Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000047.1 Hibiscus syriacus cultivar Beakdansim tig00000073_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: 112515
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1249 original size:15 final size:15
Alignment explanation
Indices: 1229--1258 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1219 ATGGAATCTA
1229 AATTGATTATCTATG
1 AATTGATTATCTATG
*
1244 AATTGATTGTCTATG
1 AATTGATTATCTATG
1259 TAACAAGCTA
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:0.30, C:0.07, G:0.17, T:0.47
Consensus pattern (15 bp):
AATTGATTATCTATG
Found at i:11476 original size:16 final size:16
Alignment explanation
Indices: 11455--11491 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
11445 ACAATGCTTG
11455 GAATGTAACCTTTCAT
1 GAATGTAACCTTTCAT
11471 GAATGTAACCTTTCAT
1 GAATGTAACCTTTCAT
11487 GAATG
1 GAATG
11492 AACATGTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (16 bp):
GAATGTAACCTTTCAT
Found at i:21375 original size:12 final size:12
Alignment explanation
Indices: 21358--21408 Score: 59
Period size: 12 Copynumber: 4.1 Consensus size: 12
21348 ACCTGAAAAG
21358 ACAAGTAAAATA
1 ACAAGTAAAATA
21370 ACAAGTAAAACTA
1 ACAAGTAAAA-TA
*
21383 TACAA-AAAAATAA
1 -ACAAGTAAAAT-A
21396 ACAAGTAAAATA
1 ACAAGTAAAATA
21408 A
1 A
21409 AAATGCTTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
12 17 0.52
13 12 0.36
14 4 0.12
ACGTcount: A:0.69, C:0.10, G:0.06, T:0.16
Consensus pattern (12 bp):
ACAAGTAAAATA
Found at i:21997 original size:21 final size:21
Alignment explanation
Indices: 21971--22012 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
21961 CCAGAATGGG
*
21971 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
*
21992 GGGAATCGATACGCCTTCATA
1 GGGAATCGATACCCCTTCATA
22013 ATATTCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:24776 original size:21 final size:21
Alignment explanation
Indices: 24750--24791 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
24740 CAGAATGGGG
*
24750 GGAATCGGTACCCCTTCATAA
1 GGAATCGATACCCCTTCATAA
24771 GGAATCGATACCCCTTCATAA
1 GGAATCGATACCCCTTCATAA
24792 TATTCAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.24
Consensus pattern (21 bp):
GGAATCGATACCCCTTCATAA
Found at i:24927 original size:19 final size:19
Alignment explanation
Indices: 24903--24977 Score: 97
Period size: 20 Copynumber: 4.1 Consensus size: 19
24893 AAACCATTCA
24903 GGGGAATCTGTACCCCCTG
1 GGGGAATCTGTACCCCCTG
24922 GGGGAATCTGT--CCCC--
1 GGGGAATCTGTACCCCCTG
24937 GGGGAAT-TGATACCCCCTGG
1 GGGGAATCTG-TACCCCCT-G
24957 GGGGAATCTGTACCCCCTG
1 GGGGAATCTGTACCCCCTG
24976 GG
1 GG
24978 CAATCTGATT
Statistics
Matches: 49, Mismatches: 0, Indels: 14
0.78 0.00 0.22
Matches are distributed among these distances:
14 2 0.04
15 8 0.16
17 8 0.16
19 14 0.29
20 15 0.31
21 2 0.04
ACGTcount: A:0.16, C:0.29, G:0.35, T:0.20
Consensus pattern (19 bp):
GGGGAATCTGTACCCCCTG
Found at i:24943 original size:34 final size:36
Alignment explanation
Indices: 24903--24972 Score: 110
Period size: 34 Copynumber: 2.0 Consensus size: 36
24893 AAACCATTCA
24903 GGGGAATCTG-TACCCCCT-GGGGGAATCTGT-CCCC
1 GGGGAAT-TGATACCCCCTGGGGGGAATCTGTACCCC
24937 GGGGAATTGATACCCCCTGGGGGGAATCTGTACCCC
1 GGGGAATTGATACCCCCTGGGGGGAATCTGTACCCC
24973 CTGGGCAATC
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
33 2 0.06
34 15 0.45
35 12 0.36
36 4 0.12
ACGTcount: A:0.17, C:0.30, G:0.33, T:0.20
Consensus pattern (36 bp):
GGGGAATTGATACCCCCTGGGGGGAATCTGTACCCC
Found at i:29134 original size:103 final size:103
Alignment explanation
Indices: 28914--29126 Score: 381
Period size: 103 Copynumber: 2.1 Consensus size: 103
28904 GGGTCTACGC
28914 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTAGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTAGTGAGACACATACTTGAT
* *
28979 CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
* *
29017 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATATTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTAGTGAGACACATACTTGAT
*
29082 CCCTAGTATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
29120 GGTCCTT
1 GGTCCTT
29127 ATGGACATTA
Statistics
Matches: 105, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 105 1.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (103 bp):
GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTAGTGAGACACATACTTGAT
CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
