118183 AGAAGGGCTATATGTCA
1 AGAAGGGTTATCTGTCA
118200 ATAAAATTGT
Statistics
Matches: 598, Mismatches: 66, Indels: 28
0.86 0.10 0.04
Matches are distributed among these distances:
163 3 0.01
164 215 0.36
165 310 0.52
166 4 0.01
167 8 0.01
168 25 0.04
169 33 0.06
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.24
Consensus pattern (163 bp):
AGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
GCAGCATAGCTTAAGTCGAGAAGGGTTATCTGACAAAGACCTCGAGTTCGATTACACTCAGCTTC
GAGGGCACATCATTTACAGCATAACTCAAGGCT
Found at i:118036 original size:329 final size:329
Alignment explanation
Indices: 117355--118146 Score: 1180
Period size: 329 Copynumber: 2.4 Consensus size: 329
117345 GCTTAAGTCA
* * * * *
117355 AGAAGGGATATATGTCACCAAAAGACCTTCGAGTTTGACTACGCTCAGCTCCGAGGCATATCATT
1 AGAAGGGTTATCTGTCACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
*
117420 TGCAGAATAGCTTAAGTCGAGAAGGGTTATCT-ACCAAAGATCCC-CGAGTTCGATTACACTCAG
65 TGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGACCAAAGA-CCCTCGAGTTCGATTACACTCAG
* * *
117483 CTTCGAGGGCACATCATTTACATCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTT
129 CTTCGAGGGCACATCATTTACAGCATAACACAAGGCTAGAAGGGTTATCTGTCACCAAACACCTT
* * * *
117548 CGAGTTCGACTACGCTCAGCTCCAATGTACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTA
194 CGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAAGGCTA
* * *
117613 TCTGCCAAAGACCTTCAAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTT
259 TCTGCCAAAGACCTTCAAGTTCGATTACACTCAGCTTCGAGGACACATCATTTACAGCATAACTG
*
117678 AAGTCG
324 AAGGCG
* * *
117684 AGAAGGGTTATCT-TCCAACCAAAGACCTTCGAGTTCGACTAAGCCCAGCTCCAAGGCGCATCAT
1 AGAAGGGTTATCTGT-C-ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCAT
* *
117748 TTACAGCATAGCTTAAGTCGAGAAGGGCTATCTGA-CAAAGACCCTCGAGTTCGATTACACTCAG
64 TTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGACCAAAGACCCTCGAGTTCGATTACACTCAG
117812 CTTCGAGGGCACATCATTTACAGCATAACACAAGGCTAGAAGGGTTATCTGTCACCAAAACACCT
129 CTTCGAGGGCACATCATTTACAGCATAACACAAGGCTAGAAGGGTTATCTGTCACC-AAACACCT
* *
117877 TCGAGTTCGACTACGCTCAGCTCTAAGGCATATCATTTGCAGCATAGCTTAAGTCGAGAAAGGCT
193 TCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAAGGCT
*
117942 ATCTGCCAAAGACAC-TCAAGTTCGATTATACTCAGCTTCGAGGACACATCATTTACAGCATAAC
258 ATCTGCCAAAGAC-CTTCAAGTTCGATTACACTCAGCTTCGAGGACACATCATTTACAGCATAAC
*
118006 TGAAGGCT
322 TGAAGGCG
* * * *
118014 ATAAGGGTTATCTGTCACCAAAGACCATCGAGTTCGACTACTCTCAGCTCAAAGGCACATCATTT
1 AGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
* *
118079 GCAGCATAGCTTAAGTCGAGAAGGGTTATCTGGCTACCAAAGACCTTTGAGTTCGATTACACTCA
66 GCAGCATAGCTTAAGTCGAGAAGGGTTATCT-G--ACCAAAGACCCTCGAGTTCGATTACACTCA
118144 GCT
128 GCT
118147 CATAGGCAAA
Statistics
Matches: 415, Mismatches: 37, Indels: 18
0.88 0.08 0.04
Matches are distributed among these distances:
328 4 0.01
329 231 0.56
330 148 0.36
331 2 0.00
332 1 0.00
333 29 0.07
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (329 bp):
AGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
GCAGCATAGCTTAAGTCGAGAAGGGTTATCTGACCAAAGACCCTCGAGTTCGATTACACTCAGCT
TCGAGGGCACATCATTTACAGCATAACACAAGGCTAGAAGGGTTATCTGTCACCAAACACCTTCG
AGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAAGGCTATC
TGCCAAAGACCTTCAAGTTCGATTACACTCAGCTTCGAGGACACATCATTTACAGCATAACTGAA
GGCG
Found at i:118837 original size:39 final size:37
Alignment explanation
Indices: 118775--119151 Score: 248
Period size: 36 Copynumber: 10.6 Consensus size: 37
118765 TTTTTATCAT
*
118775 ATATATATATATAATATAG-TTTGAAAACATTTTTAAAAA
