Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006018.1 Hibiscus syriacus cultivar Beakdansim tig00014197_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: 125683
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Found at i:15934 original size:109 final size:109
Alignment explanation
Indices: 15689--15893 Score: 259
Period size: 109 Copynumber: 1.9 Consensus size: 109
15679 ATTACTACAT
* * * **
15689 ATGACTA-AAGTGGAAAAACATGTTAAACTTAGAGGGACTAAACAACAAATATTCCAATAAACAT
1 ATGACTAGAA-TGCAAAAACATGCTAAACATAGAGGGACTAAACAACAAATAACCCAATAAACAT
* * * *
15753 TTTACATACGAGAAAAGGGGTAAATAACAATTCCAATCCTCATAG
65 ATAACATACAAGAAAAAGGGTAAATAACAATTCCAATCCTCATAG
** **
15798 ATGACTAGAATGCAAAAATGTGCTAAACATAGAGGGACTAAACAACAAATAACCCAATAAATGTA
1 ATGACTAGAATGCAAAAACATGCTAAACATAGAGGGACTAAACAACAAATAACCCAATAAACATA
* *
15863 TAACATGCAAGAAAAAGGGTAAATACCAATT
66 TAACATACAAGAAAAAGGGTAAATAACAATT
15894 TTGGTCCTTA
Statistics
Matches: 80, Mismatches: 15, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
109 78 0.98
110 2 0.03
ACGTcount: A:0.49, C:0.15, G:0.15, T:0.21
Consensus pattern (109 bp):
ATGACTAGAATGCAAAAACATGCTAAACATAGAGGGACTAAACAACAAATAACCCAATAAACATA
TAACATACAAGAAAAAGGGTAAATAACAATTCCAATCCTCATAG
Found at i:16673 original size:23 final size:23
Alignment explanation
Indices: 16647--16729 Score: 89
Period size: 23 Copynumber: 3.6 Consensus size: 23
16637 TAGGTTTTAA
*
16647 TTTGGGCTCGGGTTTGGGTTTGG
1 TTTGGGCTCGGGTTTGAGTTTGG
* * *
16670 TTTGGACTCTGGTTTAAGTTTGG
1 TTTGGGCTCGGGTTTGAGTTTGG
*
16693 TTTGGGC-CTGGGTTATGTGTTTGG
1 TTTGGGCTC-GGGTT-TGAGTTTGG
16717 TTTGGG-TCGGGTT
1 TTTGGGCTCGGGTT
16730 CTGTAAATGG
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
22 1 0.02
23 34 0.69
24 14 0.29
ACGTcount: A:0.05, C:0.08, G:0.41, T:0.46
Consensus pattern (23 bp):
TTTGGGCTCGGGTTTGAGTTTGG
Found at i:16766 original size:3 final size:3
Alignment explanation
Indices: 16758--16799 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
16748 ATGTATTTTA
* *
16758 AAT AAT AAT AAT AAT AAT AAT GAAT AAG AAT AAG AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AA
16800 AACCAATTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:16783 original size:22 final size:22
Alignment explanation
Indices: 16758--16799 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
16748 ATGTATTTTA
* *
16758 AATAATAATAATAATAATAATG
1 AATAAGAATAAGAATAATAATG
16780 AATAAGAATAAGAATAATAA
1 AATAAGAATAAGAATAATAA
16800 AACCAATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (22 bp):
AATAAGAATAAGAATAATAATG
Found at i:16789 original size:19 final size:19
Alignment explanation
Indices: 16761--16797 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
16751 TATTTTAAAT
* *
16761 AATAATAATAATAATAATG
1 AATAAGAATAAGAATAATG
16780 AATAAGAATAAGAATAAT
1 AATAAGAATAAGAATAAT
16798 AAAACCAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.08, T:0.27
Consensus pattern (19 bp):
AATAAGAATAAGAATAATG
Found at i:18148 original size:95 final size:95
Alignment explanation
Indices: 17929--18130 Score: 212
Period size: 95 Copynumber: 2.1 Consensus size: 95
17919 CTGATGTGCG
* * * * * * * **
17929 GTATCGATACTAAGAGAAAGGTATCGATAC-CTCGGAATCCAGAATG-TAGAAATGGTATTGATA
1 GTATCGATACCAGGAGAAAGGTACCGATACAAT-GGATTCTAGAAGGCT-GAAATGGTACCGATA
17992 CTGAAAGGAAGTATTGGTAACATAGTATAGAA
64 CTGAAAGGAAGTATTGGTAACATAGTATAGAA
* * * ** *
18024 GTATTGGTACTAGGAGAAAGGTATTGATACAATGGATTCTAGAAGGCTGAAATGGTACCGATATT
1 GTATCGATACCAGGAGAAAGGTACCGATACAATGGATTCTAGAAGGCTGAAATGGTACCGATACT
*
18089 GAAATGG-AGTATTGGTACCATAGTATAGAA
66 GAAA-GGAAGTATTGGTAACATAGTATAGAA
18119 GTATCGATACCA
1 GTATCGATACCA
18131 TGGTAGGAGT
Statistics
Matches: 89, Mismatches: 15, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
95 85 0.96
96 4 0.04
ACGTcount: A:0.38, C:0.10, G:0.25, T:0.27
Consensus pattern (95 bp):
GTATCGATACCAGGAGAAAGGTACCGATACAATGGATTCTAGAAGGCTGAAATGGTACCGATACT
GAAAGGAAGTATTGGTAACATAGTATAGAA
Found at i:18622 original size:81 final size:81
Alignment explanation
Indices: 18529--18785 Score: 363
Period size: 81 Copynumber: 3.2 Consensus size: 81
18519 TATTTTAAAA
* * * *
18529 TTAAAGATTAAATATATAGTTGTGTAATTGGCAGAAATGTGTCAATCATGCCAGTTAGATGAAAG
1 TTAAAGATTAAATGTCTAGTTGTGCAATTGGAAGAAATGTGTCAATCATGCCAGTTAGATGAAAG
18594 GTTAAATGCCTTTGAG
66 GTTAAATGCCTTTGAG
* * *
18610 TTAAAGATTAAATGTCTAGCTGTGCAATTGGTAG-AATGGTGCCAATCATGCCAGTTAGATGAAA
1 TTAAAGATTAAATGTCTAGTTGTGCAATTGGAAGAAAT-GTGTCAATCATGCCAGTTAGATGAAA
18674 GGTTAAATGCCTTTGAG
65 GGTTAAATGCCTTTGAG
* * * * *
18691 TTAAAGATTATATGCCTAGTTGTACAATTGGAAGAAATGTGTTAATCATGCCAGTTTGATGAAAG
1 TTAAAGATTAAATGTCTAGTTGTGCAATTGGAAGAAATGTGTCAATCATGCCAGTTAGATGAAAG
*
18756 GTTAAATGCCTTTGGG
66 GTTAAATGCCTTTGAG
* *
18772 TAAAAGACTAAATG
1 TTAAAGATTAAATG
18786 CTTAACAATG
Statistics
Matches: 156, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
80 3 0.02
81 150 0.96
82 3 0.02
ACGTcount: A:0.35, C:0.10, G:0.23, T:0.32
Consensus pattern (81 bp):
TTAAAGATTAAATGTCTAGTTGTGCAATTGGAAGAAATGTGTCAATCATGCCAGTTAGATGAAAG
GTTAAATGCCTTTGAG
Found at i:24988 original size:95 final size:95
Alignment explanation
Indices: 24883--25070 Score: 261
Period size: 95 Copynumber: 2.0 Consensus size: 95
24873 GCGGTATCGA
** * * ** *
24883 TACTAAGAGAAAGCTATCGATACCTTGGAATCTAGAATG-TAGAAATGGTATCGATACTAAAAGG
1 TACTAAGAGAAAGCTATCGATACCAGGGAATCCAGAATGCCA-AAATGACATCGATACCAAAAGG
24947 GAGTATCGGTACCATAGTATAGAAGTATCAG
65 GAGTATCGGTACCATAGTATAGAAGTATCAG
* * * *
24978 TACTAGGAGAAAGGTATCGATACCAGGGATTCCAGAATGCCAAAATGACATCGATACCGAAAGGG
1 TACTAAGAGAAAGCTATCGATACCAGGGAATCCAGAATGCCAAAATGACATCGATACCAAAAGGG
25043 AGTATCGGTACCATAGTATAGAAGTATC
66 AGTATCGGTACCATAGTATAGAAGTATC
25071 GATACCATGG
Statistics
Matches: 81, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
95 80 0.99
96 1 0.01
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.23
Consensus pattern (95 bp):
TACTAAGAGAAAGCTATCGATACCAGGGAATCCAGAATGCCAAAATGACATCGATACCAAAAGGG
AGTATCGGTACCATAGTATAGAAGTATCAG
Found at i:25731 original size:81 final size:80
Alignment explanation
Indices: 25476--25733 Score: 318
Period size: 81 Copynumber: 3.2 Consensus size: 80
25466 TATTTTAAAA
* * * * ** *
25476 TTAAAGATTAAATTCCTAGATGTGCAATTGGTAAAAAGGTGCCGATCATGCCAGTTAGATGAAAT
1 TTAAAGATTAAATGCCTAGCTGTGCAATTGGTAGAAAGGTG-CAATCATGATAGTTAGATGAAAG
*
25541 GTTAAATGCCTTTGTG
65 GTTAAATGCCTTTGGG
* * * *
25557 TTAAAGATTAAATGCCTATCTATGCAATTGGCAGAAATGTGCTAATCATGATAGTTAGATGAAAG