Found at i:29178 original size:23 final size:23
Alignment explanation
Indices: 29143--29210 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
29133 ATTATTATAT
29143 GGCACTACAGTGCAATTCTACGC
1 GGCACTACAGTGCAATTCTACGC
* * *
29166 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACAGTGCAATTCTACGC
*
29189 GGCACTTA-AGTGCAATTATACG
1 GGCAC-TACAGTGCAATTCTACG
29211 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 37 0.97
24 1 0.03
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (23 bp):
GGCACTACAGTGCAATTCTACGC
Found at i:29258 original size:16 final size:17
Alignment explanation
Indices: 29239--29272 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
29229 GTGCACAACC
29239 TCTATAG-ACTCACATG
1 TCTATAGTACTCACATG
*
29255 TCTATAGTTCTCACATG
1 TCTATAGTACTCACATG
29272 T
1 T
29273 GTACATGGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.38
Consensus pattern (17 bp):
TCTATAGTACTCACATG
Found at i:34301 original size:103 final size:103
Alignment explanation
Indices: 34117--34329 Score: 372
Period size: 103 Copynumber: 2.1 Consensus size: 103
34107 GGGTCTACGC
*
34117 GGTCTTTCGGGACATATATGTATTATTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTATTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
* *
34182 CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
*
34220 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTATTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
* *
34285 CCCTAGTATATGTATATGATTCTTAATGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
34323 GGTCCTT
1 GGTCCTT
34330 ATGGACATTA
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 104 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.37
Consensus pattern (103 bp):
GGTCCTTCGGGACATATATGTATTATTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
Found at i:34379 original size:23 final size:23
Alignment explanation
Indices: 34346--34413 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
34336 ATTATTATAT
34346 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
34369 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* *
34392 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
34414 AGCTGTGGTG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.21, C:0.28, G:0.26, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:36428 original size:22 final size:22
Alignment explanation
Indices: 36395--36458 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
36385 GGCATGTGAA
*
36395 ATATGTCACGAAGGACCTA-TGC
1 ATATGTCCCGAAGGACC-ACTGC
* *
36417 ATTTGTCCCGAAGGACCACTGT
1 ATATGTCCCGAAGGACCACTGC
*
36439 ATATGTCCTGAAGGACCACT
1 ATATGTCCCGAAGGACCACT
36459 ATCCATATGT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
21 1 0.03
22 35 0.97
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (22 bp):
ATATGTCCCGAAGGACCACTGC
Found at i:36473 original size:24 final size:22
Alignment explanation
Indices: 36420--36475 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
36410 CCTATGCATT
* *
36420 TGTCCCGAAGGACCACTGTATA
1 TGTCCTGAAGGACCACTATATA
36442 TGTCCTGAAGGACCACTATCCATA
1 TGTCCTGAAGGACCACTAT--ATA
*
36466 TGTTCTGAAG
1 TGTCCTGAAG
36476 AACATATGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 17 0.59
24 12 0.41
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (22 bp):
TGTCCTGAAGGACCACTATATA
Found at i:36496 original size:30 final size:30
Alignment explanation
Indices: 36460--36517 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
36450 AGGACCACTA
* *
36460 TCCATATGTTCTGAAGAACATATGTAACTG
1 TCCATATGTCCTGAAGAACATAGGTAACTG
*
36490 TCCATATGTCCTGAAGGACATAGGTAAC
1 TCCATATGTCCTGAAGAACATAGGTAAC
36518 CCTCGACTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (30 bp):
TCCATATGTCCTGAAGAACATAGGTAACTG
Found at i:37799 original size:20 final size:20
Alignment explanation
Indices: 37776--37830 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
37766 TTTCCTTTAG
* *
37776 GGGGTATCGATATCCTCCTT
1 GGGGTATCGATACCCACCTT
*
37796 GGGGTATCGGTACCCACCTT
1 GGGGTATCGATACCCACCTT
*
37816 GGGGTATCGGTACCC
1 GGGGTATCGATACCC
37831 TCATTGCATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.15, C:0.27, G:0.31, T:0.27
Consensus pattern (20 bp):
GGGGTATCGATACCCACCTT
Found at i:41296 original size:30 final size:30
Alignment explanation
Indices: 41260--41316 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