1 ATATATATA-AT-ATATAGTTTTTAAAACATTTTT-AAAA
* *
118814 CATATATATAATATATAGTTTTGAAAACATGTTTGAAAA
1 -ATATATATAATATATAGTTTTTAAAACAT-TTTTAAAA
* * * *
118853 CATTTATTTATTATATAGTTTTTAAAACA-TTTTGAAA
1 -ATATATATAATATATAGTTTTTAAAACATTTTTAAAA
* * *
118890 ATAAATATAATATATAGTTTTTAAAATATTTTTGAAA
1 ATATATATAATATATAGTTTTTAAAACATTTTTAAAA
*
118927 ATATATAT--TATATAGTTTTTAAAACA-TTTT---G
1 ATATATATAATATATAGTTTTTAAAACATTTTTAAAA
*
118958 A-A-A-AT-ATATATAGTTTTTAAAA-ATATTTTGAAA
1 ATATATATAATATATAGTTTTTAAAACAT-TTTTAAAA
* * * * * *
118991 ACATATATATTATATAATTTTGAAATCATTTTGAAAA
1 ATATATATAATATATAGTTTTTAAAACATTTTTAAAA
* *
119028 AT-TATATAGTATATAGTTTTAAAAACATTTTTGAAAA
1 ATATATATAATATATAGTTTTTAAAACATTTTT-AAAA
* *
119065 CTATATA-ACT-T-T-G-----AAAACATTTTTAAAAA
1 ATATATATAATATATAGTTTTTAAAACATTTTT-AAAA
* * *
119094 TATATATATAATATATA-ATTTCAAAATATTTTT-AAA
1 -ATATATATAATATATAGTTTTTAAAACATTTTTAAAA
119130 A-ATATATAATATATAGGTTTTT
1 ATATATATAATATATA-GTTTTT
119152 GAATTTTTTT
Statistics
Matches: 273, Mismatches: 36, Indels: 60
0.74 0.10 0.16
Matches are distributed among these distances:
28 3 0.01
29 32 0.12
30 11 0.04
31 3 0.01
32 1 0.00
33 2 0.01
34 20 0.07
35 20 0.07
36 57 0.21
37 48 0.18
38 22 0.08
39 42 0.15
40 12 0.04
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (37 bp):
ATATATATAATATATAGTTTTTAAAACATTTTTAAAA
Found at i:118969 original size:64 final size:65
Alignment explanation
Indices: 118898--119037 Score: 205
Period size: 66 Copynumber: 2.2 Consensus size: 65
118888 AAATAAATAT
* *
118898 AATATATAGTTTTT-AAAATATTTTTG-AAA-ATATATATTATATAGTTTTTAAAACATTTTGAA
1 AATATATAGTTTTTAAAAATA-TTTTGAAAACATATATATTATATAATTTTGAAAACATTTTGAA
118960 A
65 A
*
118961 ATATATATAGTTTTTAAAAATATTTTGAAAACATATATATTATATAATTTTGAAATCATTTTGAA
1 A-ATATATAGTTTTTAAAAATATTTTGAAAACATATATATTATATAATTTTGAAAACATTTTGAA
119026 A
65 A
119027 AATTATATAGT
1 AA-TATATAGT
119038 ATATAGTTTT
Statistics
Matches: 69, Mismatches: 3, Indels: 7
0.87 0.04 0.09
Matches are distributed among these distances:
63 1 0.01
64 18 0.26
65 10 0.14
66 40 0.58
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.46
Consensus pattern (65 bp):
AATATATAGTTTTTAAAAATATTTTGAAAACATATATATTATATAATTTTGAAAACATTTTGAAA
Found at i:118988 original size:30 final size:29
Alignment explanation
Indices: 118899--118999 Score: 121
Period size: 30 Copynumber: 3.2 Consensus size: 29
118889 AATAAATATA
118899 ATATATAGTTTTTAAAATATTTTTGAAAATATAT
1 ATATATAGTTTTTAAAATA-TTTTG--AA-A-AT
*
118933 ATTATATAGTTTTTAAAACATTTTGAAAAT
1 A-TATATAGTTTTTAAAATATTTTGAAAAT
*
118963 ATATATAGTTTTTAAAAATATTTTGAAAAC
1 ATATATAGTTTTT-AAAATATTTTGAAAAT
118993 ATATATA
1 ATATATA
119000 TTATATAATT
Statistics
Matches: 62, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
29 12 0.19
30 24 0.39
31 1 0.02
32 2 0.03
34 6 0.10
35 17 0.27
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.47
Consensus pattern (29 bp):
ATATATAGTTTTTAAAATATTTTGAAAAT
Found at i:119161 original size:102 final size:102
Alignment explanation
Indices: 118864--119151 Score: 315
Period size: 102 Copynumber: 2.8 Consensus size: 102
118854 ATTTATTTAT
* * * *
118864 TATATAGTTTTTAAAACA-TTTTGAAAATA-A-ATATAATATATAGTTTTTAAAATATTTTTGAA
1 TATATAGCTTTGAAAACATTTTTGAAAATATATATATAATATATA-ATTTTAAAATATTTTTAAA
*
118926 AATATATATTATATAGTTTTTAAAACA-TTTTGAAAATA
65 AATATATAATATATAGTTTTTAAAA-ATTTTTGAAAATA
* * * * *
118964 TATATAGTTTTTAAAA-ATATTTTGAAAACATATATAT--TATATAATTTTGAAATCATTTTGAA
1 TATATAGCTTTGAAAACAT-TTTTGAAAATATATATATAATATATAATTTTAAAAT-ATTTTTAA