1 TTAAAGATTAAATGCCTAGCTGTGCAATTGGTAGAAAGGTGC-AATCATGATAGTTAGATGAAAG
*
25622 GTTAAATGCCTTTAGG
65 GTTAAATGCCTTTGGG
* **
25638 TTAAAGATTAAATGCCTAGCTGTGCAATTGGTAGAAAGGTGTCAATCATGTTAGTTAGAAAAAAG
1 TTAAAGATTAAATGCCTAGCTGTGCAATTGGTAGAAAGGTG-CAATCATGATAGTTAGATGAAAG
25703 GTTAAATGCCTTTGGG
65 GTTAAATGCCTTTGGG
* * *
25719 TAAAACAATAAATGC
1 TTAAAGATTAAATGC
25734 TTAACAGTGC
Statistics
Matches: 151, Mismatches: 24, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
80 1 0.01
81 149 0.99
82 1 0.01
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (80 bp):
TTAAAGATTAAATGCCTAGCTGTGCAATTGGTAGAAAGGTGCAATCATGATAGTTAGATGAAAGG
TTAAATGCCTTTGGG
Found at i:29434 original size:2 final size:2
Alignment explanation
Indices: 29427--29452 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
29417 TTTACGCGAA
29427 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
29453 TTTAGTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30234 original size:83 final size:83
Alignment explanation
Indices: 29995--30320 Score: 291
Period size: 83 Copynumber: 3.9 Consensus size: 83
29985 GTATAAAAAT
* * * * * * *
29995 GTCGTAATAGGGTTCCTTTATAGTGGCTTTTTTTCCAACAAACATCGCAACAGAGTAGTATTTTA
1 GTCGCAATAGGATTCATCTATAGTGGCATTTTTT-CAACAAACACCGCAACAGAGTAGTATTGTA
* *
30060 GCGGCGTTTTTATAAAAATAC
65 GCGGCATTTTTAT-ACAAT-C
* * * ** *
30081 --CGCAATAGGATTCATCTATAGTTGCATTTTTTCAACAAATACTGCAATTGAGTTGTACTT-TA
1 GTCGCAATAGGATTCATCTATAGTGGCATTTTTTCAACAAACACCGCAACAGAGTAGTA-TTGTA
**
30143 GCAACATTTTTATACAATC
65 GCGGCATTTTTATACAATC
* * * * *
30162 GTCGTAATAGGATTCATCTATAGTGACATTTTTTCAACAAACGCCGCAGCAAAGTAGTATTGTAG
1 GTCGCAATAGGATTCATCTATAGTGGCATTTTTTCAACAAACACCGCAACAGAGTAGTATTGTAG
* *
30227 TGGCATTTTTATACAAAC
66 CGGCATTTTTATACAATC
* * * ** *
30245 GTTGCAATATGG-TTAATCTATAGTGGCATTTTTTCAACAAACGCTACAACAGAGTAGTAATGTA
1 GTCGCAATA-GGATTCATCTATAGTGGCATTTTTTCAACAAACACCGCAACAGAGTAGTATTGTA
*
30309 GTGGCGATTTTT
65 GCGGC-ATTTTT
30321 TAACAAACGC
Statistics
Matches: 194, Mismatches: 40, Indels: 14
0.78 0.16 0.06
Matches are distributed among these distances:
81 1 0.01
82 6 0.03
83 151 0.78
84 36 0.19
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (83 bp):
GTCGCAATAGGATTCATCTATAGTGGCATTTTTTCAACAAACACCGCAACAGAGTAGTATTGTAG
CGGCATTTTTATACAATC
Found at i:30311 original size:42 final size:41
Alignment explanation
Indices: 30182--30335 Score: 136
Period size: 42 Copynumber: 3.7 Consensus size: 41
30172 GATTCATCTA
* * * * *
30182 TAGTGACATTTTTTCAACAAACGCCGCAGCAAAGTAGTATTG
1 TAGTGGCATTTTTT-AACAAACGCTGCAACAGAGTAGTAATG
* * *
30224 TAGTGGCA-TTTTTATACAAACGTTGCAATATG-GT--TAATCTA
1 TAGTGGCATTTTTTA-ACAAACGCTGCAACA-GAGTAGTAA--TG
*
30265 TAGTGGCATTTTTTCAACAAACGCTACAACAGAGTAGTAATG
1 TAGTGGCATTTTTT-AACAAACGCTGCAACAGAGTAGTAATG
30307 TAGTGGCGATTTTTTAACAAACGCTGCAA
1 TAGTGGC-ATTTTTTAACAAACGCTGCAA
30336 ATTTTAAAAT
Statistics
Matches: 89, Mismatches: 13, Indels: 20
0.73 0.11 0.16
Matches are distributed among these distances:
39 2 0.02
40 1 0.01
41 28 0.31
42 47 0.53
43 8 0.09
44 3 0.03
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (41 bp):
TAGTGGCATTTTTTAACAAACGCTGCAACAGAGTAGTAATG
Found at i:36401 original size:19 final size:20
Alignment explanation
Indices: 36363--36413 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
36353 GAAACCCCTT
*
36363 TGAAAATACATAATTTTTAA
1 TGAAAATACATGATTTTTAA
36383 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
36402 TGAAGATACATG
1 TGAAAATACATG
36414 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:38730 original size:285 final size:284
Alignment explanation
Indices: 38221--38785 Score: 1013
Period size: 285 Copynumber: 2.0 Consensus size: 284
38211 TGACATTTGT
*
38221 TTTGAAACTTCAAATGGTATAACCTTTGAAACATTAAGAGACATGTCTTGTCGATCAAAAAATCA
1 TTTGAAACTTCAAATGGTATAACCTTTGAAACATTAAGAGACATGTCTTGTCGATCAAAAAATAA
* *
38286 TGCCTATTGGTCTTTCAAAGGTCACATGTTTTAGTCCTCCGAATGTCATGATTCTTGAATCATCT
66 TGCCTATTGGTCTTTCAAAGGTCACATGTTTTAGTCCTCCAAAAGTCATGATTCTTGAATCATCT
*
38351 CCCTGAAAAGATACATCTCTTGGATTATCCTGTAAAACAATAGGAAGAATAGATGAAAGAGTAAG
131 CCCTAAAAAGATACATCTCTTGGATTATCCTGTAAAACAATAGGAAGAATAGATGAAAGAGTAAG
** *
38416 GTTAGTTAAAATTTAATCTTCATTCTCCTCTTTATCTCTTAATTCATCATTTTCAACTCTCCCAT
196 GTTAGTTAAAATTTAATCTTCATTCTCCTCTTTATCTCCAAATTCATCATTTTCAACTCTCCCAC
38481 TTTCAACTCCAACGTATTCTCCCA
261 TTTCAACTCCAACGTATTCTCCCA
* *
38505 TTTGAAACTTTAAATGGTATAACCTTTGAAACATTAAGAGACATGTCTTGTGGATCAAAAAAATA
1 TTTGAAACTTCAAATGGTATAACCTTTGAAACATTAAGAGACATGTCTTGTCGATC-AAAAAATA
38570 ATGCCTATTGGTCTTTCAAAGGTCACATGTTTTAGTCCTCCAAAAGTCATGATTCTTGAATCATC
65 ATGCCTATTGGTCTTTCAAAGGTCACATGTTTTAGTCCTCCAAAAGTCATGATTCTTGAATCATC
38635 TCCCTAAAAAGATACATCTCTTGGATTATCCTGTAAAACAATAGGAAGAATAGATGAAAGAGTAA
130 TCCCTAAAAAGATACATCTCTTGGATTATCCTGTAAAACAATAGGAAGAATAGATGAAAGAGTAA
* *
38700 GGTTAGTTAAAATTTATTCTTCATTCTCCTCTTTATCTCCAAATTCATCCTTTTCAACTCTCCCA
195 GGTTAGTTAAAATTTAATCTTCATTCTCCTCTTTATCTCCAAATTCATCATTTTCAACTCTCCCA
*
38765 CTTTCAACTCCAACGTCTTCT
260 CTTTCAACTCCAACGTATTCT
38786 TCATCCACTC
Statistics
Matches: 268, Mismatches: 12, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
284 54 0.20
285 214 0.80
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.35
Consensus pattern (284 bp):
TTTGAAACTTCAAATGGTATAACCTTTGAAACATTAAGAGACATGTCTTGTCGATCAAAAAATAA
TGCCTATTGGTCTTTCAAAGGTCACATGTTTTAGTCCTCCAAAAGTCATGATTCTTGAATCATCT
CCCTAAAAAGATACATCTCTTGGATTATCCTGTAAAACAATAGGAAGAATAGATGAAAGAGTAAG
GTTAGTTAAAATTTAATCTTCATTCTCCTCTTTATCTCCAAATTCATCATTTTCAACTCTCCCAC
TTTCAACTCCAACGTATTCTCCCA
Found at i:39990 original size:27 final size:26
Alignment explanation
Indices: 39959--40009 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
39949 GATGTAAGAG
39959 TTCTTT-TATTTTCTTTTTGTTTTTTTC
1 TTCTTTCT-TTTTCTTTTT-TTTTTTTC
*
39986 TTCTTTCTTTTTGTTTTTTTTTTT
1 TTCTTTCTTTTTCTTTTTTTTTTT
40010 GTTGCAACAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 6 0.27
27 15 0.68
28 1 0.05
ACGTcount: A:0.02, C:0.10, G:0.04, T:0.84
Consensus pattern (26 bp):
TTCTTTCTTTTTCTTTTTTTTTTTTC
Found at i:40797 original size:19 final size:20
Alignment explanation
Indices: 40759--40809 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
40749 GAAATACCTT
40759 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATTTTTAA
*
40779 TGAATATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
40798 T-AAAGATACATG
1 TGAAA-ATACATG
40810 CTCTTGGCTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 2 0.07
