Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007279.1 Hibiscus syriacus cultivar Beakdansim tig00019304_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: 127154
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Found at i:1981 original size:112 final size:112
Alignment explanation
Indices: 1823--2045 Score: 446
Period size: 112 Copynumber: 2.0 Consensus size: 112
1813 CACAATCACA
1823 TCTTAAACAAAGATTGATAATGACTCCCAAAACCATATATATAGAGAGAGAGTTAGGATTCACTT
1 TCTTAAACAAAGATTGATAATGACTCCCAAAACCATATATATAGAGAGAGAGTTAGGATTCACTT
1888 ACACAACGTAAAACTCTTTAGTTTTACACAGATTTAGAACTGTTTGC
66 ACACAACGTAAAACTCTTTAGTTTTACACAGATTTAGAACTGTTTGC
1935 TCTTAAACAAAGATTGATAATGACTCCCAAAACCATATATATAGAGAGAGAGTTAGGATTCACTT
1 TCTTAAACAAAGATTGATAATGACTCCCAAAACCATATATATAGAGAGAGAGTTAGGATTCACTT
2000 ACACAACGTAAAACTCTTTAGTTTTACACAGATTTAGAACTGTTTG
66 ACACAACGTAAAACTCTTTAGTTTTACACAGATTTAGAACTGTTTG
2046 ATAAGTGAAA
Statistics
Matches: 111, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
112 111 1.00
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (112 bp):
TCTTAAACAAAGATTGATAATGACTCCCAAAACCATATATATAGAGAGAGAGTTAGGATTCACTT
ACACAACGTAAAACTCTTTAGTTTTACACAGATTTAGAACTGTTTGC
Found at i:5068 original size:28 final size:28
Alignment explanation
Indices: 5037--5101 Score: 121
Period size: 28 Copynumber: 2.3 Consensus size: 28
5027 TGGCTTGCTA
5037 ACATAATGTTTCAAGCAGTGACTCGATG
1 ACATAATGTTTCAAGCAGTGACTCGATG
*
5065 ACATAATATTTCAAGCAGTGACTCGATG
1 ACATAATGTTTCAAGCAGTGACTCGATG
5093 ACATAATGT
1 ACATAATGT
5102 AAATAAATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.29
Consensus pattern (28 bp):
ACATAATGTTTCAAGCAGTGACTCGATG
Found at i:11102 original size:43 final size:43
Alignment explanation
Indices: 11050--11133 Score: 159
Period size: 43 Copynumber: 2.0 Consensus size: 43
11040 GCATGAGTTC
*
11050 CACTCAATTATGTATTTACATTTTATTTTAATAGTTTAATACT
1 CACTCAATTATGTATTTACATTTTATTTTAATAATTTAATACT
11093 CACTCAATTATGTATTTACATTTTATTTTAATAATTTAATA
1 CACTCAATTATGTATTTACATTTTATTTTAATAATTTAATA
11134 ATAACACCCT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.35, C:0.11, G:0.04, T:0.51
Consensus pattern (43 bp):
CACTCAATTATGTATTTACATTTTATTTTAATAATTTAATACT
Found at i:12561 original size:21 final size:21
Alignment explanation
Indices: 12532--12571 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
12522 ATAATTATTA
*
12532 TAATATTTTAAAATTAATAAT
1 TAATATTTTAAAATAAATAAT
* *
12553 TAATTTTTTATAATAAATA
1 TAATATTTTAAAATAAATA
12572 TTATAAATGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TAATATTTTAAAATAAATAAT
Found at i:22378 original size:18 final size:18
Alignment explanation
Indices: 22357--22407 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
22347 TTAATAACTT
22357 AAAATTAAATATTTTTTA
1 AAAATTAAATATTTTTTA
* *
22375 AAAATTACAT-TTTTTTG
1 AAAATTAAATATTTTTTA
*
22392 AAAATAATAATATTTT
1 AAAATTA-AATATTTT
22408 CACCTCATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 12 0.44
18 11 0.41
19 4 0.15
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (18 bp):
AAAATTAAATATTTTTTA
Found at i:28674 original size:32 final size:31
Alignment explanation
Indices: 28638--28711 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
28628 AAAACATAAA
*
28638 ATTTTGATCACTTTCATTTCGTTTTAATTAAG
1 ATTTTG-TCACTTTCATCTCGTTTTAATTAAG
* **
28670 ATTTTGTCATTTTTGTCTCGTTTTAATTAAG
1 ATTTTGTCACTTTCATCTCGTTTTAATTAAG
* *