* *
119026 AAATTATATAGTATATAGTTTTAAAAACATTTTTGAAAACTA
64 AAA-TATATAATATATAGTTTTTAAAA-ATTTTTGAAAA-TA
* *
119068 TATA-A-CTTTGAAAACATTTTTAAAAATATATATATAATATATAATTTCAAAATATTTTTAAAA
1 TATATAGCTTTGAAAACATTTTTGAAAATATATATATAATATATAATTTTAAAATATTTTTAAAA
119131 ATATATAATATATAGGTTTTT
66 ATATATAATATATA-GTTTTT
119152 GAATTTTTTT
Statistics
Matches: 160, Mismatches: 16, Indels: 21
0.81 0.08 0.11
Matches are distributed among these distances:
99 1 0.01
100 24 0.15
101 25 0.16
102 59 0.37
103 31 0.19
104 20 0.12
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (102 bp):
TATATAGCTTTGAAAACATTTTTGAAAATATATATATAATATATAATTTTAAAATATTTTTAAAA
ATATATAATATATAGTTTTTAAAAATTTTTGAAAATA
Found at i:120530 original size:27 final size:25
Alignment explanation
Indices: 120503--120552 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
120493 CTTATTAATT
120503 TTTCATTTTTA-TTATATATTTTTTA
1 TTTCA-TTTTACTTATATATTTTTTA
*
120528 TTTCATTTTACTTTTATATTTTTTA
1 TTTCATTTTACTTATATATTTTTTA
120553 ACCTTTTGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.22
25 18 0.78
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (25 bp):
TTTCATTTTACTTATATATTTTTTA
Found at i:120531 original size:25 final size:24
Alignment explanation
Indices: 120503--120624 Score: 74
Period size: 25 Copynumber: 4.8 Consensus size: 24
120493 CTTATTAATT
120503 TTTCATTTTTATTATATATTTTTTA-
1 TTTCATTTTTATT-TAT-TTTTTTAC
120528 TTTCA-TTTTACTTTTATATTTTTTAACC
1 TTTCATTTTTA--TTTAT-TTTTTT-A-C
** *
120556 TTTTGTTTTTACTTTATTTTGTTA-
1 TTTCATTTTTA-TTTATTTTTTTAC
*
120580 TTT-ATTTATTTATTTATTCTTTTTAT
1 TTTCA-TT-TTTATTTATT-TTTTTAC
120606 TTTCATTTTTA-TTATTTTT
1 TTTCATTTTTATTTATTTTT
120625 ATCTTTATTT
Statistics
Matches: 80, Mismatches: 6, Indels: 24
0.73 0.05 0.22
Matches are distributed among these distances:
23 3 0.04
24 21 0.26
25 28 0.35
26 9 0.11
27 6 0.08
28 8 0.10
29 5 0.06
ACGTcount: A:0.19, C:0.07, G:0.02, T:0.73
Consensus pattern (24 bp):
TTTCATTTTTATTTATTTTTTTAC
Found at i:120575 original size:16 final size:16
Alignment explanation
Indices: 120556--120608 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
120546 TTTTTTAACC
120556 TTTTGTT-TTTACTTTA
1 TTTTGTTATTTA-TTTA
120572 TTTTGTTATTTATTTA
1 TTTTGTTATTTATTTA
*
120588 TTTAT-TTATTCTTTTTA
1 TTT-TGTTATT-TATTTA
120605 TTTT
1 TTTT
120609 CATTTTTATT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
16 20 0.61
17 13 0.39
ACGTcount: A:0.15, C:0.04, G:0.04, T:0.77
Consensus pattern (16 bp):
TTTTGTTATTTATTTA
Found at i:120583 original size:12 final size:11
Alignment explanation
Indices: 120561--120634 Score: 53
Period size: 12 Copynumber: 6.2 Consensus size: 11
120551 TAACCTTTTG
120561 TTTTTACTTTAT
1 TTTTTA-TTTAT
120573 TTTGTTATTTAT
1 TTT-TTATTTAT
120585 TTATTTATTTATT
1 TT-TTTATTTA-T
120598 CTTTTTATTT-T
1 -TTTTTATTTAT
120609 CATTTTTA-TTAT
1 --TTTTTATTTAT
*
120621 TTTTATCTTTAT
1 TTTT-TATTTAT
120633 TT
1 TT
120635 ATCCATGTTC
Statistics
Matches: 52, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
10 4 0.08
11 4 0.08
12 30 0.58
13 12 0.23
14 2 0.04
ACGTcount: A:0.18, C:0.05, G:0.01, T:0.76
Consensus pattern (11 bp):
TTTTTATTTAT
Found at i:120616 original size:21 final size:21
Alignment explanation
Indices: 120561--120634 Score: 61
Period size: 21 Copynumber: 3.7 Consensus size: 21
120551 TAACCTTTTG
*
120561 TTTTTA-CTTTA-TTTTGTTA
1 TTTTTATCTTTATTTTTATTA
* *
120580 TTTATT-TATTTA--TTTATTC
1 TTT-TTATCTTTATTTTTATTA
120599 TTTTTAT-TTTCATTTTTATTA
1 TTTTTATCTTT-ATTTTTATTA