19 14 0.50
20 12 0.43
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:41289 original size:20 final size:20
Alignment explanation
Indices: 41266--41310 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
41256 ACATGCTAGA
41266 TCCTTCAGCTAAGATGAAGC
1 TCCTTCAGCTAAGATGAAGC
41286 TCCTTCAGCTAAGATGAAGC
1 TCCTTCAGCTAAGATGAAGC
41306 TCCTT
1 TCCTT
41311 AAGTGATGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.29
Consensus pattern (20 bp):
TCCTTCAGCTAAGATGAAGC
Found at i:43511 original size:30 final size:30
Alignment explanation
Indices: 43477--43547 Score: 124
Period size: 30 Copynumber: 2.4 Consensus size: 30
43467 CACTCTAGAA
* *
43477 CTTCAAGGCTTTTACTAGTCCTCTTCTAGT
1 CTTCAACGCTCTTACTAGTCCTCTTCTAGT
43507 CTTCAACGCTCTTACTAGTCCTCTTCTAGT
1 CTTCAACGCTCTTACTAGTCCTCTTCTAGT
43537 CTTCAACGCTC
1 CTTCAACGCTC
43548 AAGCCTTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.17, C:0.32, G:0.11, T:0.39
Consensus pattern (30 bp):
CTTCAACGCTCTTACTAGTCCTCTTCTAGT
Found at i:48439 original size:21 final size:21
Alignment explanation
Indices: 48413--48458 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
48403 TGATTTATTA
48413 TTATGGAGTTCAAGTTTGTTG
1 TTATGGAGTTCAAGTTTGTTG
*
48434 TTATGGATTTCAAGTTTGTTG
1 TTATGGAGTTCAAGTTTGTTG
48455 TTAT
1 TTAT
48459 TAATGTCAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.20, C:0.04, G:0.24, T:0.52
Consensus pattern (21 bp):
TTATGGAGTTCAAGTTTGTTG
Found at i:48467 original size:21 final size:21
Alignment explanation
Indices: 48422--48467 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
48412 ATTATGGAGT
* *
48422 TCAAGTTTGTTGTTATGGATT
1 TCAAGTTTGTTGTTATGAATG
*
48443 TCAAGTTTGTTGTTATTAATG
1 TCAAGTTTGTTGTTATGAATG
48464 TCAA
1 TCAA
48468 TGCTATATGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.24, C:0.07, G:0.20, T:0.50
Consensus pattern (21 bp):
TCAAGTTTGTTGTTATGAATG
Found at i:49517 original size:21 final size:20
Alignment explanation
Indices: 49476--49526 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
49466 AATCTCAATT
* *
49476 ACTAAACCTCAAACTCCAAA
1 ACTAAAACTCAAACACCAAA
*
49496 ATCTAAAACTCAAACACTAAA
1 A-CTAAAACTCAAACACCAAA
*
49517 ACTTAAACTC
1 ACTAAAACTC
49527 TTACCCTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.51, C:0.29, G:0.00, T:0.20
Consensus pattern (20 bp):
ACTAAAACTCAAACACCAAA
Found at i:49597 original size:34 final size:34
Alignment explanation
Indices: 49559--49628 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
49549 ATGTAAGTTA
49559 AAGAAATATTTATTTATGAGTAAAAATTTAAATT
1 AAGAAATATTTATTTATGAGTAAAAATTTAAATT
*
49593 AAGAAATATTTATTTATGAGTAATAATTTAAATT
1 AAGAAATATTTATTTATGAGTAAAAATTTAAATT
49627 AA
1 AA
49629 ATATAACTCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (34 bp):
AAGAAATATTTATTTATGAGTAAAAATTTAAATT
Found at i:52198 original size:16 final size:16
Alignment explanation
Indices: 52179--52214 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
52169 TGTTAACCGA
*
52179 TAACTTTTCTAACAAC
1 TAACATTTCTAACAAC
*
52195 TAACATTTCTAACAGC
1 TAACATTTCTAACAAC
52211 TAAC
1 TAAC
52215 CACAAACTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.39, C:0.25, G:0.03, T:0.33
Consensus pattern (16 bp):
TAACATTTCTAACAAC
Found at i:53000 original size:5 final size:5
Alignment explanation
Indices: 52990--53037 Score: 62
Period size: 5 Copynumber: 9.8 Consensus size: 5
52980 TATTATCTTG
* * *
52990 TTTTA TTTTA TTTTA TTTTA TCTTA -TTCA TTTTA TTTTA TTATA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
53038 TGTCTTCTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
4 2 0.06
5 34 0.94
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:53005 original size:23 final size:23
Alignment explanation
Indices: 52964--53032 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
52954 GTTTTTTTTT
* **
52964 TTGTTTTTTTTTACCTTATTATC
1 TTGTTTTATTTTATTTTATTATC
52987 TTGTTTTATTTTATTTTATTTTATC
1 TTGTTTTATTTTATTTTA--TTATC
* *
53012 TT-ATTCATTTTATTTTATTAT
1 TTGTTTTATTTTATTTTATTAT
53033 ATTTTTGTCT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
22 4 0.10
23 15 0.38
24 13 0.33
25 7 0.18
ACGTcount: A:0.17, C:0.07, G:0.03, T:0.72
Consensus pattern (23 bp):
TTGTTTTATTTTATTTTATTATC
Found at i:53015 original size:33 final size:34
Alignment explanation
Indices: 52957--53037 Score: 92
Period size: 33 Copynumber: 2.4 Consensus size: 34
52947 TTCGATAGTT
* * * *
52957 TTTTTTTTTGTTTTTTTTTACCTTATT-ATCTTG
1 TTTTATTTTATTTTATTTTACCTTATTCATCTTA
* *
52990 TTTTATTTTATTTTATTTTATCTTATTCATTTTA
1 TTTTATTTTATTTTATTTTACCTTATTCATCTTA
*
53024 TTTTATTATATTTT
1 TTTTATTTTATTTT
53038 TGTCTTCTAT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
33 23 0.57
34 17 0.43
ACGTcount: A:0.16, C:0.06, G:0.02, T:0.75
Consensus pattern (34 bp):
TTTTATTTTATTTTATTTTACCTTATTCATCTTA
Found at i:56654 original size:17 final size:18
Alignment explanation
Indices: 56616--56664 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 18
56606 GAAAAAAACA
56616 AAGATAAAAAGAAATATGAG
1 AAGA-AAAAAGAAATA-GAG
56636 AAGAAAAAAGAAATA-AG
1 AAGAAAAAAGAAATAGAG
56653 AAG-AAAAAGAAA
1 AAGAAAAAAGAAA
56665 GAAAAAGGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.31
17 5 0.17
19 11 0.38
20 4 0.14
ACGTcount: A:0.73, C:0.00, G:0.18, T:0.08
Consensus pattern (18 bp):
AAGAAAAAAGAAATAGAG
Found at i:56657 original size:20 final size:21
Alignment explanation
Indices: 56623--56690 Score: 74
Period size: 20 Copynumber: 3.4 Consensus size: 21
56613 ACAAAGATAA
*
56623 AAAGAAATATG-AGAAGAAA-
1 AAAGAAATAAGAAGAAGAAAG
56642 AAAGAAATAAGAAGAA-AAAG
1 AAAGAAATAAGAAGAAGAAAG
56662 AAAGAAA-AAGGAA-AAGAAAG
1 AAAGAAATAA-GAAGAAGAAAG
56682 AAAGCAAAT
1 AAAG-AAAT
56691 CAAGTATTTC
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
19 17 0.40
20 22 0.52
21 3 0.07
ACGTcount: A:0.72, C:0.01, G:0.21, T:0.06
Consensus pattern (21 bp):
AAAGAAATAAGAAGAAGAAAG
Found at i:56661 original size:16 final size:16
Alignment explanation
Indices: 56621--56680 Score: 66
Period size: 16 Copynumber: 3.6 Consensus size: 16
56611 AAACAAAGAT
56621 AAAAAGAAATATGAGAAG
1 AAAAAGAAATA--AGAAG
56639 AAAAAAGAAATAAGAAG
1 -AAAAAGAAATAAGAAG
* *
56656 AAAAAGAAAGAAAAAG
1 AAAAAGAAATAAGAAG
*
56672 GAAAAGAAA
1 AAAAAGAAA
56681 GAAAGCAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
16 22 0.58
17 5 0.13
19 11 0.29
ACGTcount: A:0.75, C:0.00, G:0.20, T:0.05
Consensus pattern (16 bp):
AAAAAGAAATAAGAAG