41250 AGGACCACTA
*
41260 TCCATATGT-TCTGAAGAACATAGGTAATTG
1 TCCATATGTCCCT-AAGAACATAGGTAATTG
*
41290 TCCATATGTCCCTAAGGACATAGGTAA
1 TCCATATGTCCCTAAGAACATAGGTAA
41317 CCCTCGACTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 22 0.92
31 2 0.08
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (30 bp):
TCCATATGTCCCTAAGAACATAGGTAATTG
Found at i:48732 original size:17 final size:17
Alignment explanation
Indices: 48710--48751 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
48700 ACACTTTATA
48710 ATGGAAGCCATGTGAGT
1 ATGGAAGCCATGTGAGT
48727 ATGGAAGCCATGTGAGT
1 ATGGAAGCCATGTGAGT
*
48744 ATAGAAGC
1 ATGGAAGC
48752 AACAACGCCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.33, C:0.12, G:0.33, T:0.21
Consensus pattern (17 bp):
ATGGAAGCCATGTGAGT
Found at i:52203 original size:17 final size:17
Alignment explanation
Indices: 52181--52213 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
52171 TTATCAGATT
52181 AAAAACCGGTTTTTTTA
1 AAAAACCGGTTTTTTTA
52198 AAAAACCGGTTTTTTT
1 AAAAACCGGTTTTTTT
52214 CAAACCGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (17 bp):
AAAAACCGGTTTTTTTA
Found at i:58821 original size:29 final size:31
Alignment explanation
Indices: 58763--58823 Score: 108
Period size: 30 Copynumber: 2.0 Consensus size: 31
58753 ACAATTTAAG
58763 ACAAAATGGTTTTTGGACTTGAATTGAATTT
1 ACAAAATGGTTTTTGGACTTGAATTGAATTT
58794 ACAAAAT-GTTTTTGGACTT-AATTGAATTT
1 ACAAAATGGTTTTTGGACTTGAATTGAATTT
58823 A
1 A
58824 TTCAAAGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.37
30 12 0.40
31 7 0.23
ACGTcount: A:0.34, C:0.07, G:0.16, T:0.43
Consensus pattern (31 bp):
ACAAAATGGTTTTTGGACTTGAATTGAATTT
Found at i:58929 original size:21 final size:21
Alignment explanation
Indices: 58903--58959 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
58893 AGGGTGTCAA
*
58903 AGTGCATCCATGTACCCCTAC
1 AGTGCATCCATGCACCCCTAC
* **
58924 AGTGCATCCATGCATCCCTGT
1 AGTGCATCCATGCACCCCTAC
58945 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
58960 ATGCACTAGT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.23, C:0.35, G:0.18, T:0.25
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTAC
Found at i:63383 original size:18 final size:18
Alignment explanation
Indices: 63362--63415 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
63352 ATGTAAATAT
63362 TTATGAGATTTTAAATTA
1 TTATGAGATTTTAAATTA
*
63380 TTATGAG----TAATTTGA
1 TTATGAGATTTTAAATT-A
63395 TTCATGAGATTTTAAATTA
1 TT-ATGAGATTTTAAATTA
63414 TT
1 TT
63416 TTAGGAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 11
0.68 0.05 0.27
Matches are distributed among these distances:
14 5 0.18
15 3 0.11
16 5 0.18
18 7 0.25
19 3 0.11
20 5 0.18
ACGTcount: A:0.35, C:0.02, G:0.13, T:0.50
Consensus pattern (18 bp):
TTATGAGATTTTAAATTA
Found at i:65693 original size:58 final size:58
Alignment explanation
Indices: 65603--65740 Score: 276
Period size: 58 Copynumber: 2.4 Consensus size: 58
65593 TTAAGCAGAC
65603 AAGATTATATATTTTATATTTGAGAAAGATTTTAAGTTGAAAAATCATTTGTTTTTCA
1 AAGATTATATATTTTATATTTGAGAAAGATTTTAAGTTGAAAAATCATTTGTTTTTCA
65661 AAGATTATATATTTTATATTTGAGAAAGATTTTAAGTTGAAAAATCATTTGTTTTTCA
1 AAGATTATATATTTTATATTTGAGAAAGATTTTAAGTTGAAAAATCATTTGTTTTTCA
65719 AAGATTATATATTTTATATTTG
1 AAGATTATATATTTTATATTTG
65741 TTTTTAAGTT
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 80 1.00
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.48
Consensus pattern (58 bp):
AAGATTATATATTTTATATTTGAGAAAGATTTTAAGTTGAAAAATCATTTGTTTTTCA
Found at i:68175 original size:71 final size:70
Alignment explanation
Indices: 68046--68183 Score: 215
Period size: 71 Copynumber: 2.0 Consensus size: 70
68036 ATTGAGATGC
* *
68046 CTTCAAGTTCAAGTGAAAGCCATTCAACTACAGCTTGTTCGACCTAAATGTCGGTATCATGGAGG
1 CTTCAAGTTCAAGGGAAAGACATTCAACTACAGCTTGTTCGACCTAAATGTCGGTATCATGGAGG
68111 AATTA
66 AATTA
* *
68116 CTTCAAGTTCAAGGGAAAGACATTCATCTACCATCTTGTTCGACCTAAATG-CTGGTATCATGGA
1 CTTCAAGTTCAAGGGAAAGACATTCAACTA-CAGCTTGTTCGACCTAAATGTC-GGTATCATGGA
68180 GGAA
64 GGAA
68184 CCCTCATCTT
Statistics
Matches: 62, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
70 28 0.45
71 34 0.55
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.28
Consensus pattern (70 bp):
CTTCAAGTTCAAGGGAAAGACATTCAACTACAGCTTGTTCGACCTAAATGTCGGTATCATGGAGG
AATTA
Found at i:68521 original size:70 final size:71
Alignment explanation
Indices: 68437--68570 Score: 198