120620 TTTTTATCTTTATTT
1 TTTTTATCTTTATTT
120635 ATCCATGTTC
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
18 5 0.11
19 13 0.30
20 6 0.14
21 17 0.39
22 3 0.07
ACGTcount: A:0.18, C:0.05, G:0.01, T:0.76
Consensus pattern (21 bp):
TTTTTATCTTTATTTTTATTA
Found at i:120654 original size:3 final size:3
Alignment explanation
Indices: 120646--120692 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
120636 TCCATGTTCT
120646 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
120693 ACATTTTTGT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:122057 original size:15 final size:15
Alignment explanation
Indices: 122037--122094 Score: 55
Period size: 15 Copynumber: 3.8 Consensus size: 15
122027 ATTAATTTAA
122037 ATAAATAATAATTAT
1 ATAAATAATAATTAT
* *
122052 ATAAATATTATTTTAAT
1 ATAAATAATA-ATT-AT
* *
122069 AAAAATAATATTTAT
1 ATAAATAATAATTAT
122084 ATAAAT-ATAAT
1 ATAAATAATAAT
122095 AATAAAAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
14 4 0.11
15 16 0.46
16 5 0.14
17 10 0.29
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATAAATAATAATTAT
Found at i:122080 original size:17 final size:17
Alignment explanation
Indices: 122039--122095 Score: 64
Period size: 17 Copynumber: 3.5 Consensus size: 17
122029 TAATTTAAAT
*
122039 AAATAATAATTATATAA
1 AAATAATATTTATATAA
* *
122056 ATATTAT-TTTA-ATAA
1 AAATAATATTTATATAA
122071 AAATAATATTTATATAA
1 AAATAATATTTATATAA
*
122088 ATATAATA
1 AAATAATA
122096 ATAAAAAATA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
15 9 0.28
16 7 0.22
17 16 0.50
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AAATAATATTTATATAA
Found at i:122176 original size:10 final size:10
Alignment explanation
Indices: 122161--122187 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
122151 GGGATGCGCC
122161 TTAATGGTAT
1 TTAATGGTAT
122171 TTAATGGTAT
1 TTAATGGTAT
122181 TTAATGG
1 TTAATGG
122188 ATGGGGGCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.48
Consensus pattern (10 bp):
TTAATGGTAT
Found at i:123117 original size:34 final size:33
Alignment explanation
Indices: 123041--123147 Score: 85
Period size: 34 Copynumber: 3.1 Consensus size: 33
123031 GTGGTAAGAA
* *
123041 ATTTATTTTTATGTTAGTAT-TTT-TTTAAATAGTT
1 ATTT-TTTTTAT-TTAATATATTTATATAAATA-TT
*
123075 ATTATTTTTTATATTAATATATTTATGTAAATATT
1 ATT-TTTTTTAT-TTAATATATTTATATAAATATT
* *
123110 A-TTTTTTTATTAAAATAATATTTATATAATTATT
1 ATTTTTTTTATT-TAAT-ATATTTATATAAATATT
123144 ATTT
1 ATTT
123148 ATTTAGAATT
Statistics
Matches: 61, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
32 1 0.02
33 11 0.18
34 33 0.54
35 9 0.15
36 7 0.11
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (33 bp):
ATTTTTTTTATTTAATATATTTATATAAATATT
Found at i:123129 original size:36 final size:34
Alignment explanation
Indices: 123074--123152 Score: 101
Period size: 34 Copynumber: 2.4 Consensus size: 34
123064 TTTAAATAGT
*
123074 TATTATTTTTTATATT--AAT-ATATTTATGTAAA
1 TATTATTTTTT-TATTAAAATAATATTTATATAAA
*
123106 TATTATTTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTTATTAAAATAATATTTATATAAA
*
123140 TATTATTTATTTA
1 TATTATTTTTTTA
123153 GAATTATTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
31 4 0.10
32 11 0.27
33 3 0.07
34 23 0.56
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (34 bp):
TATTATTTTTTTATTAAAATAATATTTATATAAA
Found at i:123313 original size:17 final size:17
Alignment explanation
Indices: 123291--123344 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
123281 AATGTTAATA