Found at i:57582 original size:25 final size:25
Alignment explanation
Indices: 57535--57596 Score: 83
Period size: 25 Copynumber: 2.5 Consensus size: 25
57525 GGGCAATTTT
*
57535 TTTTCAAAA-TTTTTGATTAAATAA
1 TTTTCAAAATTTTTTAATTAAATAA
*
57559 TTTTCAAAATTCTTTTAATT-AATAT
1 TTTTCAAAATT-TTTTAATTAAATAA
57584 TTTTCAAAATTTT
1 TTTTCAAAATTTT
57597 GGAAATAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 11 0.32
25 16 0.47
26 7 0.21
ACGTcount: A:0.37, C:0.06, G:0.02, T:0.55
Consensus pattern (25 bp):
TTTTCAAAATTTTTTAATTAAATAA
Found at i:67046 original size:21 final size:21
Alignment explanation
Indices: 66979--67038 Score: 102
Period size: 21 Copynumber: 2.9 Consensus size: 21
66969 TTCTATGTGG
* *
66979 TTCTTTGGGATATATATGTAA
1 TTCTTTGGAACATATATGTAA
67000 TTCTTTGGAACATATATGTAA
1 TTCTTTGGAACATATATGTAA
67021 TTCTTTGGAACATATATG
1 TTCTTTGGAACATATATG
67039 CGGTTCTTCG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.30, C:0.08, G:0.17, T:0.45
Consensus pattern (21 bp):
TTCTTTGGAACATATATGTAA
Found at i:67123 original size:21 final size:21
Alignment explanation
Indices: 67094--67167 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
67084 TCGTTAAGGA
* *
67094 GTGGCCCTTTGAGACATATAT
1 GTGGTCCTTCGAGACATATAT
* * *
67115 GTGGTCCTTCGGGATATCTAT
1 GTGGTCCTTCGAGACATATAT
* *
67136 GTGGTCATTCAAGACATATAT
1 GTGGTCCTTCGAGACATATAT
*
67157 GTGGTCATTCG
1 GTGGTCCTTCG
67168 GAACAAATTC
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.35
Consensus pattern (21 bp):
GTGGTCCTTCGAGACATATAT
Found at i:69323 original size:22 final size:19
Alignment explanation
Indices: 69274--69347 Score: 69
Period size: 20 Copynumber: 3.7 Consensus size: 19
69264 AATCTAAATT
*
69274 GGGTATTGATACCTAGATG
1 GGGTATCGATACCTAGATG
69293 GGGTATCGATACCGTAGTATAG
1 GGGTATCGATACC-TAG-AT-G
* *
69315 GGTTATCGATACC-ATGGTG
1 GGGTATCGATACCTA-GATG
69334 AGGGTATCGATACC
1 -GGGTATCGATACC
69348 AGGCTATACC
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
19 13 0.28
20 17 0.37
21 3 0.07
22 13 0.28
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (19 bp):
GGGTATCGATACCTAGATG
Found at i:69343 original size:20 final size:21
Alignment explanation
Indices: 69293--69348 Score: 69
Period size: 22 Copynumber: 2.7 Consensus size: 21
69283 TACCTAGATG
* *
69293 GGGTATCGATACCGTAGTATA
1 GGGTATCGATACCATAGTAGA
*
69314 GGGTTATCGATACCATGGT-GA
1 GGG-TATCGATACCATAGTAGA
69335 GGGTATCGATACCA
1 GGGTATCGATACCA
69349 GGCTATACCG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 11 0.35
21 7 0.23
22 13 0.42
ACGTcount: A:0.27, C:0.16, G:0.30, T:0.27
Consensus pattern (21 bp):
GGGTATCGATACCATAGTAGA
Found at i:69418 original size:22 final size:22
Alignment explanation
Indices: 69390--69431 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
69380 CATTAAGGGG
* *
69390 GTATCGATACCCTAATAGGGTA
1 GTATCGATACCATAAAAGGGTA
69412 GTATCGATACCATAAAAGGG
1 GTATCGATACCATAAAAGGG
69432 GTAATGATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.24
Consensus pattern (22 bp):
GTATCGATACCATAAAAGGGTA
Found at i:69815 original size:58 final size:58
Alignment explanation
Indices: 69753--69897 Score: 173
Period size: 59 Copynumber: 2.5 Consensus size: 58
69743 TACCAAATGA
*
69753 CACTTTGTGTGCAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGG
1 CACTTTGTGTGCAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGG
* * ** * * *
69811 CACTTCGTGTCCTAGCATGATAAGAAATTCATACTAAGTGTGTGAATTTCGGTATTGGG
1 CACTTTGTGTGC-AAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGG
** * *
69870 CACCCTGTGTGCTAAAGGATAAGAAATT
1 CACTTTGTGTGCAAAATGATAAGAAATT
69898 TATGATAAAT
Statistics
Matches: 70, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
58 22 0.31
59 48 0.69
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.32
Consensus pattern (58 bp):
CACTTTGTGTGCAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGG
Found at i:70377 original size:68 final size:68
Alignment explanation
Indices: 70292--70685 Score: 581
Period size: 68 Copynumber: 5.8 Consensus size: 68
70282 TAAATAATCA
* * * *
70292 TGAGGCCTAATTGTGCATATGATAGAAATGTGTCATTAATGCCAGTTAGATGAAAGATTAAGTGT
1 TGAGGCCTAACTGTGCATATGATAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGT
70357 CTT
66 CTT
** *
70360 TGAGGCCTAACAATGCATATGATAGAAAGGTGTCATTTATGCGAGTTAGATGAAAGACTAAGTGT
1 TGAGGCCTAACTGTGCATATGATAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGT
70425 CTT
66 CTT
** * * * *
70428 TGAGGCCTAACAATGCATATGATATAAATGTGTCATTTATTCCAGTTAGATGAAAGGCTAAGTGT
1 TGAGGCCTAACTGTGCATATGATAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGT
70493 CTT
66 CTT
* * * * *
70496 TAAGGCCTAACTGTGCATATGATAGAAATGTGTCATTTATGTCATTTAGATGAAAGACTAAGTAT
1 TGAGGCCTAACTGTGCATATGATAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGT
70561 CTT
66 CTT
* * *
70564 TGGGGCTTAACTGTGCATATGATAGAAAGGTATCATTTATGCCAGTTAGATGAAAGACTAAGTGT
1 TGAGGCCTAACTGTGCATATGATAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGT
70629 CTT
66 CTT
* *
70632 TGGGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAA
1 TGAGGCCTAACTGTGCATATGATAGAAAGGTGTCATTTATGCCAGTTAGATGAA
70686 CGGTTAGGTA
Statistics
Matches: 294, Mismatches: 32, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
68 294 1.00
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.32
Consensus pattern (68 bp):
TGAGGCCTAACTGTGCATATGATAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGT
CTT
Found at i:74457 original size:22 final size:22
Alignment explanation
Indices: 74431--74472 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
74421 CATTAAGGGG
* *
74431 GTATCGATACCCTAATAGGGTA
1 GTATCGATACCATAAAAGGGTA
*
74453 GTATCTATACCATAAAAGGG
1 GTATCGATACCATAAAAGGG
74473 GTATTGATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (22 bp):
GTATCGATACCATAAAAGGGTA
Found at i:74954 original size:58 final size:59
Alignment explanation
Indices: 74817--74960 Score: 202
Period size: 59 Copynumber: 2.5 Consensus size: 59
74807 AAATGTTACC
* * *
74817 AAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCGTGTGCTAGCATGATAAG
1 AAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACCTCGTGTGCTAGAAGGATAAG
** * *
74876 AAATTCATACTAAGCATATGAATTTCTGTATTGGGCATCCT-GTGTGCTA-AAGGATAAG
1 AAATTCATACTAAGTGTATGAATTTCCGTATAGGGCA-CCTCGTGTGCTAGAAGGATAAG
74934 AAATTCATACTAAGTGTATGAATTTCC
1 AAATTCATACTAAGTGTATGAATTTCC
74961 TTATGGGAAA
Statistics
Matches: 74, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
58 31 0.42
59 41 0.55