28701 ATGTAGTCACT
1 ATTTTGTCACT
28712 GAAGGTTAAC
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
31 29 0.83
32 6 0.17
ACGTcount: A:0.23, C:0.12, G:0.12, T:0.53
Consensus pattern (31 bp):
ATTTTGTCACTTTCATCTCGTTTTAATTAAG
Found at i:30332 original size:31 final size:31
Alignment explanation
Indices: 30297--30408 Score: 111
Period size: 31 Copynumber: 3.6 Consensus size: 31
30287 ATTTAACGTC
30297 CAAGTGATCAAAACTTAATAAAATGATAACG
1 CAAGTGATCAAAACTTAATAAAATGATAACG
* **
30328 CAAGTGACCAAAACTTAATAAAACAATAACG
1 CAAGTGATCAAAACTTAATAAAATGATAACG
* * * *
30359 TAAGTGATAAAAAATGT-ATAAATATGAGAA-G
1 CAAGTGATCAAAACT-TAATAAA-ATGATAACG
* *
30390 AAAGTGATTAAAACTTAAT
1 CAAGTGATCAAAACTTAAT
30409 TCACGTATTA
Statistics
Matches: 65, Mismatches: 13, Indels: 6
0.77 0.15 0.07
Matches are distributed among these distances:
30 1 0.02
31 59 0.91
32 5 0.08
ACGTcount: A:0.54, C:0.10, G:0.13, T:0.23
Consensus pattern (31 bp):
CAAGTGATCAAAACTTAATAAAATGATAACG
Found at i:31755 original size:74 final size:74
Alignment explanation
Indices: 31629--31776 Score: 287
Period size: 74 Copynumber: 2.0 Consensus size: 74
31619 TTTTGGTCAC
*
31629 ATTCTTTTTATATCTATACACTTTTGGTCACTTGCGTTATTGTTTTTCTTGGCTACAACTATCAG
1 ATTCCTTTTATATCTATACACTTTTGGTCACTTGCGTTATTGTTTTTCTTGGCTACAACTATCAG
31694 GATTCAGGG
66 GATTCAGGG
31703 ATTCCTTTTATATCTATACACTTTTGGTCACTTGCGTTATTGTTTTTCTTGGCTACAACTATCAG
1 ATTCCTTTTATATCTATACACTTTTGGTCACTTGCGTTATTGTTTTTCTTGGCTACAACTATCAG
31768 GATTCAGGG
66 GATTCAGGG
31777 CGCCTTGGGA
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 73 1.00
ACGTcount: A:0.20, C:0.18, G:0.16, T:0.45
Consensus pattern (74 bp):
ATTCCTTTTATATCTATACACTTTTGGTCACTTGCGTTATTGTTTTTCTTGGCTACAACTATCAG
GATTCAGGG
Found at i:44205 original size:28 final size:28
Alignment explanation
Indices: 44173--44230 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
44163 AAGGAGGTTA
44173 TATCTGTCACCCGCTGAATCATCTACGT
1 TATCTGTCACCCGCTGAATCATCTACGT
44201 TATCTGTCACCCGCTGAATCATCTACGT
1 TATCTGTCACCCGCTGAATCATCTACGT
44229 TA
1 TA
44231 GTTCCTCTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.22, C:0.31, G:0.14, T:0.33
Consensus pattern (28 bp):
TATCTGTCACCCGCTGAATCATCTACGT
Found at i:51672 original size:20 final size:20
Alignment explanation
Indices: 51649--51715 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
51639 AATTTGTAAA
51649 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
51669 TCGCAACGC-GATAGTCAAAT
1 TCGCAACACAGA-AGTCAAAT
* * *
51689 TCGCAACACAAAAATTAAAT
1 TCGCAACACAGAAGTCAAAT
51709 TCGCAAC
1 TCGCAAC
51716 GCCATAATCA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
19 2 0.05
20 37 0.93
21 1 0.03
ACGTcount: A:0.43, C:0.25, G:0.13, T:0.18
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAT
Found at i:51693 original size:40 final size:40
Alignment explanation
Indices: 51628--51735 Score: 121
Period size: 40 Copynumber: 2.7 Consensus size: 40
51618 GAACTCCAAT
* * *
51628 TTCGCAACGCGAATTTGT-AAA-TCGCAACACAGAAGTCAAA
1 TTCGCAACGCG-A-TAGTCAAATTCGCAACACAAAAATCAAA
*
51668 TTCGCAACGCGATAGTCAAATTCGCAACACAAAAATTAAA
1 TTCGCAACGCGATAGTCAAATTCGCAACACAAAAATCAAA
* * *
51708 TTCGCAACGCCATAATCAAATTTGCAAC
1 TTCGCAACGCGATAGTCAAATTCGCAAC
51736 GCGAAACACA
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
38 3 0.05
39 4 0.07
40 52 0.88
ACGTcount: A:0.41, C:0.24, G:0.14, T:0.21
Consensus pattern (40 bp):