123291 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
123308 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
123325 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
123342 TTT
1 TTT
123345 TTATAATATA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:124899 original size:21 final size:21
Alignment explanation
Indices: 124869--124916 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
124859 GCAGGGGTAC
* *
124869 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
124890 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
124911 ATGCCA
1 ATGCCA
124917 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:124987 original size:21 final size:21
Alignment explanation
Indices: 124926--124993 Score: 102
Period size: 21 Copynumber: 3.2 Consensus size: 21
124916 ATCTCCGCAG
*
124926 GGTTACATTCCGAGCCCG-CA
1 GGTTACATTCCTAGCCCGCCA
124946 GGGTTACATTCCTAGCCCGCCA
1 -GGTTACATTCCTAGCCCGCCA
*
124968 GGTTACATGCCTAGCCCGCCA
1 GGTTACATTCCTAGCCCGCCA
124989 GGTTA
1 GGTTA
124994 TAGCCCGCAG
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
21 42 0.95
22 2 0.05
ACGTcount: A:0.19, C:0.34, G:0.25, T:0.22
Consensus pattern (21 bp):
GGTTACATTCCTAGCCCGCCA
Found at i:125559 original size:28 final size:27
Alignment explanation
Indices: 125527--125620 Score: 89
Period size: 28 Copynumber: 3.2 Consensus size: 27
125517 GATAAATGTT
*
125527 TTTAAAATACAAATTATATTATTCAAAA
1 TTTAAAATAAAAATTATATTATTC-AAA
125555 TTTAAAATAAAAATAAAAATAATATTATTCAAA
1 TTTAAAATAAAAAT-----T-ATATTATTCAAA
* *
125588 TTTAAAATATAAATTATAGTATTCGAAA
1 TTTAAAATAAAAATTATATTATTC-AAA
125616 TTTAA
1 TTTAA
125621 CATTAAATTT
Statistics
Matches: 56, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
27 8 0.14
28 22 0.39
33 17 0.30
34 9 0.16
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.38
Consensus pattern (27 bp):
TTTAAAATAAAAATTATATTATTCAAA
Found at i:125589 original size:33 final size:34
Alignment explanation
Indices: 125530--125601 Score: 110
Period size: 34 Copynumber: 2.1 Consensus size: 34
125520 AAATGTTTTT
* *
125530 AAAATACAAATTATATTATTCAAAATTTAAAATA
1 AAAATAAAAATAATATTATTCAAAATTTAAAATA
125564 AAAATAAAAATAATATTATTC-AAATTTAAAATA
1 AAAATAAAAATAATATTATTCAAAATTTAAAATA
*
125597 TAAAT
1 AAAAT
125602 TATAGTATTC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
33 16 0.46
34 19 0.54
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (34 bp):
AAAATAAAAATAATATTATTCAAAATTTAAAATA
Found at i:125627 original size:27 final size:27
Alignment explanation
Indices: 125564--125629 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
125554 ATTTAAAATA
* * *
125564 AAAATAAAAATAATATTATTCAAATTT
1 AAAATATAAATTATAGTATTCAAATTT
125591 AAAATATAAATTATAGTATTCGAAATTT
1 AAAATATAAATTATAGTATTC-AAATTT
*
125619 AACAT-TAAATT
1 AAAATATAAATT
125630 TCAACTTAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 24 0.71
28 10 0.29
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (27 bp):
AAAATATAAATTATAGTATTCAAATTT
Found at i:126236 original size:128 final size:128
Alignment explanation
Indices: 126008--126598 Score: 1137
Period size: 128 Copynumber: 4.6 Consensus size: 128
125998 TTTAAGTTAT
* *
126008 TCCCCGAGTGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
*
126073 GCGCACCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
*
126136 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
126201 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
*
126264 TCCCCGAGGGACATGAATGACATAATAGGACAATGATAACATATTCTCTGACGAAATAATGGAAG