Period size: 71 Copynumber: 1.9 Consensus size: 71
68427 TTATCAGTTA
* *
68437 AAGTTCAAGTGAAAGCCATTCAACTA-CAGCTTGTTCGACCTAAATATCAGTATCATGGAGGAAT
1 AAGTTCAAGGGAAAGACATTCAACTACCAGCTTGTTCGACCTAAATATCAGTATCATGGAGGAAT
68501 TACTTC
66 TACTTC
* * * **
68507 AAGTTCAAGGGAAAGACATTCATCTACCATCTTGTTCGACCTAAATGTTGGTATCATGGAGGAA
1 AAGTTCAAGGGAAAGACATTCAACTACCAGCTTGTTCGACCTAAATATCAGTATCATGGAGGAA
68571 CCCTCATCTT
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
70 23 0.41
71 33 0.59
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (71 bp):
AAGTTCAAGGGAAAGACATTCAACTACCAGCTTGTTCGACCTAAATATCAGTATCATGGAGGAAT
TACTTC
Found at i:68764 original size:387 final size:387
Alignment explanation
Indices: 68050--68824 Score: 1487
Period size: 387 Copynumber: 2.0 Consensus size: 387
68040 AGATGCCTTC
* *
68050 AAGTTCAAGTGAAAGCCATTCAACTACAGCTTGTTCGACCTAAATGTCGGTATCATGGAGGAATT
1 AAGTTCAAGTGAAAGCCATTCAACTACAGCTTGTTCGACCTAAATATCAGTATCATGGAGGAATT
68115 ACTTCAAGTTCAAGGGAAAGACATTCATCTACCATCTTGTTCGACCTAAATGCTGGTATCATGGA
66 ACTTCAAGTTCAAGGGAAAGACATTCATCTACCATCTTGTTCGACCTAAATGCTGGTATCATGGA
68180 GGAACCCTCATCTTCATCAGAAGAACCTCTTCATGAGCCAGGTGTGGATGGTGCTGAGACTATAC
131 GGAACCCTCATCTTCATCAGAAGAACCTCTTCATGAGCCAGGTGTGGATGGTGCTGAGACTATAC
68245 TATTCGTTTAGCCAGAATCACCACAATACAACATGGACTCCGATGATGATGATGATGTAGATGAA
196 TATTCGTTTAGCCAGAATCACCACAATACAACATGGACTCCGATGATGATGATGATGTAGATGAA
68310 GTTCCAACAAGTACGGTATACACCGAACCTCCAGCACATATGTATGAAGCTGACTATGGTGTAAT
261 GTTCCAACAAGTACGGTATACACCGAACCTCCAGCACATATGTATGAAGCTGACTATGGTGTAAT
* *
68375 GTACGAGCCATAATTTATGGATATGCCTAATTTTGGTGACTACGGATTTAACTTATCAGTTA
326 GTACGAGCCATAATTTACGGATATGCCTAATGTTGGTGACTACGGATTTAACTTATCAGTTA
68437 AAGTTCAAGTGAAAGCCATTCAACTACAGCTTGTTCGACCTAAATATCAGTATCATGGAGGAATT
1 AAGTTCAAGTGAAAGCCATTCAACTACAGCTTGTTCGACCTAAATATCAGTATCATGGAGGAATT
*
68502 ACTTCAAGTTCAAGGGAAAGACATTCATCTACCATCTTGTTCGACCTAAATGTTGGTATCATGGA
66 ACTTCAAGTTCAAGGGAAAGACATTCATCTACCATCTTGTTCGACCTAAATGCTGGTATCATGGA
*
68567 GGAACCCTCATCTTCATCAGAAGAACCTCTTCGTGAGCCAGGTGTGGATGGTGCTGAGACTATAC
131 GGAACCCTCATCTTCATCAGAAGAACCTCTTCATGAGCCAGGTGTGGATGGTGCTGAGACTATAC
*
68632 TATTCGTTTAGCTAGAATCACCACAATACAACATGGACTCCGATGATGATGATGATGTAGATGAA
196 TATTCGTTTAGCCAGAATCACCACAATACAACATGGACTCCGATGATGATGATGATGTAGATGAA
68697 GTTCCAACAAGTACGGTATACACCGAACCTCCAGCACATATGTATGAAGCTGACTATGGTGTAAT
261 GTTCCAACAAGTACGGTATACACCGAACCTCCAGCACATATGTATGAAGCTGACTATGGTGTAAT
68762 GTACGAGCCATAATTTACGGATATGCCTAATGTTGGTGACTACGGATTTAACTTATCAGTTA
326 GTACGAGCCATAATTTACGGATATGCCTAATGTTGGTGACTACGGATTTAACTTATCAGTTA
68824 A
1 A
68825 TGATAGTGAG
Statistics
Matches: 381, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
387 381 1.00
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (387 bp):
AAGTTCAAGTGAAAGCCATTCAACTACAGCTTGTTCGACCTAAATATCAGTATCATGGAGGAATT
ACTTCAAGTTCAAGGGAAAGACATTCATCTACCATCTTGTTCGACCTAAATGCTGGTATCATGGA
GGAACCCTCATCTTCATCAGAAGAACCTCTTCATGAGCCAGGTGTGGATGGTGCTGAGACTATAC
TATTCGTTTAGCCAGAATCACCACAATACAACATGGACTCCGATGATGATGATGATGTAGATGAA
GTTCCAACAAGTACGGTATACACCGAACCTCCAGCACATATGTATGAAGCTGACTATGGTGTAAT
GTACGAGCCATAATTTACGGATATGCCTAATGTTGGTGACTACGGATTTAACTTATCAGTTA
Found at i:73128 original size:18 final size:17
Alignment explanation
Indices: 73105--73165 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 17
73095 ATTGAATATT
73105 TGTCCCGAACGACCACTA
1 TGTCCCGAA-GACCACTA
*
73123 TGTCCCAAAGGACCACTGA
1 TGTCCCGAA-GACCACT-A
*
73142 TTGTTCCGAAGAACCACTA
1 -TGTCCCGAAG-ACCACTA
73161 TGTCC
1 TGTCC
73166 ATAAGGACCA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
18 19 0.54
19 3 0.09
20 13 0.37
ACGTcount: A:0.28, C:0.33, G:0.18, T:0.21
Consensus pattern (17 bp):
TGTCCCGAAGACCACTA
Found at i:73177 original size:18 final size:17
Alignment explanation
Indices: 73115--73177 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 17
73105 TGTCCCGAAC
73115 GACCACTATGTCCCAAAG
1 GACCACTATGT-CCAAAG
*
73133 GACCACTGATTGTTCCGAAG
1 GACCACT-A-TG-TCCAAAG
*
73153 AACCACTATGTCCATAAG
1 GACCACTATGTCCA-AAG
73171 GACCACT
1 GACCACT
73178 GATTATCCCT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
17 3 0.08
18 18 0.49
19 2 0.05
20 13 0.35
21 1 0.03
ACGTcount: A:0.32, C:0.30, G:0.17, T:0.21
Consensus pattern (17 bp):
GACCACTATGTCCAAAG
Found at i:84531 original size:12 final size:12
Alignment explanation
Indices: 84514--84543 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
84504 TAGGGCCATT