TTCGCAACGCGATAGTCAAATTCGCAACACAAAAATCAAA
Found at i:51728 original size:20 final size:20
Alignment explanation
Indices: 51663--51737 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
51653 AACACAGAAG
* *
51663 TCAAATTCGCAACGCGATAG
1 TCAAATTCGCAACGCAATAA
* *
51683 TCAAATTCGCAACACAAAAA
1 TCAAATTCGCAACGCAATAA
* *
51703 TTAAATTCGCAACGCCATAA
1 TCAAATTCGCAACGCAATAA
*
51723 TCAAATTTGCAACGC
1 TCAAATTCGCAACGC
51738 GAAACACAAT
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.41, C:0.25, G:0.12, T:0.21
Consensus pattern (20 bp):
TCAAATTCGCAACGCAATAA
Found at i:51872 original size:22 final size:22
Alignment explanation
Indices: 51847--51901 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
51837 CTCTCTACGG
51847 CGAAATCCGTCCCCATCTCCGA
1 CGAAATCCGTCCCCATCTCCGA
51869 CGAAATCCGTCCCCATCTCCGA
1 CGAAATCCGTCCCCATCTCCGA
51891 CGAAATCCGTC
1 CGAAATCCGTC
51902 TATCTCCATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.24, C:0.44, G:0.15, T:0.18
Consensus pattern (22 bp):
CGAAATCCGTCCCCATCTCCGA
Found at i:61541 original size:17 final size:17
Alignment explanation
Indices: 61488--61542 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
61478 AATAAATTAA
*
61488 TTTCTTAAAAAATATTT
1 TTTCTTAAAAATTATTT
* * *
61505 TTATAATTAAAATTTTTTT
1 TT-T-CTTAAAAATTATTT
61524 TTTCTTAAAAATTATTT
1 TTTCTTAAAAATTATTT
61541 TT
1 TT
61543 AAAAAATACC
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
17 15 0.52
18 2 0.07
19 12 0.41
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTCTTAAAAATTATTT
Found at i:64569 original size:32 final size:32
Alignment explanation
Indices: 64533--64685 Score: 231
Period size: 32 Copynumber: 4.8 Consensus size: 32
64523 GAGTCGAGGG
*
64533 TTACCTATGTCTTTCGAGACATATGGACAGAA
1 TTACCTATGTCTTTCGGGACATATGGACAGAA
*
64565 TTACCTATGTCTTTCGGGACATATGGACAGTA
1 TTACCTATGTCTTTCGGGACATATGGACAGAA
*
64597 TTACCTATGTTTTTCGGGACATATGGACAGAA
1 TTACCTATGTCTTTCGGGACATATGGACAGAA
64629 TTACCTATGTCTTTCGGGACATATGGAC--AA
1 TTACCTATGTCTTTCGGGACATATGGACAGAA
* *
64659 TTACCTATGT-TCTTAGGAACATATGGA
1 TTACCTATGTCT-TTCGGGACATATGGA
64686 TAGGTTCTTC
Statistics
Matches: 113, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
29 1 0.01
30 25 0.22
32 87 0.77
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (32 bp):
TTACCTATGTCTTTCGGGACATATGGACAGAA
Found at i:65579 original size:2 final size:2
Alignment explanation
Indices: 65572--65604 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
65562 ATTTAAGTAT
65572 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 T
65605 TTGAATTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:67479 original size:21 final size:20
Alignment explanation
Indices: 67442--67483 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
67432 TAGAAACACG
67442 ATAATTTTTTTAATTTAATTA
1 ATAATTTTTTTAATTT-ATTA
*
67463 ATAATTTTATTT-TTTTATTA
1 ATAATTTT-TTTAATTTATTA
67483 A
1 A
67484 AAACAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 5 0.26
21 11 0.58
22 3 0.16
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
ATAATTTTTTTAATTTATTA
Found at i:75679 original size:19 final size:20
Alignment explanation
Indices: 75639--75681 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
75629 TGGTACAATT
75639 AACTCAATTTTTTAATTAAA
1 AACTCAATTTTTTAATTAAA
75659 AACTCAATTTTTTAATTAAA
1 AACTCAATTTTTTAATTAAA
75679 AAC
1 AAC
75682 CTAACTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.42