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
126329 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
126392 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
126457 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
126520 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
126585 GCGCGCCCCCGGGA
66 GCGCGCCCCCGGGA
126599 TGACGAGGAT
Statistics
Matches: 458, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
128 458 1.00
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.22
Consensus pattern (128 bp):
TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
Found at i:128799 original size:12 final size:13
Alignment explanation
Indices: 128766--128803 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
128756 AAATACATAA
128766 ATATATTTAATAT
1 ATATATTTAATAT
*
128779 ATTTATTTAATAT
1 ATATATTTAATAT
128792 A-ATATTTAATAT
1 ATATATTTAATAT
128804 TATTAGTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
ATATATTTAATAT
Found at i:131409 original size:31 final size:31
Alignment explanation
Indices: 131374--131519 Score: 229
Period size: 31 Copynumber: 4.7 Consensus size: 31
131364 ATTATATGTG
*
131374 TAGTACCTAAACTATCAATTTTAATTTGTTT
1 TAGTACCTAAACTATCAATTTTAATTCGTTT
131405 TAGTACCTAAACTATCAATTTTAATTCGTTT
1 TAGTACCTAAACTATCAATTTTAATTCGTTT
131436 TAGTACCTAAACTATCAATTTTAATTCGTTT
1 TAGTACCTAAACTATCAATTTTAATTCGTTT
* * *
131467 TAGTACCTAAACTATCAGTTTTGATCCGTTT
1 TAGTACCTAAACTATCAATTTTAATTCGTTT
* * *
131498 TATTACCTAAACTTTCATTTTT
1 TAGTACCTAAACTATCAATTTT
131520 TTTAAAATCA
Statistics
Matches: 108, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 108 1.00
ACGTcount: A:0.30, C:0.16, G:0.07, T:0.47
Consensus pattern (31 bp):
TAGTACCTAAACTATCAATTTTAATTCGTTT
Found at i:134512 original size:13 final size:13
Alignment explanation
Indices: 134494--134536 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
134484 AGGTTCCTAA
134494 ATACCTTTCTGAT
1 ATACCTTTCTGAT
134507 ATACCTTTCTG--
1 ATACCTTTCTGAT
134518 ATACCTTTCTGAT
1 ATACCTTTCTGAT
*
134531 ACACCT
1 ATACCT
134537 AACAAATCGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
11 11 0.41
13 16 0.59
ACGTcount: A:0.23, C:0.28, G:0.07, T:0.42
Consensus pattern (13 bp):
ATACCTTTCTGAT
Found at i:134523 original size:11 final size:11
Alignment explanation
Indices: 134494--134532 Score: 60
Period size: 11 Copynumber: 3.4 Consensus size: 11
134484 AGGTTCCTAA
134494 ATACCTTTCTG
1 ATACCTTTCTG
134505 ATATACCTTTCTG
1 --ATACCTTTCTG
134518 ATACCTTTCTG
1 ATACCTTTCTG
134529 ATAC
1 ATAC
134533 ACCTAACAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 15 0.58
13 11 0.42
ACGTcount: A:0.23, C:0.26, G:0.08, T:0.44
Consensus pattern (11 bp):
ATACCTTTCTG
Found at i:134692 original size:216 final size:216
Alignment explanation
Indices: 134318--134728 Score: 777
Period size: 216 Copynumber: 1.9 Consensus size: 216
134308 GACTCGATTT
*
134318 CCTAACAAATCGACATGAATCTTGAATATCATAAATCATTGTTTCACCCTTATTGAATTAATTTT
1 CCTAACAAATCGACATGAATCTTGAATATCATAAATCATTGTTTCACCCTTATTGAATTAATTTG
*
134383 CTAAGAATCTACTAGAAATCAAAGTGTCCAAAATACCCCTGATGTCCTAAATAATGGAATCACTC
66 CTAAGAATCTACTAGAAATCAAAATGTCCAAAATACCCCTGATGTCCTAAATAATGGAATCACTC
* *
134448 TGGTTATATTTGAAATCTTTATTTATTCTGATATAAAGGTTCCTAAATACCTTTCTGATATACCT
131 TGGTTATATCTGAAATCTTTATTTATTCTGATATAAAGGTTCCTAAATACCTTTCTGATACACCT
134513 TTCTGATACCTTTCTGATACA
196 TTCTGATACCTTTCTGATACA
134534 CCTAACAAATCGACATGAATCTTGAATATCATAAATCATTGTTTCACCCTTATTGAATTAATTTG