60 2 0.03
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (59 bp):
AAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACCTCGTGTGCTAGAAGGATAAG
Found at i:75585 original size:135 final size:136
Alignment explanation
Indices: 75335--75657 Score: 540
Period size: 135 Copynumber: 2.4 Consensus size: 136
75325 AAAGATCATG
*
75335 AGGCCTAATTGTGCATATGATGGAAAGGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGTCT
1 AGGCCTAATTGTGCATATGATAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGTCT
*
75400 TTGAGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTA
66 TTGAGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAATTAGATGAAAGACTAAGTA
75465 TCTTTA
131 TCTTTA
* * *
75471 ATGCCTAACTGTGCATATAATAGAAAGGTGTCATTTATG-CAGTTAGATGAAAGACTAAGTGTCT
1 AGGCCTAATTGTGCATATGATAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGTCT
* * *
75535 TTGAGGCCTAACTGTGCATATGACAGAGATGTGTCATTTATGCCAATTAGATGAAAGACTAAGTG
66 TTGAGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAATTAGATGAAAGACTAAGTA
*
75600 TCTTTG
131 TCTTTA
* *
75606 AGGCCTAATTGTGCACATGATAGAAAGGTGTCATTTATGTCAGTTAGATGAA
1 AGGCCTAATTGTGCATATGATAGAAAGGTGTCATTTATGCCAGTTAGATGAA
75658 CTGTTAGGTA
Statistics
Matches: 173, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
135 126 0.73
136 47 0.27
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.31
Consensus pattern (136 bp):
AGGCCTAATTGTGCATATGATAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGTCT
TTGAGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAATTAGATGAAAGACTAAGTA
TCTTTA
Found at i:75675 original size:68 final size:68
Alignment explanation
Indices: 75333--75657 Score: 517
Period size: 68 Copynumber: 4.8 Consensus size: 68
75323 TAAAAGATCA
* *
75333 TGAGGCCTAATTGTGCATATGATGGAAAGGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGT
1 TGAGGCCTAACTGTGCATATGATAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGT
75398 CTT
66 CTT
* *
75401 TGAGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTAT
1 TGAGGCCTAACTGTGCATATGATAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGT
75466 CTT
66 CTT
* * *
75469 TAATGCCTAACTGTGCATATAATAGAAAGGTGTCATTTATG-CAGTTAGATGAAAGACTAAGTGT
1 TGAGGCCTAACTGTGCATATGATAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGT
75533 CTT
66 CTT
* * * *
75536 TGAGGCCTAACTGTGCATATGACAGAGATGTGTCATTTATGCCAATTAGATGAAAGACTAAGTGT
1 TGAGGCCTAACTGTGCATATGATAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGT
75601 CTT
66 CTT
* * *
75604 TGAGGCCTAATTGTGCACATGATAGAAAGGTGTCATTTATGTCAGTTAGATGAA
1 TGAGGCCTAACTGTGCATATGATAGAAAGGTGTCATTTATGCCAGTTAGATGAA
75658 CTGTTAGGTA
Statistics
Matches: 233, Mismatches: 23, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
67 60 0.26
68 173 0.74
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.31
Consensus pattern (68 bp):
TGAGGCCTAACTGTGCATATGATAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGT
CTT
Found at i:76199 original size:49 final size:49
Alignment explanation
Indices: 76100--76213 Score: 158
Period size: 49 Copynumber: 2.3 Consensus size: 49
76090 TGTATACTCA
* * * **
76100 GCAAATAAATAATGAAAGGGAAAAATATACAGAATGGTAGGTATTCTGG
1 GCAAATAAAGAATAAAAGGGAAAAATATACAGAATGATAGGTATAATGG
76149 GCAAATAAAGAATAAAAGGGAAAAATATACAGAATGATAGGTATAATGG
1 GCAAATAAAGAATAAAAGGGAAAAATATACAGAATGATAGGTATAATGG
*
76198 GCATACT-AAGAATAAA
1 GCA-AATAAAGAATAAA
76214 TTCCATGATG
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
49 56 0.97
50 2 0.03
ACGTcount: A:0.52, C:0.06, G:0.22, T:0.20
Consensus pattern (49 bp):
GCAAATAAAGAATAAAAGGGAAAAATATACAGAATGATAGGTATAATGG
Found at i:82292 original size:19 final size:19
Alignment explanation
Indices: 82263--82299 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 19
82253 AGATTTAAAT
82263 CAAACCCAAACCCAAAAAAA
1 CAAACCCAAA-CCAAAAAAA
82283 CAAA-CCAAACCAAAAAA
1 CAAACCCAAACCAAAAAA
82300 CCCGACTCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 5 0.29
20 4 0.24
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (19 bp):
CAAACCCAAACCAAAAAAA
Found at i:83613 original size:15 final size:16
Alignment explanation
Indices: 83586--83616 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
83576 GATAATTATT
83586 TTACTTGTATTATATA
1 TTACTTGTATTATATA
83602 TTACTT-TATTATATA
1 TTACTTGTATTATATA
83617 CCTAATATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.58
Consensus pattern (16 bp):
TTACTTGTATTATATA
Found at i:95607 original size:8 final size:8
Alignment explanation
Indices: 95584--95686 Score: 57
Period size: 8 Copynumber: 12.0 Consensus size: 8
95574 ACTATGCTTG
*
95584 AAGAAACA
1 AAGAAAAA
95592 AA-AAAAA
1 AAGAAAAA
95599 AAGAAAAA
1 AAGAAAAA
* *
95607 AAG-GACA
1 AAGAAAAA
*
95614 AAGAAAGA
1 AAGAAAAA
95622 AAGAATAAA
1 AAGAA-AAA
95631 AAGATGAAAA
1 AAGA--AAAA
*
95641 ATGAAAAA
1 AAGAAAAA
95649 AATGAAATGAAA
1 AA-G-AA--AAA
95661 AATGAAAAA
1 AA-GAAAAA
95670 AAGAGAAAA
1 AAGA-AAAA
*
95679 GAGAAAAA
1 AAGAAAAA
95687 TAAGGGTTCG
Statistics
Matches: 76, Mismatches: 9, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
7 11 0.14
8 28 0.37
9 19 0.25
10 8 0.11
11 3 0.04
12 7 0.09
ACGTcount: A:0.76, C:0.02, G:0.17, T:0.06
Consensus pattern (8 bp):
AAGAAAAA
Found at i:96823 original size:105 final size:105
Alignment explanation
Indices: 96629--97237 Score: 799
Period size: 105 Copynumber: 5.8 Consensus size: 105
96619 TGATCCACTG
* * * * * **
96629 CAGAAGCAGGTGAACCAACATTTCCAGAAGAGTTCCTAATAGGAAGAACTCGTTGTAAAGGAGAA
1 CAGAAGGAGGTGAAACAACATTTCCAGAAGAGTTCATAATAAGAAGAACTCATCCTAAAGGAGAA
* * *
96694 AGTCCGTAATGAGAAGAACATGTTCCTTTCAAATTCACCC
66 AGTTCATAATGAGAAGAACATGTTCCTTTCAAATCCACCC
* * * ** *
96734 CATAAAGAGGTGAAACAACGTTTTTAGAAGAGTTCATAATAAGAAGAACTCGTCCTAAAGGAGAA
1 CAGAAGGAGGTGAAACAACATTTCCAGAAGAGTTCATAATAAGAAGAACTCATCCTAAAGGAGAA
* * *
96799 AGTTCGTAGTGAGAAGAACCTGTTCCTTTCAAATCCACCC
66 AGTTCATAATGAGAAGAACATGTTCCTTTCAAATCCACCC
* * *
96839 CAGAAAGTAGGTGAAACAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCTAAAAGAGA
1 CAG-AAGGAGGTGAAACAACATTTCCAGAAGAGTTCATAATAAGAAGAACTCATCCTAAAGGAGA
*
96904 AAGTTCATAATGAGAATAACATGTTCCTTTCAAATCCACCC
65 AAGTTCATAATGAGAAGAACATGTTCCTTTCAAATCCACCC
* * * *
96945 TAGAAGGAGATGAAACAACATTTCCAGAAGAGTTCATAATAAGAAGAACTCTTTCTAAAGGAGAA
1 CAGAAGGAGGTGAAACAACATTTCCAGAAGAGTTCATAATAAGAAGAACTCATCCTAAAGGAGAA
* **
97010 AGTTCATAATGAGAGGAACATGTTCCTTTCAAATAAACCC
66 AGTTCATAATGAGAAGAACATGTTCCTTTCAAATCCACCC
* * * * *