Consensus pattern (20 bp):
AACTCAATTTTTTAATTAAA
Found at i:76510 original size:60 final size:60
Alignment explanation
Indices: 76443--76583 Score: 246
Period size: 60 Copynumber: 2.3 Consensus size: 60
76433 TCGGATGACC
*
76443 ATTTTGTAACTTTTAATAGTCGAGGGACTCAACAGAGCAACACTGTATAGTTAAAGGACT
1 ATTTTGTAACTTTTAATAGTCGAGGGACTCAACAGAGCAACACTGTATAGTTAAAGGAAT
* *
76503 ATTTTGTAATTTTTAATAGTCGAGGGACTCAACAGAGCAATACTGTATAGTTAAAGGAAT
1 ATTTTGTAACTTTTAATAGTCGAGGGACTCAACAGAGCAACACTGTATAGTTAAAGGAAT
76563 ATTTTGTAAACTTTTAATAGT
1 ATTTTGT-AACTTTTAATAGT
76584 TAAAGGACTT
Statistics
Matches: 76, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
60 64 0.84
61 12 0.16
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.35
Consensus pattern (60 bp):
ATTTTGTAACTTTTAATAGTCGAGGGACTCAACAGAGCAACACTGTATAGTTAAAGGAAT
Found at i:77105 original size:22 final size:24
Alignment explanation
Indices: 77063--77106 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
77053 ACCATAATCC
77063 TCACCATCCAAACCCTCATCATGG
1 TCACCATCCAAACCCTCATCATGG
*
77087 TCACCAT-C-AACTCTCATCAT
1 TCACCATCCAAACCCTCATCAT
77107 CAAAGCCTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 11 0.58
23 1 0.05
24 7 0.37
ACGTcount: A:0.30, C:0.41, G:0.05, T:0.25
Consensus pattern (24 bp):
TCACCATCCAAACCCTCATCATGG
Found at i:81255 original size:21 final size:21
Alignment explanation
Indices: 81231--81294 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
81221 GCAAATTCGC
*
81231 GTTGCATTTCGCGTTGAGATA
1 GTTGCATTTCGCGTTGCGATA
* **
81252 GTTGAAAATCGCGTTGCGAT-
1 GTTGCATTTCGCGTTGCGATA
* *
81272 TTTCCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
81293 GT
1 GT
81295 GGAGATCGCA
Statistics
Matches: 32, Mismatches: 10, Indels: 2
0.73 0.23 0.05
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.19, C:0.17, G:0.27, T:0.38
Consensus pattern (21 bp):
GTTGCATTTCGCGTTGCGATA
Found at i:81394 original size:20 final size:20
Alignment explanation
Indices: 81369--81406 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
81359 TCGTTGCGAT
81369 TTTCCAAATTCCCATTAGTG
1 TTTCCAAATTCCCATTAGTG
81389 TTTCCAAATTCCCATTAG
1 TTTCCAAATTCCCATTAG
81407 GCATTCGCGA
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:0.26, C:0.26, G:0.08, T:0.39
Consensus pattern (20 bp):
TTTCCAAATTCCCATTAGTG
Found at i:81899 original size:6 final size:6
Alignment explanation
Indices: 81879--81922 Score: 72
Period size: 6 Copynumber: 7.5 Consensus size: 6
81869 GTCCATCTCG
*
81879 GGTCG- GGTAGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
81923 AATACGTGTC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
5 4 0.11
6 32 0.89
ACGTcount: A:0.02, C:0.14, G:0.52, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:82077 original size:41 final size:41
Alignment explanation
Indices: 82007--82221 Score: 191
Period size: 41 Copynumber: 5.0 Consensus size: 41
81997 TCAACGAATT
* *
82007 TGGAAAATCGCAACGAC-AACTGCAGACTATCGCAACGCGAAA
1 TGGAAAATCGCAACG-CGAATTTCA-ACTATCGCAACGCGAAA
*
82049 TGGAAAATCGCAATGCGAATTTCAACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGAATTTCAACTATCGCAACGCGAAA
* *
82090 TGGAAAATCGCAACGCGAATTTCAACTATCGTAACGCGAATT
1 TGGAAAATCGCAACGCGAATTTCAACTATCGCAACGCGAA-A
*** *
82132 TGCGATAGTGGAGATCGCGTTGCG-ATTTCAACTATGGCAACGCGAAA
1 TG-GA-A----A-ATCGCAACGCGAATTTCAACTATCGCAACGCGAAA
* * ** * *
82179 TGGAAAAACGTAACGCGTTTTTCAATTATCGCAATGCGAAA