1 CCTAACAAATCGACATGAATCTTGAATATCATAAATCATTGTTTCACCCTTATTGAATTAATTTG
*
134599 CTAAGAATCTGCTAGAAATCAAAATGTCCAAAATACCCCTGATGTCCTAAATAATGGAATCACTC
66 CTAAGAATCTACTAGAAATCAAAATGTCCAAAATACCCCTGATGTCCTAAATAATGGAATCACTC
134664 TGGTTATATCTGAAATCTTTATTTATTCTGATATAAAGGTTCCTAAATACCTTTCTGATACACCT
131 TGGTTATATCTGAAATCTTTATTTATTCTGATATAAAGGTTCCTAAATACCTTTCTGATACACCT
134729 AAAATCTTAA
Statistics
Matches: 190, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
216 190 1.00
ACGTcount: A:0.34, C:0.19, G:0.10, T:0.36
Consensus pattern (216 bp):
CCTAACAAATCGACATGAATCTTGAATATCATAAATCATTGTTTCACCCTTATTGAATTAATTTG
CTAAGAATCTACTAGAAATCAAAATGTCCAAAATACCCCTGATGTCCTAAATAATGGAATCACTC
TGGTTATATCTGAAATCTTTATTTATTCTGATATAAAGGTTCCTAAATACCTTTCTGATACACCT
TTCTGATACCTTTCTGATACA
Found at i:152623 original size:22 final size:22
Alignment explanation
Indices: 152585--152628 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
152575 TTTGTTTCGA
152585 AAATAAAACAAAACATT-TTTG
1 AAATAAAACAAAACATTCTTTG
* *
152606 AAATAATAATAAAGCATTCTTTG
1 AAATAA-AACAAAACATTCTTTG
152629 TAACATATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 6 0.32
22 9 0.47
23 4 0.21
ACGTcount: A:0.52, C:0.09, G:0.07, T:0.32
Consensus pattern (22 bp):
AAATAAAACAAAACATTCTTTG
Found at i:153213 original size:49 final size:49
Alignment explanation
Indices: 153131--153351 Score: 291
Period size: 49 Copynumber: 4.5 Consensus size: 49
153121 TAATACCATG
* * *
153131 AGTGGCACATTTTATGCCGAAAATGCACCGTTATGCATTTAACTTTCATT
1 AGTGACACCTTTTATGCC-AAAATGCACCGTTATACATTTAACTTTCATT
* * *
153181 AATGACACCTTTTATGCCAAAATGCACTGTTATACATTTTACTTTCATT
1 AGTGACACCTTTTATGCCAAAATGCACCGTTATACATTTAACTTTCATT
** * * *
153230 AGCAACACCTTTTATGCCAAAATGCACCGTTATGCATTTAATTTTTATT
1 AGTGACACCTTTTATGCCAAAATGCACCGTTATACATTTAACTTTCATT
*
153279 AGTGTA-ATCTTTTATGCCAAAATGCACCGTTATACATTTAACTTTCATT
1 AGTG-ACACCTTTTATGCCAAAATGCACCGTTATACATTTAACTTTCATT
* *
153328 AGTGACATCTTTTATGCCGAAATG
1 AGTGACACCTTTTATGCCAAAATG
153352 TACCTATGAC
Statistics
Matches: 148, Mismatches: 21, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
48 1 0.01
49 131 0.89
50 16 0.11
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.38
Consensus pattern (49 bp):
AGTGACACCTTTTATGCCAAAATGCACCGTTATACATTTAACTTTCATT
Found at i:163804 original size:37 final size:36
Alignment explanation
Indices: 163739--163854 Score: 164
Period size: 35 Copynumber: 3.2 Consensus size: 36
163729 TTATCCCATT
* * *
163739 ATCATTTTTC-AACAAGCATCTACCAAACTTTGAAAA
1 ATCATTTTTCAAAGAAACATTTACCAAACTTTG-AAA
*
163775 ATTATTTTTCAAAGAAACATTTACCAAACTTTGAAA
1 ATCATTTTTCAAAGAAACATTTACCAAACTTTGAAA
*
163811 ACCA-TTTTCAAAGAAACATTTACCAAACTTTGAAA
1 ATCATTTTTCAAAGAAACATTTACCAAACTTTGAAA
163846 ATCATTTTT
1 ATCATTTTT
163855 TAAAAGTTGG
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
35 34 0.48
36 18 0.25
37 19 0.27
ACGTcount: A:0.42, C:0.18, G:0.05, T:0.34
Consensus pattern (36 bp):
ATCATTTTTCAAAGAAACATTTACCAAACTTTGAAA
Found at i:163816 original size:21 final size:20
Alignment explanation
Indices: 163789--163852 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
163779 TTTTTCAAAG
163789 AAACATTTACCAAACTTTGA
1 AAACATTTACCAAACTTTGA
*
163809 AAACCATTT-TCAAA----G-
1 AAA-CATTTACCAAACTTTGA
163824 AAACATTTACCAAACTTTGA
1 AAACATTTACCAAACTTTGA
163844 AAATCATTT
1 AAA-CATTT
163853 TTTAAAAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.15
15 7 0.21
16 1 0.03
19 1 0.03
20 10 0.29
21 10 0.29
ACGTcount: A:0.45, C:0.19, G:0.05, T:0.31
Consensus pattern (20 bp):