97050 CAGAAGGAGGTGAATCAACATTTTCAGAAGAGTTCATAATGAGAAGAACTCATCTTAAAGGGGAA
1 CAGAAGGAGGTGAAACAACATTTCCAGAAGAGTTCATAATAAGAAGAACTCATCCTAAAGGAGAA
* **
97115 AGTTC-TAATGAGAAGAACTTGTTCCTTTCAAATCCACTG
66 AGTTCATAATGAGAAGAACATGTTCCTTTCAAATCCACCC
* * * * *
97154 CATAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAATAACTCA-CCTTAAAGGAGG
1 CAGAAGGAGGTGAAACAACATTTCCAGAAGAGTTCATAATAAGAAGAACTCATCC-TAAAGGAGA
97218 AAGTTCATAATGAGAAGAAC
65 AAGTTCATAATGAGAAGAAC
97238 TTTCTCAACT
Statistics
Matches: 440, Mismatches: 61, Indels: 6
0.87 0.12 0.01
Matches are distributed among these distances:
103 1 0.00
104 89 0.20
105 258 0.59
106 92 0.21
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (105 bp):
CAGAAGGAGGTGAAACAACATTTCCAGAAGAGTTCATAATAAGAAGAACTCATCCTAAAGGAGAA
AGTTCATAATGAGAAGAACATGTTCCTTTCAAATCCACCC
Found at i:97005 original size:211 final size:207
Alignment explanation
Indices: 96629--97237 Score: 806
Period size: 211 Copynumber: 2.9 Consensus size: 207
96619 TGATCCACTG
* * * * **
96629 CAGAAGCAGGTGAACCAACATTTCCAGAAGAGTTCCTAAT-AGGAAGAACTCGTTGTAAAGGAGA
1 CAGAAGGAGGTGAAACAACATTTCCAGAAGAGTTCATAATGA-GAAGAACTCATCCTAAAGGAGA
* * * * *
96693 AAGTCCGTAATGAGAAGAACATGTTCCTTTCAAATTCACCCCATAAAGAGGTGAAACAACGTTTT
65 AAGTTC-TAATGAGAAGAACATGTTCCTTTCAAATCCA-CCCATAAGGAGGTGAAACAACATTTC
* * * *
96758 TAGAAGAGTTCATAATAAGAAGAACTCGTCCTAAAGGAGAAAGTTCGTAGTGAGAAGAACCTGTT
128 CAGAAGAGTTCATAATAAGAAGAACTC-TCCTAAAGGAGAAAGTTCATAATGAGAAGAACATGTT
**
96823 CCTTTCAAATCCACCC
192 CCTTTCAAATAAACCC
* *
96839 CAGAAAGTAGGTGAAACAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCTAAAAGAGA
1 CAG-AAGGAGGTGAAACAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCTAAAGGAGA
* * *
96904 AAGTTCATAATGAGAATAACATGTTCCTTTCAAATCCACCCTAGAAGGAGATGAAACAACATTTC
65 AAGTTC-TAATGAGAAGAACATGTTCCTTTCAAATCCACCC-ATAAGGAGGTGAAACAACATTTC
* *
96969 CAGAAGAGTTCATAATAAGAAGAACTCTTTCTAAAGGAGAAAGTTCATAATGAGAGGAACATGTT
128 CAGAAGAGTTCATAATAAGAAGAACTC-TCCTAAAGGAGAAAGTTCATAATGAGAAGAACATGTT
97034 CCTTTCAAATAAACCC
192 CCTTTCAAATAAACCC
* * * *
97050 CAGAAGGAGGTGAATCAACATTTTCAGAAGAGTTCATAATGAGAAGAACTCATCTTAAAGGGGAA
1 CAGAAGGAGGTGAAACAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCTAAAGGAGAA
* * *
97115 AGTTCTAATGAGAAGAACTTGTTCCTTTCAAATCCACTGCATAAGGAGGTGAACCAACATTTCCA
66 AGTTCTAATGAGAAGAACATGTTCCTTTCAAATCCAC-CCATAAGGAGGTGAAACAACATTTCCA
* * * *
97180 GAAGAGTTCATAATGAGAATAACTCACCTTAAAGGAGGAAGTTCATAATGAGAAGAAC
130 GAAGAGTTCATAATAAGAAGAACTCTCC-TAAAGGAGAAAGTTCATAATGAGAAGAAC
97238 TTTCTCAACT
Statistics
Matches: 351, Mismatches: 43, Indels: 11
0.87 0.11 0.03
Matches are distributed among these distances:
208 1 0.00
209 102 0.29
210 68 0.19
211 179 0.51
212 1 0.00
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (207 bp):
CAGAAGGAGGTGAAACAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCTAAAGGAGAA
AGTTCTAATGAGAAGAACATGTTCCTTTCAAATCCACCCATAAGGAGGTGAAACAACATTTCCAG
AAGAGTTCATAATAAGAAGAACTCTCCTAAAGGAGAAAGTTCATAATGAGAAGAACATGTTCCTT
TCAAATAAACCC
Found at i:98834 original size:15 final size:16
Alignment explanation
Indices: 98808--98838 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
98798 GATATTTATT
98808 TTACTTGTATTATATA
1 TTACTTGTATTATATA
98824 TTACTT-TATTATATA
1 TTACTTGTATTATATA
98839 CCTAATATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.58
Consensus pattern (16 bp):
TTACTTGTATTATATA
Found at i:102111 original size:43 final size:43
Alignment explanation
Indices: 102050--102136 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
102040 CATAAATATA
102050 TATATATATATATATATATTGTTAAATAGATTCAATCTCAAAT
1 TATATATATATATATATATTGTTAAATAGATTCAATCTCAAAT
102093 TATATATATATATATATATTGTTAAATAGATTCAATCTCAAAT
1 TATATATATATATATATATTGTTAAATAGATTCAATCTCAAAT
102136 T
1 T
102137 TTAGTATAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.45
Consensus pattern (43 bp):
TATATATATATATATATATTGTTAAATAGATTCAATCTCAAAT
Found at i:103315 original size:37 final size:37
Alignment explanation
Indices: 103265--103338 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
103255 TACGATTTAC
* *
103265 ATTAACTTCGAGTCGTAATTTCATAAACTCGACTTGA
1 ATTAACTTCGAGTCATAATTTCATAAACTCAACTTGA
103302 ATTAACTTCGAGTCATAATTTCATAAACTCAACTTGA
1 ATTAACTTCGAGTCATAATTTCATAAACTCAACTTGA
103339 TTTGAAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (37 bp):
ATTAACTTCGAGTCATAATTTCATAAACTCAACTTGA
Found at i:107283 original size:3 final size:3
Alignment explanation
Indices: 107277--107363 Score: 63
Period size: 3 Copynumber: 27.3 Consensus size: 3
107267 CTACAGAAGA
107277 AAT AAT AAT AAAT AAT AAAT AA- ATAT AAT ATAT AAT GAAT AAT AAT
1 AAT AAT AAT -AAT AAT -AAT AAT A-AT AAT A-AT AAT -AAT AAT AAT
* *
107323 AAT ATAT AAT AAAT AA- ATAT AAT AAT AAA AAC AAT -AT AAT A
1 AAT A-AT AAT -AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT A
107364 CTATATTTAA
Statistics
Matches: 70, Mismatches: 3, Indels: 22
0.74 0.03 0.23
Matches are distributed among these distances:
2 4 0.06
3 46 0.66
4 20 0.29
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:107292 original size:7 final size:7
Alignment explanation
Indices: 107280--107351 Score: 76
Period size: 7 Copynumber: 10.3 Consensus size: 7
107270 CAGAAGAAAT
107280 AATAATA
1 AATAATA
107287 AATAATA
1 AATAATA
107294 AATAA-A
1 AATAATA
*
107300 TATAATA
1 AATAATA
* *
107307 TATAATG
1 AATAATA
107314 AATAAT-
1 AATAATA
107320 AATAATA
1 AATAATA
*
107327 TATAATA
1 AATAATA
107334 AATAAATA
1 AAT-AATA
107342 TAATAATA
1 -AATAATA
107350 AA
1 AA
107352 AACAATATAA
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
6 11 0.20
7 34 0.61
8 8 0.14
9 3 0.05
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (7 bp):
AATAATA
Found at i:107304 original size:13 final size:13
Alignment explanation
Indices: 107288--107351 Score: 71
Period size: 13 Copynumber: 4.9 Consensus size: 13
107278 ATAATAATAA
107288 ATAATAAATAAAT
1 ATAATAAATAAAT
*
107301 ATAATATAT-AAT
1 ATAATAAATAAAT
107313 GAATAAT-AATAATAT
1 --ATAATAAATAA-AT
107328 ATAATAAATAAAT
1 ATAATAAATAAAT
107341 ATAAT-AATAAA
1 ATAATAAATAAA
107352 AACAATATAA
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
12 9 0.20
13 22 0.50
14 11 0.25
15 2 0.05
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (13 bp):
ATAATAAATAAAT
Found at i:107306 original size:20 final size:20
Alignment explanation
Indices: 107276--107363 Score: 94
Period size: 20 Copynumber: 4.5 Consensus size: 20
107266 CCTACAGAAG
107276 AAATAATAATAAATAATAAAT