1 TGGAAAATCGCAACGCGAATTTCAACTATCGCAACGCGAAA
82220 TG
1 TG
82222 CAACTTGAAT
Statistics
Matches: 142, Mismatches: 21, Indels: 21
0.77 0.11 0.11
Matches are distributed among these distances:
40 6 0.04
41 78 0.55
42 21 0.15
43 2 0.01
44 1 0.01
45 1 0.01
46 2 0.01
47 2 0.01
48 21 0.15
49 8 0.06
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.21
Consensus pattern (41 bp):
TGGAAAATCGCAACGCGAATTTCAACTATCGCAACGCGAAA
Found at i:82081 original size:21 final size:21
Alignment explanation
Indices: 82032--82132 Score: 98
Period size: 20 Copynumber: 4.9 Consensus size: 21
82022 ACAACTGCAG
* **
82032 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAATTTCA
* *
82053 A-AATCGCAATGCGAATTTCA
1 ACTATCGCAACGCGAATTTCA
* **
82073 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAATTTCA
*
82094 A-AATCGCAACGCGAATTTCA
1 ACTATCGCAACGCGAATTTCA
*
82114 ACTATCGTAACGCGAATTT
1 ACTATCGCAACGCGAATTT
82133 GCGATAGTGG
Statistics
Matches: 62, Mismatches: 16, Indels: 4
0.76 0.20 0.05
Matches are distributed among these distances:
20 31 0.50
21 31 0.50
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.21
Consensus pattern (21 bp):
ACTATCGCAACGCGAATTTCA
Found at i:82267 original size:19 final size:19
Alignment explanation
Indices: 82243--82295 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
82233 TGCGATAGTG
82243 GAGATCGCAATGCGAATTA
1 GAGATCGCAATGCGAATTA
82262 GAGATCGCAATGCGAATTA
1 GAGATCGCAATGCGAATTA
*
82281 GAGATCGCATTGCGA
1 GAGATCGCAATGCGA
82296 TTTTGTTGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.34, C:0.17, G:0.28, T:0.21
Consensus pattern (19 bp):
GAGATCGCAATGCGAATTA
Found at i:83340 original size:31 final size:31
Alignment explanation
Indices: 83305--83381 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 31
83295 TCAAAAAACA
* *
83305 TAATATATTGTCACTTTCGTTTTTATTTAAT
1 TAATATATGGTCACTTTCATTTTTATTTAAT
*
83336 TAATATATGGTCACTTTTATTTTTATTTAAT
1 TAATATATGGTCACTTTCATTTTTATTTAAT
* *
83367 TAAAATGTGGTCACT
1 TAATATATGGTCACT
83382 CTGAGTTAAC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.53
Consensus pattern (31 bp):
TAATATATGGTCACTTTCATTTTTATTTAAT
Found at i:87047 original size:3 final size:3
Alignment explanation
Indices: 87039--87067 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
87029 ATGTGCACAT
87039 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
87068 AATCCTTATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:89279 original size:21 final size:24
Alignment explanation
Indices: 89241--89287 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
89231 AAATACAAAA
89241 TCTAATAATCTATAATATAAATAT
1 TCTAATAATCTATAATATAAATAT
*
89265 TCTAAT-AT-TATATATATATATAT
1 TCTAATAATCTATA-ATATAAATAT
89288 AAATAAAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 4 0.19
23 11 0.52
24 6 0.29
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (24 bp):
TCTAATAATCTATAATATAAATAT
Found at i:89708 original size:20 final size:20
Alignment explanation
Indices: 89667--89708 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
89657 GATATGGTCT
*
89667 TTAGAAATGATTGAAGTTTA
1 TTAGAAATGATTGAAATTTA
*
89687 TTAGAGATGATT-AAATTATA
1 TTAGAAATGATTGAAATT-TA
89707 TT
1 TT
89709 TAATTTCTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.43
Consensus pattern (20 bp):
TTAGAAATGATTGAAATTTA
Found at i:92458 original size:2 final size:2
Alignment explanation