AAACATTTACCAAACTTTGA
Found at i:170515 original size:21 final size:21
Alignment explanation
Indices: 170469--170522 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
170459 TGTATGATCA
*
170469 GTATCGATACAATATGAAGGAG
1 GTATCGATAC-CTATGAAGGAG
*
170491 GTATCGATACCTATG-TGGAG
1 GTATCGATACCTATGAAGGAG
*
170511 TGTATTGATACC
1 -GTATCGATACC
170523 CAGGGAAACA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 4 0.14
21 14 0.50
22 10 0.36
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.30
Consensus pattern (21 bp):
GTATCGATACCTATGAAGGAG
Found at i:171621 original size:20 final size:20
Alignment explanation
Indices: 171598--171643 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
171588 ATGGTATATG
*
171598 TGATATATGACGTGTATAAA
1 TGATAAATGACGTGTATAAA
171618 TGATAAATGACGTGTATAAA
1 TGATAAATGACGTGTATAAA
171638 TGATAA
1 TGATAA
171644 GTTCAGGATC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.43, C:0.04, G:0.20, T:0.33
Consensus pattern (20 bp):
TGATAAATGACGTGTATAAA
Found at i:174743 original size:50 final size:50
Alignment explanation
Indices: 174664--174769 Score: 160
Period size: 50 Copynumber: 2.1 Consensus size: 50
174654 GTTGAATGGG
* *
174664 TACC-GATACTACAAGGCCATTTATGAGGAATGGATGCGTGGGGTATCGA
1 TACCTGATACTACAAGGCCATTTATGAGGAATGAATGCATGGGGTATCGA
* *
174713 TACCTGATACTACAAGGTCATTTATGAGGAATGAATGCATGGGGTATTGA
1 TACCTGATACTACAAGGCCATTTATGAGGAATGAATGCATGGGGTATCGA
*
174763 TATCTGA
1 TACCTGA
174770 ATGAACAATA
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
49 4 0.08
50 47 0.92
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.28
Consensus pattern (50 bp):
TACCTGATACTACAAGGCCATTTATGAGGAATGAATGCATGGGGTATCGA
Found at i:176025 original size:22 final size:24
Alignment explanation
Indices: 175977--176025 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 24
175967 TAATAAGTAT
*
175977 ATATGTGTATTTGTATATGAGATG
1 ATATGTGTATTTGTATATGAGAGG
*
176001 ATATGTG-A-TTGTATATGATAGG
1 ATATGTGTATTTGTATATGAGAGG
176023 ATA
1 ATA
176026 GTAGTAATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 15 0.65
23 1 0.04
24 7 0.30
ACGTcount: A:0.33, C:0.00, G:0.24, T:0.43
Consensus pattern (24 bp):
ATATGTGTATTTGTATATGAGAGG
Found at i:187140 original size:20 final size:20
Alignment explanation
Indices: 187111--187150 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
187101 TTTGGGAAAA
* *
187111 ATCGGTTTTTTTTTAACCGG
1 ATCGGATTTTTTTAAACCGG
187131 ATCGGATTTTTTTAAACCGG
1 ATCGGATTTTTTTAAACCGG
187151 TTATTTTAAC
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:0.20, C:0.15, G:0.20, T:0.45
Consensus pattern (20 bp):
ATCGGATTTTTTTAAACCGG
Found at i:187222 original size:15 final size:13
Alignment explanation
Indices: 187201--187241 Score: 57
Period size: 12 Copynumber: 3.1 Consensus size: 13
187191 TTTTATCGGA
187201 TAAAAAACCGGTT
1 TAAAAAACCGGTT
187214 TGAAAAAAACCGG-T
1 T--AAAAAACCGGTT
187228 TAAAAAACCGGTT
1 TAAAAAACCGGTT
187241 T
1 T
187242 TTATCCAGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 10 0.40
13 3 0.12
14 2 0.08
15 10 0.40
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (13 bp):
TAAAAAACCGGTT
Found at i:189301 original size:21 final size:21
Alignment explanation
Indices: 189277--189316 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
189267 TTTATTTTAT
189277 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
189298 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
189317 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Done.