84514 AGTTTTACATCA
1 AGTTTTACATCA
*
84526 AGTTTTACATTA
1 AGTTTTACATCA
84538 AGTTTT
1 AGTTTT
84544 CTTTATTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (12 bp):
AGTTTTACATCA
Found at i:88436 original size:18 final size:17
Alignment explanation
Indices: 88413--88474 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 17
88403 ACTGAATATT
88413 TGTCCCGAAATACCACTA
1 TGTCCCGAAA-ACCACTA
88431 TGTCCCGAAGAACCACTGA
1 TGTCCCGAA-AACCACT-A
* *
88450 TTGTTCCAAAGAACCACTA
1 -TGTCCCGAA-AACCACTA
88469 TGTCCC
1 TGTCCC
88475 AAAGGACCAC
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
18 20 0.53
19 3 0.08
20 15 0.39
ACGTcount: A:0.31, C:0.32, G:0.15, T:0.23
Consensus pattern (17 bp):
TGTCCCGAAAACCACTA
Found at i:88463 original size:20 final size:20
Alignment explanation
Indices: 88431--88494 Score: 78
Period size: 20 Copynumber: 3.3 Consensus size: 20
88421 AATACCACTA
*
88431 TGTCCCGAAGAACCACTGAT
1 TGTCCCAAAGAACCACTGAT
*
88451 TGTTCCAAAGAACCACT-A-
1 TGTCCCAAAGAACCACTGAT
*
88469 TGTCCCAAAGGACCACTGAT
1 TGTCCCAAAGAACCACTGAT
*
88489 TATCCC
1 TGTCCC
88495 TCGACTCTTG
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
18 15 0.41
19 2 0.05
20 20 0.54
ACGTcount: A:0.31, C:0.31, G:0.16, T:0.22
Consensus pattern (20 bp):
TGTCCCAAAGAACCACTGAT
Found at i:88478 original size:18 final size:18
Alignment explanation
Indices: 88424--88485 Score: 79
Period size: 18 Copynumber: 3.3 Consensus size: 18
88414 GTCCCGAAAT
*
88424 ACCACTATGTCCCGAAGA
1 ACCACTATGTCCCAAAGA
*
88442 ACCACTGATTGTTCCAAAGA
1 ACCACT-A-TGTCCCAAAGA
*
88462 ACCACTATGTCCCAAAGG
1 ACCACTATGTCCCAAAGA
88480 ACCACT
1 ACCACT
88486 GATTATCCCT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
18 21 0.55
19 2 0.05
20 15 0.39
ACGTcount: A:0.34, C:0.32, G:0.15, T:0.19
Consensus pattern (18 bp):
ACCACTATGTCCCAAAGA
Found at i:88721 original size:21 final size:21
Alignment explanation
Indices: 88697--88743 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
88687 CATGTTAAAT
*
88697 TATAAATGAATATGAAATCAC
1 TATAAATGAATATGAAATCAA
*
88718 TATAAATGAATATGTAATCAA
1 TATAAATGAATATGAAATCAA
88739 TATAA
1 TATAA
88744 CATTAATACA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.53, C:0.06, G:0.09, T:0.32
Consensus pattern (21 bp):
TATAAATGAATATGAAATCAA
Found at i:98946 original size:21 final size:21
Alignment explanation
Indices: 98904--98948 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
98894 GATTTAACTA
* * *
98904 AAAAGTTTTAATATGCAATAT
1 AAAAGTTCTAAAAAGCAATAT
*
98925 AAAAGTTCTAAAAAGCAGTAT
1 AAAAGTTCTAAAAAGCAATAT
98946 AAA
1 AAA
98949 TGACTTCTAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.53, C:0.07, G:0.11, T:0.29
Consensus pattern (21 bp):
AAAAGTTCTAAAAAGCAATAT
Found at i:103526 original size:425 final size:424
Alignment explanation
Indices: 102534--103621 Score: 1132
Period size: 425 Copynumber: 2.5 Consensus size: 424
102524 TGTGAGAGTT
* * * * * * * *
102534 TGTCTATCTGTAAAATAATTTGTTGATTTGTGAGAATCTGTCAATTTATGATATTTTTTGTCTTG
1 TGTCTATCTGTAAAGTAATTTGTTGATATGTGAGAATCTGTCAATCTATTACA-CTTTTATCGTG
* * * *
102599 ATTTAAGTAAATGTATATAACGTTTCAGAAAAGAAAT-TTGATTTTAAAATTTTGAACGTCTTTT
65 ATTTAAGTAAATGCATAGAACGTTTAAGAAAA-AAATATTAATTTTAAAATTTTGAACGTCTTTT
* * * * * * * *
102663 TAAGTTTTCATGAATAAGTTTTTTTTGTAGATAATTACAAGTGATTCGTATTTAACATGTATTGA
129 TAAGTTTTCATGAATAAG-TCTCTTTGAAGATGATTACACGTGTTTTGTATTTAACATTTATTGA
* * * * *
102728 AAAGTTAAATAAACTCACACAACGAATAAATTCTTGATGT-TTTAACTTTTTTTTTATATGTAAT
193 AAAATTAAATAAACTCA-AC-A-G--TGAA--C-TGAT-TCTTCAAC-TTTTTCTTATATGTAAC
* * **
102792 ATTTATGAATTTCAAAATGATTAATTTTCGAGAAGATGAAGATATCACTAGACCTCTTAAATCAT
248 ATTTATGAACTTCAAAAGGATTAACGTTCGAGAAGATGAAGATATCACTAGACCTCTTAAATCAT
* * *
102857 GTTTAGTATTTTGTTTTTGTTGTAGCAAATTTGAATAAAAACATACATATTTTAATTGATTTCTA
313 GTTTAGTATTTTGTTTTTGTTGCAACAAATTTGAATAAAAACATAAATATTTTAATTGATTTCTA
** * ** *
102922 AGAATTATTTTTTCATCTGTAAAGTAATTTATTGATTTGTAAGAATG
378 AGAATTATTGATTCATCTGTAAAGTAATTTATTAATTACTAAGAATC
* * ** * *
102969 TGAT-TATCTGAAAAGTAATTTGTTGATGTGTGAGAATCTGTCGGTCTGTCT-CACTTTTTTCGT
1 TG-TCTATCTGTAAAGTAATTTGTTGATATGTGAGAATCTGTCAATCTAT-TACACTTTTATCGT
* * * *
103032 GATTTAAGTAAATACAAAGAACGTTTTAA-AATAAAAA-ATTAATTTTGAAATTTTGAACGTCTC
64 GATTTAAGTAAATGCATAGAACG-TTTAAGAA-AAAAATATTAATTTTAAAATTTTGAACGTCTT
*
103095 TTTAAGTTTTCATGAATAAGTCTCTTTGAAGATGATTACACGTGTTTTTTTATTTAACATTTATT
127 TTTAAGTTTTCATGAATAAGTCTCTTTGAAGATGATTACACGTG-TTTTGTATTTAACATTTATT