Indices: 92451--92476 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
92441 TTTCTCTAAT
92451 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
92477 CATGTATAGA
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):
TA
Found at i:92570 original size:33 final size:33
Alignment explanation
Indices: 92531--92596 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
92521 CCTCTAAATT
92531 ATAAAATAGATTTATAATTTTATTTTTGAATAA
1 ATAAAATAGATTTATAATTTTATTTTTGAATAA
92564 ATAAAATAGATTTATAATTTTATTTTTGAATAA
1 ATAAAATAGATTTATAATTTTATTTTTGAATAA
92597 GAGATTTGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (33 bp):
ATAAAATAGATTTATAATTTTATTTTTGAATAA
Found at i:92601 original size:27 final size:29
Alignment explanation
Indices: 92538--92603 Score: 73
Period size: 33 Copynumber: 2.2 Consensus size: 29
92528 ATTATAAAAT
*
92538 AGATTTATAATTTTATTTTTGAATAAATAAAAT
1 AGATTTATAATTTTATTTTTG---AAAT-AAAG
92571 AGATTTATAATTTTATTTTTG-AAT-AAG
1 AGATTTATAATTTTATTTTTGAAATAAAG
92598 AGATTT
1 AGATTT
92604 GTGAGGAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
27 8 0.25
29 3 0.09
33 21 0.66
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (29 bp):
AGATTTATAATTTTATTTTTGAAATAAAG
Found at i:93021 original size:26 final size:27
Alignment explanation
Indices: 92966--93026 Score: 90
Period size: 26 Copynumber: 2.3 Consensus size: 27
92956 AACACCAAAT
*
92966 ATAATAATAATATTATTTATTAATAAA
1 ATAATAATAATAATATTTATTAATAAA
92993 ATAATAATAAATAATA-TT-TTAATAAA
1 ATAATAAT-AATAATATTTATTAATAAA
93019 ATAATAAT
1 ATAATAAT
93027 GTTATTTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
26 16 0.50
27 10 0.31
28 6 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (27 bp):
ATAATAATAATAATATTTATTAATAAA
Found at i:93173 original size:24 final size:24
Alignment explanation
Indices: 93146--93191 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
93136 ACAAATTATA
93146 TGTTAATAAT-TAAAATATAAATAT
1 TGTTAA-AATATAAAATATAAATAT
*
93170 TGTTAAAATATAAATTATAAAT
1 TGTTAAAATATAAAATATAAAT
93192 TAGAATTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.41
Consensus pattern (24 bp):
TGTTAAAATATAAAATATAAATAT
Found at i:93361 original size:32 final size:35
Alignment explanation
Indices: 93325--93402 Score: 83
Period size: 32 Copynumber: 2.3 Consensus size: 35
93315 GTATAATATT
93325 ATATTTAATAATATAATTAT-AAC-AGTA-AAA-TA
1 ATATTTAATAATA-AATTATCAACAAGTATAAACTA
* *
93357 ATATTATATTATTAAATTATCAACAAGTATAAACTA
1 ATATT-TAATAATAAATTATCAACAAGTATAAACTA
*
93393 ATAATTAATA
1 ATATTTAATA
93403 TATTTATTAG
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
32 11 0.30
33 9 0.24
34 4 0.11
35 7 0.19
36 6 0.16
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (35 bp):
ATATTTAATAATAAATTATCAACAAGTATAAACTA
Found at i:97471 original size:101 final size:102
Alignment explanation
Indices: 97315--97509 Score: 333
Period size: 101 Copynumber: 1.9 Consensus size: 102
97305 TATTTTTTTA
97315 TTAAATTATAAAATTTATTTTAACCAATTTTTACTAATAATATTTTAACAATTTAAATTGAATAA
1 TTAAATTATAAAATTTA--TTAACCAATTTTTACTAATAATATTTTAACAATTTAAATTGAAT-A
97380 TATTAAA-TTTATTTCATAAATAATAGGTGACACTAAATT
63 TATTAAATTTTATTTCATAAATAATAGGTGACACTAAATT
97419 TTAAATTATAAAATTTA-TAACC-ATTTTATACTAATAATATTTTAACAATTTAAATTGAATATA
1 TTAAATTATAAAATTTATTAACCAATTTT-TACTAATAATATTTTAACAATTTAAATTGAATATA
97482 TTAAATTTTATTTCATAAATAATAGGTG
65 TTAAATTTTATTTCATAAATAATAGGTG