1 AAAT-ATAATAAATAATAAAT
* *
107297 AAATATAATATATAATGAAT
1 AAATATAATAAATAATAAAT
*
107317 -AATAATAATATATAATAAAT
1 AAAT-ATAATAAATAATAAAT
107337 AAATATAAT-AATAA-AAA-
1 AAATATAATAAATAATAAAT
*
107354 CAATATAATA
1 AAATATAATA
107364 CTATATTTAA
Statistics
Matches: 59, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
17 8 0.14
18 3 0.05
19 7 0.12
20 34 0.58
21 7 0.12
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.31
Consensus pattern (20 bp):
AAATATAATAAATAATAAAT
Found at i:107361 original size:23 final size:23
Alignment explanation
Indices: 107318--107361 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
107308 ATAATGAATA
* *
107318 ATAATAATATATAATAAATAAAT
1 ATAATAATATAAAACAAATAAAT
107341 ATAATAATA-AAAACAATATAA
1 ATAATAATATAAAACAA-ATAA
107362 TACTATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (23 bp):
ATAATAATATAAAACAAATAAAT
Found at i:107362 original size:40 final size:40
Alignment explanation
Indices: 107277--107369 Score: 125
Period size: 40 Copynumber: 2.3 Consensus size: 40
107267 CTACAGAAGA
* * **
107277 AATAATAATAAATAATAAATAAATATAATATATAATGAAT
1 AATAATAATATATAATAAATAAATATAATATAAAAACAAT
107317 AATAATAATATATAATAAATAAATATAATAATAAAAACAAT
1 AATAATAATATATAATAAATAAATATAAT-ATAAAAACAAT
*
107358 -ATAATACTATAT
1 AATAATAATATAT
107370 TTAAAAAATA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
40 39 0.83
41 8 0.17
ACGTcount: A:0.65, C:0.02, G:0.01, T:0.32
Consensus pattern (40 bp):
AATAATAATATATAATAAATAAATATAATATAAAAACAAT
Found at i:107559 original size:75 final size:75
Alignment explanation
Indices: 107459--107756 Score: 306
Period size: 75 Copynumber: 4.0 Consensus size: 75
107449 TCAAAGTCGT
* * * *
107459 TTTTTTTAAAATATATATGTTATACGTTTTCAAAAATATTTT-CAAAAACTATAT-TTATACATT
1 TTTTTTTAAAAAATATATATTATACGTTTTCAAAAATATTTTAAAAAAACTATATATTATACGTT
107522 TACAAAAAATG
66 T-CAAAAAATG
*
107533 TTTTTTTAAAAAAATATATATTATACGTTTTCAAAAATATTTTTAAAAAAAACTATATATTTTAC
1 TTTTTTT-AAAAAATATATATTATACGTTTTCAAAAATA-TTTT-AAAAAAACTATATATTATAC
*
107598 GTTTTAAAAAAT-
63 GTTTCAAAAAATG
* * * *
107610 ATTTTTT-AAAACTATATATTATACGTTTTCAAATATGTTTTTTAAAAAAACTATATATTATACG
1 TTTTTTTAAAAAATATATATTATACGTTTTCAAA-A-ATATTTTAAAAAAACTATATATTATACG
*
107674 TGTTC---AAATA
64 T-TTCAAAAAATG
* * * * * *
107684 TATTTTTAAAAACTATATATTATACGAGTTCCAAACATATTTT-CAAAAACTATATATTATACGT
1 TTTTTTTAAAAAATATATATTATACG-TTTTCAAAAATATTTTAAAAAAACTATATATTATACG-
107748 TTTCAAAAA
64 TTTCAAAAA
107757 CATATACTAT
Statistics
Matches: 189, Mismatches: 20, Indels: 28
0.80 0.08 0.12
Matches are distributed among these distances:
73 26 0.14
74 18 0.10
75 93 0.49
76 19 0.10
77 7 0.04
78 18 0.10
79 8 0.04
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (75 bp):
TTTTTTTAAAAAATATATATTATACGTTTTCAAAAATATTTTAAAAAAACTATATATTATACGTT
TCAAAAAATG
Found at i:107569 original size:39 final size:37
Alignment explanation
Indices: 107458--107756 Score: 268
Period size: 39 Copynumber: 8.0 Consensus size: 37
107448 TTCAAAGTCG
* * *
107458 TTTTTTTTAAAATATATATGTTATACGTTTTCAAAAA
1 TTTTTTTAAAAAAATATATATTATACGTTTTCAAAAA
* * * * *
107495 -TATTTTCAAAAACTATAT-TTATACATTTACAAAAAA
1 TTTTTTTAAAAAAATATATATTATACGTTTTC-AAAAA
107531 TGTTTTTTTAAAAAAATATATATTATACGTTTTCAAAAA
1 --TTTTTTTAAAAAAATATATATTATACGTTTTCAAAAA
* * *
107570 TATTTTTAAAAAAAACTATATATTTTACGTTTTAAAAAA
1 T-TTTTTTAAAAAAA-TATATATTATACGTTTTCAAAAA
* *
107609 TATTTTTT--AAAACTATATATTATACGTTTTCAAATA
1 T-TTTTTTAAAAAAATATATATTATACGTTTTCAAAAA
* *
107645 TGTTTTTTAAAAAAACTATATATTATACGTGTTCAAATA
1 T-TTTTTTAAAAAAA-TATATATTATACGTTTTCAAAAA
* * * * *
107684 TATTTTT-AAAAACTATATATTATACGAGTTCCAAACA
1 TTTTTTTAAAAAAATATATATTATACG-TTTTCAAAAA
* * *
107721 -TATTTTCAAAAACTATATATTATACGTTTTCAAAAA
1 TTTTTTTAAAAAAATATATATTATACGTTTTCAAAAA
107757 CATATACTAT
Statistics
Matches: 217, Mismatches: 33, Indels: 25
0.79 0.12 0.09
Matches are distributed among these distances:
35 10 0.05
36 70 0.32
37 35 0.16
38 21 0.10
39 71 0.33
40 10 0.05
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.44
Consensus pattern (37 bp):
TTTTTTTAAAAAAATATATATTATACGTTTTCAAAAA
Found at i:107590 original size:114 final size:112
Alignment explanation
Indices: 107461--107756 Score: 393
Period size: 114 Copynumber: 2.6 Consensus size: 112
107451 AAAGTCGTTT
* * *
107461 TTTTTAAAATA-TATATGTTATACGTTTTCAAAAATATTTTCAAAAACTATAT-TTATACATTTA
1 TTTTTAAAA-ACTATATATTATACGTTTTCAAAAATATTTTCAAAAACTATATATTATACGTTTT
*
107524 CAAAAAATGTTTTTTTAAAAAAA-TATATATTATACGTTTTCAAAAATA
65 CAAAAAATG-TTTTTTAAAAAAACTATATATTATACGTGTTCAAAAATA
* * **
107572 TTTTTAAAAAAAACTATATATTTTACGTTTTAAAAAATATTTTTTAAAACTATATATTATACGTT
1 TTTTT---AAAAACTATATATTATACGTTTTCAAAAATATTTTCAAAAACTATATATTATACGTT
* *
107637 TTC-AAATATGTTTTTTAAAAAAACTATATATTATACGTGTTCAAATATA
63 TTCAAAAAATGTTTTTTAAAAAAACTATATATTATACGTGTTCAAAAATA
* * *
107686 TTTTTAAAAACTATATATTATACGAGTTCCAAACATATTTTCAAAAACTATATATTATACGTTTT
1 TTTTTAAAAACTATATATTATACG-TTTTCAAAAATATTTTCAAAAACTATATATTATACGTTTT
107751 CAAAAA
65 CAAAAA
107757 CATATACTAT
Statistics
Matches: 159, Mismatches: 18, Indels: 14
0.83 0.09 0.07
Matches are distributed among these distances:
111 23 0.14
112 35 0.22
113 17 0.11
114 74 0.47
115 10 0.06
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (112 bp):
TTTTTAAAAACTATATATTATACGTTTTCAAAAATATTTTCAAAAACTATATATTATACGTTTTC
AAAAAATGTTTTTTAAAAAAACTATATATTATACGTGTTCAAAAATA
Found at i:107780 original size:24 final size:24
Alignment explanation
Indices: 107720--107779 Score: 86
Period size: 23 Copynumber: 2.5 Consensus size: 24
107710 AGTTCCAAAC
*
107720 ATATTTTCAAAAACTATATATTAT
1 ATATTTTCAAAAACTATATACTAT
**
107744 ACGTTTTCAAAAAC-ATATACTAT
1 ATATTTTCAAAAACTATATACTAT
107767 ATATTTTCAAAAA
1 ATATTTTCAAAAA
107780 AGTACATTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
23 19 0.61
24 12 0.39
ACGTcount: A:0.47, C:0.12, G:0.02, T:0.40
Consensus pattern (24 bp):
ATATTTTCAAAAACTATATACTAT
Found at i:118241 original size:20 final size:20
Alignment explanation
Indices: 118216--118254 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
118206 CCTTTGTCCA
118216 TTAATGCAA-ATTATTTGTGT
1 TTAATG-AACATTATTTGTGT
*
118236 TTAATGAACATTTTTTGTG
1 TTAATGAACATTATTTGTG
118255 GATCAAACCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.28, C:0.05, G:0.15, T:0.51
Consensus pattern (20 bp):
TTAATGAACATTATTTGTGT
Found at i:120888 original size:20 final size:20
Alignment explanation
Indices: 120851--120929 Score: 83