* * *
103160 GAAAAAAAATAAATAAACTCTACAGTGAAC-GATTCTTCAAC-TTTTCTTATATGTAACGTTTAT
191 G--AAAAATTAAATAAACTCAACAGTGAACTGATTCTTCAACTTTTTCTTATATGTAACATTTAT
* * **
103223 GAGCTTCAAAAGGATTAGCGTTC-ATGAAGATGAAGATATCACTTTACCTCTTAAATCATGTTTA
254 GAACTTCAAAAGGATTAACGTTCGA-GAAGATGAAGATATCACTAGACCTCTTAAATCATGTTTA
* * *
103287 CG-A-TTTGTTTTTGTTGCAACAAATTTGAATAAATAA-ATAAATAAATTTTTATTGATTTTTTA
318 -GTATTTTGTTTTTGTTGCAACAAATTTGAATAAA-AACATAAAT--ATTTTAATTGATTTCTAA
* * **
103349 GAA-T-TTGATT-ATCTGTCAAGTAATTTGTTAATTACTAATTATC
379 GAATTATTGATTCATCTGTAAAGTAATTTATTAATTACTAAGAATC
*
103392 TGTCTATATGTAAAGTAATTTGTTGATATGTGAGAATCTGTCAATCTATTACA-TTTTCATCGTG
1 TGTCTATCTGTAAAGTAATTTGTTGATATGTGAGAATCTGTCAATCTATTACACTTTT-ATCGTG
* *
103456 ATTTAAGTAAATGCATAGAACGTTTAAGAACAAAAATAATAATTTTAAAATTTTGAGCACCT-TT
65 ATTTAAGTAAATGCATAGAACGTTTAAGAA-AAAAATATTAATTTTAAAATTTTGA--ACGTCTT
* * *
103520 TTTAAGTTTTTATGAATAAGTCTCTTT-ATAGATGATTACACGTATTTTGTATTTAACGTTTATT
127 TTTAAGTTTTCATGAATAAGTCTCTTTGA-AGATGATTACACGTGTTTTGTATTTAACATTTATT
* **
103584 GAAAAATTAAATAAACTCAACAGCGAACAAATTCTTCA
191 GAAAAATTAAATAAACTCAACAGTGAACTGATTCTTCA
103622 TTTATTAATA
Statistics
Matches: 547, Mismatches: 83, Indels: 58
0.80 0.12 0.08
Matches are distributed among these distances:
422 35 0.06
423 108 0.20
424 75 0.14
425 118 0.22
426 23 0.04
427 8 0.01
429 1 0.00
431 3 0.01
433 20 0.04
434 91 0.17
435 49 0.09
436 16 0.03
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.42
Consensus pattern (424 bp):
TGTCTATCTGTAAAGTAATTTGTTGATATGTGAGAATCTGTCAATCTATTACACTTTTATCGTGA
TTTAAGTAAATGCATAGAACGTTTAAGAAAAAAATATTAATTTTAAAATTTTGAACGTCTTTTTA
AGTTTTCATGAATAAGTCTCTTTGAAGATGATTACACGTGTTTTGTATTTAACATTTATTGAAAA
ATTAAATAAACTCAACAGTGAACTGATTCTTCAACTTTTTCTTATATGTAACATTTATGAACTTC
AAAAGGATTAACGTTCGAGAAGATGAAGATATCACTAGACCTCTTAAATCATGTTTAGTATTTTG
TTTTTGTTGCAACAAATTTGAATAAAAACATAAATATTTTAATTGATTTCTAAGAATTATTGATT
CATCTGTAAAGTAATTTATTAATTACTAAGAATC
Found at i:108906 original size:8 final size:8
Alignment explanation
Indices: 108893--108932 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
108883 TCATTTTCAA
108893 AGAATTTG
1 AGAATTTG
108901 AGAATTT-
1 AGAATTTG
*
108908 AGAGTTTG
1 AGAATTTG
*
108916 GGAATTTG
1 AGAATTTG
108924 AGAATTTG
1 AGAATTTG
108932 A
1 A
108933 AAGCTTGTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.35, C:0.00, G:0.28, T:0.38
Consensus pattern (8 bp):
AGAATTTG
Found at i:109258 original size:124 final size:125
Alignment explanation
Indices: 109013--109847 Score: 1183
Period size: 124 Copynumber: 6.7 Consensus size: 125
109003 ACTATTCACA
* * * *
109013 TGAAGGCGCGTTCACGGGGGCGCGTCTTCCATTATTTTTTCAGAGAATATGTTATCATT---CTA
1 TGAAGGCGCG-TCCCCGGGGCGCGCCTTCCATTATTTTGTCAGAGAATA--TTATCATTGCCCTA
*
109075 TTATATCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
63 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
*
109138 TGAAGGCGCGTCCCCGGGACGCGCCTTCCATTATTTTGTCAGAGAATA-TATCATTGCCCTATTA
1 TGAAGGCGCGTCCCCGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATTATCATTGCCCTATTA
*
109202 TGTCACTCATGTCCCTCGGGGACACTATTCATATCATTACCTATTATTTCTCAGGGGACT
66 TGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
*
109262 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCG-TCCCCGGGGCGCGCCTTCCATTATTTTGTCAGAGAATA--TTATCATTGCCCTA
* *
109327 TTATGTCACTCATGTCCCTCGGGG--ACTATTCATATCATTACCTATTATTTCTCAAGGGACT
63 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
* * *
109388 TGAAGGCGCATTCCCGGGG-GCGCCTTCCCATTATTTTATCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTCCCCGGGGCGCGCCTT-CCATTATTTTGTCAGAGAATA--TTATCATTGCCCTA
109452 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCA-GGGACT
63 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
* *
109514 TGAA-G-GCGTTCCCGGGGGGCGCCTTCCATTA--TTGTCAGAGAATATGTTATCATTGCCCTAT
1 TGAAGGCGCGTCCCCGGGGCGCGCCTTCCATTATTTTGTCAGAGAATA--TTATCATTGCCCTAT
*
109575 TATGTCACTCATGTCCCTCGGGGACACTATTCATATCATTACCTATTATTTCTCAGGGGACT
64 TATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
* *
109637 TGAAGGCACGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTG-CCTA
1 TGAAGGCGCG-TCCCCGGGGCGCGCCTTCCATTATTTTGTCAGAGAATA--TTATCATTGCCCTA
* *
109701 TTATGTCACTCATGTCCCTCGGGGACACTATTC-TATTAGTACC---TATTTCTCAAGGGACT
63 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
* *
109760 TGAAGGCGCGTTCCCGAGGGCACGCCTTCCATTA-TTTGTCAGAG-A-ATT-T-ATTGCCCTATT