97510 GTTAGAAGAT
Statistics
Matches: 89, Mismatches: 0, Indels: 7
0.93 0.00 0.07
Matches are distributed among these distances:
100 13 0.15
101 59 0.66
104 17 0.19
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (102 bp):
TTAAATTATAAAATTTATTAACCAATTTTTACTAATAATATTTTAACAATTTAAATTGAATATAT
TAAATTTTATTTCATAAATAATAGGTGACACTAAATT
Found at i:98935 original size:2 final size:2
Alignment explanation
Indices: 98897--98925 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
98887 GATATTCATT
98897 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 T
98926 TAACATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:100544 original size:22 final size:21
Alignment explanation
Indices: 100520--100592 Score: 76
Period size: 22 Copynumber: 3.3 Consensus size: 21
100510 CAGTGCTAGT
*
100520 GCACTTTTGTATCAGTGTGAAT
1 GCACTTTTGTATCAGTGT-AAG
100542 GCACTTTTG-ATTCAGTGCTAAG
1 GCACTTTTGTA-TCAGTG-TAAG
* *
100564 GCACTTTAGTATTAGTGTTAAG
1 GCACTTTTGTATCAGTG-TAAG
100586 GCACTTT
1 GCACTTT
100593 CGTTATATAA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
21 1 0.02
22 41 0.93
23 2 0.05
ACGTcount: A:0.23, C:0.15, G:0.22, T:0.40
Consensus pattern (21 bp):
GCACTTTTGTATCAGTGTAAG
Found at i:114319 original size:22 final size:23
Alignment explanation
Indices: 114294--114336 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
114284 ACTAATAAGC
114294 TGATAACAT-ATGT-TCGATAAAA
1 TGATAA-ATAATGTATCGATAAAA
114316 TGATAAATAATGTATCGATAA
1 TGATAAATAATGTATCGATAA
114337 TATTAATGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 2 0.11
22 10 0.53
23 7 0.37
ACGTcount: A:0.47, C:0.07, G:0.14, T:0.33
Consensus pattern (23 bp):
TGATAAATAATGTATCGATAAAA
Found at i:114943 original size:31 final size:31
Alignment explanation
Indices: 114905--114967 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
114895 AATAGGGTGA
114905 AATCCACAGTGTTGGCCGTAGGTCGTCATGC
1 AATCCACAGTGTTGGCCGTAGGTCGTCATGC
114936 AATCCACAGTGTTGGCCGTAGGTCGTCATGC
1 AATCCACAGTGTTGGCCGTAGGTCGTCATGC
114967 A
1 A
114968 CTCCGGGCGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.21, C:0.25, G:0.29, T:0.25
Consensus pattern (31 bp):
AATCCACAGTGTTGGCCGTAGGTCGTCATGC
Found at i:114995 original size:29 final size:29
Alignment explanation
Indices: 114953--115009 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
114943 AGTGTTGGCC
*
114953 GTAGGTCGTCATGCACTCCGGGCGACCTT
1 GTAGGTCGCCATGCACTCCGGGCGACCTT
114982 GTAGGTCGCCATGCACTCCGGGCGACCT
1 GTAGGTCGCCATGCACTCCGGGCGACCT
115010 ACCCTTGCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.14, C:0.33, G:0.32, T:0.21
Consensus pattern (29 bp):
GTAGGTCGCCATGCACTCCGGGCGACCTT
Found at i:115143 original size:14 final size:14
Alignment explanation
Indices: 115121--115187 Score: 71
Period size: 14 Copynumber: 4.4 Consensus size: 14
115111 CCTCGCATAG
*
115121 CTCGTTCGGATGGC
1 CTCGGTCGGATGGC
115135 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
115149 CTCGGATGCTCTTGGATGGC
1 CTC-G--G-TC--GGATGGC
115169 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
115183 CTCGG
1 CTCGG
115188 ATGCCCAGCG
Statistics
Matches: 46, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
14 28 0.61
15 1 0.02
16 2 0.04
17 2 0.04
18 2 0.04
19 1 0.02
20 10 0.22
ACGTcount: A:0.07, C:0.28, G:0.39, T:0.25
Consensus pattern (14 bp):
CTCGGTCGGATGGC
Found at i:115267 original size:29 final size:30
Alignment explanation