Period size: 20 Copynumber: 4.0 Consensus size: 20
120841 CAAAAGAAAC
* *
120851 AATAATAAACAATAAATAAAT
1 AATAATATATAAT-AATAAAT
120872 AA-AATATATAATGAAT-AAT
1 AATAATATATAAT-AATAAAT
*
120891 AATAATATATAATATATAATT
1 AATAATATATAATA-ATAAAT
120912 AATAA-ATATAATAATAAA
1 AATAATATATAATAATAAA
120930 AACTATATAA
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
19 10 0.20
20 31 0.62
21 9 0.18
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (20 bp):
AATAATATATAATAATAAAT
Found at i:120891 original size:27 final size:27
Alignment explanation
Indices: 120852--120941 Score: 85
Period size: 27 Copynumber: 3.2 Consensus size: 27
120842 AAAAGAAACA
*
120852 ATAATAAACAATAAATAAATAAAATAT
1 ATAATAAATAATAAATAAATAAAATAT
* *
120879 ATAATGAATAAT-AATAATATATAATAT
1 ATAATAAATAATAAATAA-ATAAAATAT
*
120906 ATAATTAATAAATATAAT-AATAAAAACTAT
1 ATAATAAAT-AATA-AATAAAT-AAAA-TAT
120936 ATAATA
1 ATAATA
120942 CTATATTTTC
Statistics
Matches: 51, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
26 5 0.10
27 26 0.51
28 5 0.10
29 4 0.08
30 11 0.22
ACGTcount: A:0.64, C:0.02, G:0.01, T:0.32
Consensus pattern (27 bp):
ATAATAAATAATAAATAAATAAAATAT
Found at i:120902 original size:7 final size:7
Alignment explanation
Indices: 120861--120928 Score: 58
Period size: 7 Copynumber: 10.3 Consensus size: 7
120851 AATAATAAAC
*
120861 AATAAAT
1 AATATAT
*
120868 AA-ATAA
1 AATATAT
120874 AATATAT
1 AATATAT
120881 AATGA-AT
1 AAT-ATAT
120888 AATA-AT
1 AATATAT
120894 AATATAT
1 AATATAT
120901 AATATAT
1 AATATAT
120908 AAT-TAAT
1 AATAT-AT
120915 AA-ATAT
1 AATATAT
120921 AATA-AT
1 AATATAT
120927 AA
1 AA
120929 AAACTATATA
Statistics
Matches: 52, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
6 20 0.38
7 31 0.60
8 1 0.02
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (7 bp):
AATATAT
Found at i:121035 original size:36 final size:37
Alignment explanation
Indices: 120982--121203 Score: 278
Period size: 36 Copynumber: 6.1 Consensus size: 37
120972 CGTTTTAAAA
*
120982 TAAAAA-TATATATTATACGTTTTC-AAATGTATTTT
1 TAAAAACTATATATTATACGTTTTCAAAATATATTTT
*
121017 TAAAAATTATATATTATACGTTTTCAAAAT-TATTTT
1 TAAAAACTATATATTATACGTTTTCAAAATATATTTT
* * *
121053 AAAAAACTATATATTATACGTTTCCAAAAAAATATTTTTT
1 TAAAAACTATATATTATACGTTTTC---AAAATATATTTT
* * *
121093 TAAAAACTATATGTTATATGTTTTCCAAAATATTTTTT
1 TAAAAACTATATATTATACGTTTT-CAAAATATATTTT
121131 TAAAAAC--TATATTATACGTTTTCAAAA-ATATTTT
1 TAAAAACTATATATTATACGTTTTCAAAATATATTTT
121165 TAAAAAACTATATATTATACGTTTTC-AAATATATTTT
1 T-AAAAACTATATATTATACGTTTTCAAAATATATTTT
121202 TA
1 TA
121204 GTGTTCTAAA
Statistics
Matches: 165, Mismatches: 11, Indels: 21
0.84 0.06 0.11
Matches are distributed among these distances:
34 7 0.04
35 17 0.10
36 63 0.38
37 28 0.17
38 19 0.12
39 5 0.03
40 25 0.15
41 1 0.01
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (37 bp):
TAAAAACTATATATTATACGTTTTCAAAATATATTTT
Found at i:121081 original size:112 final size:111
Alignment explanation
Indices: 120960--121201 Score: 294
Period size: 112 Copynumber: 2.2 Consensus size: 111
120950 TCAAAAATAT
* *
120960 GTTTTCAAAAATCGTTTTAAAATAAAAA-TATATATTATACGTTTT-C-AAATGTATTTTTAAAA
1 GTTTTCAAAAAT-ATTTT--AATAAAAACTATATATTATACGTTTTCCAAAATATATTTTTAAAA
*
121022 ATTATATATTATACGTTTTCAAAATTA-TTTTAAAAAACTATATATTATAC
63 A--ATATATTATACGTTTTCAAAAATATTTTTAAAAAACTATATATTATAC
* ** * * *
121072 GTTTCCAAAAAAATATTTTTTTAAAAACTATATGTTATATGTTTTCCAAAATATTTTTTTAAAAA
1 GTTTTC--AAAAATATTTTAATAAAAACTATATATTATACGTTTTCCAAAATATATTTTTAAAAA
*
121137 CTATATTATACGTTTTCAAAAATATTTTTAAAAAACTATATATTATAC
64 ATATATTATACGTTTTCAAAAATATTTTTAAAAAACTATATATTATAC
*
121185 GTTTTCAAATATATTTT
1 GTTTTCAAAAATATTTT
121202 TAGTGTTCTA
Statistics
Matches: 112, Mismatches: 12, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
111 16 0.14
112 42 0.38
113 33 0.29
114 21 0.19
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (111 bp):
GTTTTCAAAAATATTTTAATAAAAACTATATATTATACGTTTTCCAAAATATATTTTTAAAAAAT
ATATTATACGTTTTCAAAAATATTTTTAAAAAACTATATATTATAC
Found at i:121096 original size:76 final size:72
Alignment explanation
Indices: 120982--121201 Score: 259
Period size: 76 Copynumber: 3.0 Consensus size: 72
120972 CGTTTTAAAA
* ** *
120982 TAAAAATA-TATATTATACGTTTTCAAATGTA-TTTTTAAAAATTATATATTATACGTTTTCAAA
1 TAAAAA-ACTATATTATACGTTTCCAAAAATATTTTTTAAAAACTATATATTATACGTTTTCAAA
121045 AT-TATTT
65 ATATATTT
* *
121052 TAAAAAACTATATATTATACGTTTCCAAAAAAATATTTTTTTAAAAACTATATGTTATATGTTTT
1 TAAAAAAC--TATATTATACGTTTCC--AAAAATA-TTTTTTAAAAACTATATATTATACGTTTT
*
121117 CCAAAATATTTTT
61 -CAAAATATATTT
* * *
121130 TTAAAAACTATATTATACGTTTTCAAAAATATTTTTAAAAAACTATATATTATACGTTTTC-AAA
1 TAAAAAACTATATTATACGTTTCCAAAAATATTTTTTAAAAACTATATATTATACGTTTTCAAAA
121194 TATATTT
66 TATATTT
121201 T
1 T
121202 TAGTGTTCTA
Statistics
Matches: 128, Mismatches: 13, Indels: 17
0.81 0.08 0.11
Matches are distributed among these distances:
69 1 0.01
70 6 0.05
71 10 0.08
72 16 0.12
73 26 0.20
74 12 0.09
76 40 0.31
77 6 0.05
78 11 0.09
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (72 bp):
TAAAAAACTATATTATACGTTTCCAAAAATATTTTTTAAAAACTATATATTATACGTTTTCAAAA
TATATTT
Found at i:121927 original size:2 final size:2
Alignment explanation
Indices: 121920--121946 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
121910 TCTATTATGA
121920 AT 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 AT A
121947 CACACATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:122108 original size:2 final size:2
Alignment explanation
Indices: 122069--122126 Score: 59
Period size: 2 Copynumber: 30.5 Consensus size: 2
122059 TGCGTGCATT
* * * *
122069 TA TA TT TA TA TA -A TA -A TA AA TA T- TA AA TA TA AA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
122108 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
122127 TAATTAAGTC
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
1 3 0.07
2 42 0.93
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:125543 original size:34 final size:34
Alignment explanation
Indices: 125505--125579 Score: 87
Period size: 34 Copynumber: 2.2 Consensus size: 34
125495 GTTTATGCTA
* *
125505 AAACTCTACCGAAAATTCTGCATGTTTAATACTG
1 AAACTCTACCCAAAATTCTGCACGTTTAATACTG
* * * * *
125539 AAACTTTGCCCAAAATTTTGCCCGTTTCATACTG
1 AAACTCTACCCAAAATTCTGCACGTTTAATACTG
125573 AAACTCT
1 AAACTCT
125580 GCCTGAATGA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.33
Consensus pattern (34 bp):
AAACTCTACCCAAAATTCTGCACGTTTAATACTG
Done.