1 TGAAGGCGCGTCCCCG-GGGCGCGCCTTCCATTATTTTGTCAGAGAATATTATCATTGCCCTATT
109820 ATGTCACTCATGTCCCTCGGGGACACTA
65 ATGTCACTCATGTCCCTCGGGGACACTA
109848 GATGGATTGT
Statistics
Matches: 662, Mismatches: 29, Indels: 46
0.90 0.04 0.06
Matches are distributed among these distances:
116 4 0.01
117 35 0.05
118 2 0.00
120 1 0.00
121 8 0.01
122 97 0.15
123 50 0.08
124 132 0.20
125 123 0.19
126 83 0.13
127 66 0.10
128 61 0.09
ACGTcount: A:0.21, C:0.25, G:0.20, T:0.33
Consensus pattern (125 bp):
TGAAGGCGCGTCCCCGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATTATCATTGCCCTATTA
TGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
Found at i:109653 original size:249 final size:252
Alignment explanation
Indices: 109013--109847 Score: 1302
Period size: 249 Copynumber: 3.4 Consensus size: 252
109003 ACTATTCACA
* * *
109013 TGAAGGCGCGTTCACGGGGGCGCGTCTTCCATTATTTTTTCAGAGAATATGTTATCATT---CTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTA-TTTGTCAGAGAATATGTTATCATTGCCCTA
* *
109075 TTATATCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTG
65 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCATTACCTATTATTTCTCAGGGGACTTG
* *
109140 AAGGCGCGTCCCCGGGACGCGCCTTCCATTATTTTGTCAGAGAATA---TATCATTGCCCTATTA
130 AAGGCGCGTTCCCGGG-GGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTA
*
109202 TGTCACTCATGTCCCTCGGGGACACTATTCATATCATTACCTATTATTTCTCAGGGGACT
194 TGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCA-GGGACT
109262 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTA-TTTGTCAGAGAATATGTTATCATTGCCCTA
*
109327 TTATGTCACTCATGTCCCTCGGGG--ACTATTCATATCATTACCTATTATTTCTCAAGGGACTTG
65 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCATTACCTATTATTTCTCAGGGGACTTG
* *
109390 AAGGCGCATTCCCGGGGGCGCCTTCCCATTATTTTATCAGAGAATATGTTATCATTGCCCTATTA
130 AAGGCGCGTTCCCGGGGGCGCCTT-CCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTA
109455 TGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGACT
194 TGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGACT
109514 TGAA-G-GCGTTCCCGGGGG-GCGCCTTCCATTA-TTGTCAGAGAATATGTTATCATTGCCCTAT
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTGTCAGAGAATATGTTATCATTGCCCTAT
109575 TATGTCACTCATGTCCCTCGGGGACACTATTCATATCATTACCTATTATTTCTCAGGGGACTTGA
66 TATGTCACTCATGTCCCTCGGGGACACTATTCATATCATTACCTATTATTTCTCAGGGGACTTGA
*
109640 AGGCACGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTG-CCTATTA
131 AGGCGCGTTCCC-GGGG-GCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTA
*
109704 TGTCACTCATGTCCCTCGGGGACACTATTC-TATTAGTACC---TATTTCTCAAGGGACT
194 TGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTC-AGGGACT
* *
109760 TGAAGGCGCGTTCCCGAGGGCACGCCTTCCATTATTTGTCAGAG-A-A--TT-T-ATTGCCCTAT
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTGTCAGAGAATATGTTATCATTGCCCTAT
109819 TATGTCACTCATGTCCCTCGGGGACACTA
66 TATGTCACTCATGTCCCTCGGGGACACTA
109848 GATGGATTGT
Statistics
Matches: 552, Mismatches: 18, Indels: 37
0.91 0.03 0.06
Matches are distributed among these distances:
244 39 0.07
245 9 0.02
246 13 0.02
247 54 0.10
248 22 0.04
249 175 0.32
250 128 0.23
251 8 0.01
252 36 0.07
253 68 0.12
ACGTcount: A:0.21, C:0.25, G:0.20, T:0.33
Consensus pattern (252 bp):
TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTGTCAGAGAATATGTTATCATTGCCCTAT
TATGTCACTCATGTCCCTCGGGGACACTATTCATATCATTACCTATTATTTCTCAGGGGACTTGA
AGGCGCGTTCCCGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATG
TCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGACT
Found at i:109746 original size:375 final size:372
Alignment explanation
Indices: 109013--109847 Score: 1324
Period size: 375 Copynumber: 2.2 Consensus size: 372
109003 ACTATTCACA
* *
109013 TGAAGGCGCGTTCACGGGGGCGCGTCTTCCATTATTTTTTCAGAGAATATGTTATCATT---CTA
1 TGAAGGCGCGTTCCCGGGGGCGC--CTTCCATTATTTTATCAGAGAATATGTTATCATTGCCCTA
*
109075 TTATATCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTG
64 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTG
109140 AAGGCGCGTCCCCGGGACGCGCCTTCCATTATTTTGTCAGAGAATATATCATTGCCCTATTATGT
129 AAGGCGCGTCCCCGGGACGCGCCTTCCATTA-TTTGTCAGAGAATATATCATTGCCCTATTATGT
*
109205 CACTCATGTCCCTCGGGGACACTATTCATATCATTACCTATTATTTCTCAGGGGACTTGAAGGCG
193 CACTCATGTCCCTCGGGGACACTATTCATATCATTACCTATTATTTCTCAGGGGACTTGAAGGCA
109270 CGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCA
258 CGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCA
*
109335 CTCATGTCCCTCGGGGACTATTCATATCATTACCTATTATTTCTCAAGGGACT
323 CTCATGTCCCTCGGGGACTATTCATATCAGTACC---TATTTCTCAAGGGACT
*
109388 TGAAGGCGCATTCCCGGGGGCGCCTTCCCATTATTTTATCAGAGAATATGTTATCATTGCCCTAT
1 TGAAGGCGCGTTCCCGGGGGCGCCTT-CCATTATTTTATCAGAGAATATGTTATCATTGCCCTAT
109453 TATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCA-GGGACTTGA
65 TATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTGA
* **
109517 A-G-GCGTTCCCGGGGGGCGCCTTCCATTA-TTGTCAGAGAATATGTTATCATTGCCCTATTATG
130 AGGCGCGTCCCCGGGACGCGCCTTCCATTATTTGTCAGAGAATA---TATCATTGCCCTATTATG
109579 TCACTCATGTCCCTCGGGGACACTATTCATATCATTACCTATTATTTCTCAGGGGACTTGAAGGC
192 TCACTCATGTCCCTCGGGGACACTATTCATATCATTACCTATTATTTCTCAGGGGACTTGAAGGC
109644 ACGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTG-CCTATTATGTC
257 ACGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTC
*
109708 ACTCATGTCCCTCGGGGACACTATTC-TATTAGTACCTATTTCTCAAGGGACT
322 ACTCATGTCCCTCGGGG--ACTATTCATATCAGTACCTATTTCTCAAGGGACT
* *
109760 TGAAGGCGCGTTCCCGAGGGCACGCCTTCCATTA-TTTGTCAGAG-A-A--TT-T-ATTGCCCTA
1 TGAAGGCGCGTTCCCG-GGG-GCGCCTTCCATTATTTTATCAGAGAATATGTTATCATTGCCCTA
109818 TTATGTCACTCATGTCCCTCGGGGACACTA
64 TTATGTCACTCATGTCCCTCGGGGACACTA
109848 GATGGATTGT
Statistics
Matches: 436, Mismatches: 13, Indels: 31
0.91 0.03 0.06
Matches are distributed among these distances:
366 39 0.09
367 1 0.00
368 2 0.00
370 1 0.00
371 1 0.00
372 53 0.12
373 12 0.03
374 87 0.20
375 165 0.38
376 17 0.04
377 58 0.13
ACGTcount: A:0.21, C:0.25, G:0.20, T:0.33
Consensus pattern (372 bp):
TGAAGGCGCGTTCCCGGGGGCGCCTTCCATTATTTTATCAGAGAATATGTTATCATTGCCCTATT
ATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTGAA
GGCGCGTCCCCGGGACGCGCCTTCCATTATTTGTCAGAGAATATATCATTGCCCTATTATGTCAC
TCATGTCCCTCGGGGACACTATTCATATCATTACCTATTATTTCTCAGGGGACTTGAAGGCACGT
TCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTC
ATGTCCCTCGGGGACTATTCATATCAGTACCTATTTCTCAAGGGACT
Found at i:110315 original size:33 final size:33
Alignment explanation
Indices: 110245--110342 Score: 126
Period size: 33 Copynumber: 3.0 Consensus size: 33
110235 AAATTTAATG
*
110245 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATAT-ATTTATATTTTAAAT
* * *
110279 TTAAATTTCGAATAATATATTTTTATTTTTATT
1 TTAAATTTCGAATAATATATTTATATTTTAAAT
* *
110312 TTAAATTTTGAATAATA-ATTTGTATTTTAAA
1 TTAAATTTCGAATAATATATTTATATTTTAAA
110343 AACATTTATC
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
32 11 0.20
33 28 0.50
34 17 0.30
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (33 bp):
TTAAATTTCGAATAATATATTTATATTTTAAAT
Found at i:110878 original size:21 final size:20
Alignment explanation
Indices: 110848--110955 Score: 137
Period size: 21 Copynumber: 5.2 Consensus size: 20
110838 TATGGTATAA
*
110848 AACCTTGCGGGCTAGGCATGT
1 AACC-TGCGGGCTAGGAATGT
110869 AACCTGGCGGGCTAGGAATGT
1 AACCT-GCGGGCTAGGAATGT
*
110890 AACCATGCGGGCTCGGAATGT
1 AACC-TGCGGGCTAGGAATGT
110911 AACCTGGCGGGCTAGGAATGT
1 AACCT-GCGGGCTAGGAATGT
*
110932 AACCCTGCGGGCTCGGAAT-T
1 AA-CCTGCGGGCTAGGAATGT
110952 AACC
1 AACC
110956 CTCGGAGATG
Statistics
Matches: 79, Mismatches: 4, Indels: 10
0.85 0.04 0.11
Matches are distributed among these distances:
19 2 0.03
20 5 0.06
21 68 0.86
22 4 0.05
ACGTcount: A:0.23, C:0.24, G:0.33, T:0.19
Consensus pattern (20 bp):
AACCTGCGGGCTAGGAATGT
Found at i:110912 original size:42 final size:42
Alignment explanation
Indices: 110848--110955 Score: 173
Period size: 42 Copynumber: 2.6 Consensus size: 42
110838 TATGGTATAA
* * *
110848 AACCTTGCGGGCTAGGCATGTAACCTGGCGGGCTAGGAATGT
1 AACCATGCGGGCTCGGAATGTAACCTGGCGGGCTAGGAATGT
110890 AACCATGCGGGCTCGGAATGTAACCTGGCGGGCTAGGAATGT
1 AACCATGCGGGCTCGGAATGTAACCTGGCGGGCTAGGAATGT
*
110932 AACCCTGCGGGCTCGGAAT-TAACC
1 AACCATGCGGGCTCGGAATGTAACC
110956 CTCGGAGATG
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
41 5 0.08
42 57 0.92
ACGTcount: A:0.23, C:0.24, G:0.33, T:0.19
Consensus pattern (42 bp):
AACCATGCGGGCTCGGAATGTAACCTGGCGGGCTAGGAATGT
Found at i:110990 original size:21 final size:20
Alignment explanation
Indices: 110964--111004 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
110954 CCCTCGGAGA
*
110964 TGACATATGAATTGGTGGGCT
1 TGACATATGAA-TGGAGGGCT
110985 TGACATATGAATGGAGGGCT
1 TGACATATGAATGGAGGGCT
111005 GGGCATGTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.27, C:0.10, G:0.34, T:0.29
Consensus pattern (20 bp):
TGACATATGAATGGAGGGCT
Done.