Indices: 115230--115288 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
115220 ACAATCTCTT
*
115230 GTAGCTCGCCGGGAAGACAT-AGCGACCTA
1 GTAGCTCGCCCGGAAGACATGAGCGACCTA
* * *
115259 GTAGGTCGCCCGGAAGGCATGGGCGACCTA
1 GTAGCTCGCCCGGAAGACATGAGCGACCTA
115289 CGGCCAACAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.24, C:0.27, G:0.36, T:0.14
Consensus pattern (30 bp):
GTAGCTCGCCCGGAAGACATGAGCGACCTA
Found at i:115565 original size:2 final size:2
Alignment explanation
Indices: 115558--115587 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
115548 AAGAACTGTA
115558 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
115588 TCTTCCATGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:119269 original size:55 final size:55
Alignment explanation
Indices: 119071--119270 Score: 242
Period size: 55 Copynumber: 3.6 Consensus size: 55
119061 ACAAGTAGTA
* * * * *
119071 CCGATACGATCGTTCATAAACTTATTATGAATTTTGTGGTTTTACACACATAAAG
1 CCGATACGGTCGTTCATAAACATATTATGAATTCTGTGGTTTTACACACTTAATG
* * * * * *
119126 CTGATACGGTCGTTTATAAATATATTATGAATT-TCGTGGTTTTGCACATTTAGTG
1 CCGATACGGTCGTTCATAAACATATTATGAATTCT-GTGGTTTTACACACTTAATG
* *
119181 TCGATACGGTCGTTCATAAACATATTACGAATTCTGTGGTTTTACACACTTAATG
1 CCGATACGGTCGTTCATAAACATATTATGAATTCTGTGGTTTTACACACTTAATG
*
119236 CCGATTA-GGTCATTCATAAACATATTATGAATTCT
1 CCGA-TACGGTCGTTCATAAACATATTATGAATTCT
119271 TTTCGGTCAC
Statistics
Matches: 121, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
54 1 0.01
55 117 0.97
56 3 0.02
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.39
Consensus pattern (55 bp):
CCGATACGGTCGTTCATAAACATATTATGAATTCTGTGGTTTTACACACTTAATG
Found at i:120079 original size:20 final size:20
Alignment explanation
Indices: 120042--120080 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
120032 TGAAAATAAT
*
120042 ATAATTAATATTTTAATTTA
1 ATAATTAATATTTAAATTTA
* *
120062 ATAATTTATCTTTAAATTT
1 ATAATTAATATTTAAATTT
120081 TTAACTAATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (20 bp):
ATAATTAATATTTAAATTTA
Found at i:120130 original size:20 final size:20
Alignment explanation
Indices: 120105--120168 Score: 58
Period size: 20 Copynumber: 3.0 Consensus size: 20
120095 ATTATAAGTT
120105 AAATTTTTTAAAAAATTTTA
1 AAATTTTTTAAAAAATTTTA
*
120125 AAATTTTATAAATTAAATTATTA
1 AAATTTTTTAAA--AAATT-TTA
* *
120148 ATTATTTTTT-TAAAATTTTA
1 A-AATTTTTTAAAAAATTTTA
120168 A
1 A
120169 TTTTTTATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
20 15 0.42
21 5 0.14
22 5 0.14
23 5 0.14
24 6 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AAATTTTTTAAAAAATTTTA
Found at i:122898 original size:12 final size:13
Alignment explanation
Indices: 122883--122921 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
122873 TAAAAGAAAT
122883 TTTAAATTTAA-A
1 TTTAAATTTAATA
*
122895 TTTAAATTCAATA
1 TTTAAATTTAATA
122908 TTTAATATTTAATA
1 TTTAA-ATTTAATA
122922 ACTTTATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 10 0.43
13 6 0.26
14 7 0.30
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (13 bp):
TTTAAATTTAATA
Found at i:127048 original size:13 final size:12
Alignment explanation
Indices: 127017--127041 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
127007 GTATTATTTA
127017 AATAAAAAAATT
1 AATAAAAAAATT
127029 AATAAAAAAATT
1 AATAAAAAAATT
127041 A
1 A
127042 CTTAAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AATAAAAAAATT
Done.