Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005617.1 Hibiscus syriacus cultivar Beakdansim tig00013064_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: 88853
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.32
Found at i:9 original size:1 final size:1
Alignment explanation
Indices: 4--69 Score: 69
Period size: 1 Copynumber: 66.0 Consensus size: 1
1 TTC
* * * * * * *
4 TTTTTTTCTTTTTTTTTTTCTTTTTTTCTTTTTTTCTTTTTTTTTTCTTTCTTTTTTTCTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
69 T
1 T
70 CTTCAAATAA
Statistics
Matches: 51, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 51 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (1 bp):
T
Found at i:13 original size:8 final size:8
Alignment explanation
Indices: 1--72 Score: 100
Period size: 8 Copynumber: 9.6 Consensus size: 8
1 TTCTTTTT
1 TTCTTTTT
9 TTC---TT
1 TTCTTTTT
14 TT-TTTTT
1 TTCTTTTT
21 TTCTTTTT
1 TTCTTTTT
29 TTCTTTTT
1 TTCTTTTT
37 TTCTTTTT
1 TTCTTTTT
*
45 TT-TTTCT
1 TTCTTTTT
52 TTCTTTTT
1 TTCTTTTT
60 TTCTTTTT
1 TTCTTTTT
68 TTCTT
1 TTCTT
73 CAAATAATAT
Statistics
Matches: 57, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
5 4 0.07
7 10 0.18
8 43 0.75
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (8 bp):
TTCTTTTT
Found at i:55 original size:31 final size:31
Alignment explanation
Indices: 12--72 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
2 TCTTTTTTTC
*
12 TTTTTTTT-TTTCTTTTTTTCTTTTTTTCTT
1 TTTTTTTTCTTCCTTTTTTTCTTTTTTTCTT
*
42 TTTTTTTTCTTTCTTTTTTTCTTTTTTTCTT
1 TTTTTTTTCTTCCTTTTTTTCTTTTTTTCTT
73 CAAATAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 8 0.27
31 22 0.73
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (31 bp):
TTTTTTTTCTTCCTTTTTTTCTTTTTTTCTT
Found at i:7310 original size:15 final size:15
Alignment explanation
Indices: 7287--7318 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
7277 TGAAATGAAT
7287 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
7302 AATGCATGTATGCAA
1 AATGAATGTATGCAA
7317 AA
1 AA
7319 AGGTATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:10637 original size:28 final size:29
Alignment explanation
Indices: 10606--10678 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 29
10596 AAAATGAAAC
*
10606 ATATAAATATTATGAAAA-TAATAAGTAA
1 ATATAAATATTATGAAAAGAAATAAGTAA
* * *
10634 ATATAAAAATTTTGAAAAGAAATAATTAA
1 ATATAAATATTATGAAAAGAAATAAGTAA
*
10663 AAATTAAATA-TATGAA
1 ATA-TAAATATTATGAA
10679 CTTTTAATTT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
28 16 0.44
29 15 0.42
30 5 0.14
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.32
Consensus pattern (29 bp):
ATATAAATATTATGAAAAGAAATAAGTAA
Found at i:12643 original size:3 final size:3
Alignment explanation
Indices: 12625--12699 Score: 87
Period size: 3 Copynumber: 24.7 Consensus size: 3
12615 TGTAATATTA
* * * * *
12625 AAT AAT ATAT ATT AAT AAT AAT AAT AAT TAT TAT TAT AAT AAT TAT
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
12671 AAT AAT AAT AAT TAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
12700 CATTAAAATG
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
3 60 0.95
4 3 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
AAT
Found at i:12665 original size:15 final size:15
Alignment explanation
Indices: 12617--12697 Score: 105
Period size: 15 Copynumber: 5.5 Consensus size: 15
12607 TTTGGGCTTG
12617 TAAT-ATTA-AATAA
1 TAATAATTATAATAA
12630 T-ATATATTAATAATAA
1 TAATA-ATT-ATAATAA
* *
12646 TAATAATTATTATTA
1 TAATAATTATAATAA
12661 TAATAATTATAATAA
1 TAATAATTATAATAA
12676 TAATAATTATAATAA
1 TAATAATTATAATAA
12691 TAATAAT
1 TAATAAT
12698 AACATTAAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
12 2 0.03
13 1 0.02
14 3 0.05
15 41 0.69
16 9 0.15
17 3 0.05
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TAATAATTATAATAA
Found at i:16961 original size:65 final size:64
Alignment explanation
Indices: 16892--17047 Score: 176
Period size: 65 Copynumber: 2.4 Consensus size: 64
16882 TACACTAGGG
* * * *
16892 GTGCATCGATACACTAATTAT-ATTCGATGTTTCAA-AAGAGCCAGGAGTGCATCGATGCATGGT
1 GTGCATCGGTACACTAA-AATCATTCGATGTTTCAATAA-AGCCAAGAGTGCATCGATGCAT-GA
16955 CT
63 CT
* **
16957 GTGCATCGGTAC-GTAAAATGCATTCGATGTTTCAATAAATTCAAGAGTGCATCGATGCATGACT
1 GTGCATCGGTACACTAAAAT-CATTCGATGTTTCAATAAAGCCAAGAGTGCATCGATGCATGACT
17021 GTGCATCGGTACAC-AAAATGCATTCGA
1 GTGCATCGGTACACTAAAAT-CATTCGA
17048 AATAGGGTGT
Statistics
Matches: 79, Mismatches: 8, Indels: 9
0.82 0.08 0.09
Matches are distributed among these distances:
63 2 0.03
64 31 0.39
65 44 0.56
66 2 0.03
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (64 bp):
GTGCATCGGTACACTAAAATCATTCGATGTTTCAATAAAGCCAAGAGTGCATCGATGCATGACT
Found at i:17469 original size:72 final size:72
Alignment explanation
Indices: 17347--17484 Score: 258
Period size: 72 Copynumber: 1.9 Consensus size: 72
17337 AACCTACTAC
17347 ATTTAATCTAAATGACTTACATATGGTATAGTTGAGTCAAGAGTGAGTTACATTTGATGCTATAC
1 ATTTAATCTAAATGACTTACATATGGTATAGTTGAGTCAAGAGTGAGTTACATTTGATGCTATAC
17412 TGCTTAT
66 TGCTTAT
* *
17419 ATTTCATCTAAATGACTTACATATGGTATAGTTGAGTCAAGAGTGAGTTACCTTTGATGCTATAC
1 ATTTAATCTAAATGACTTACATATGGTATAGTTGAGTCAAGAGTGAGTTACATTTGATGCTATAC
17484 T
66 T
17485 ACTAGAAACG
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 64 1.00
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.38
Consensus pattern (72 bp):
ATTTAATCTAAATGACTTACATATGGTATAGTTGAGTCAAGAGTGAGTTACATTTGATGCTATAC
TGCTTAT
Found at i:23449 original size:110 final size:111
Alignment explanation
Indices: 23283--23501 Score: 269
Period size: 110 Copynumber: 2.0 Consensus size: 111
23273 AATTCATAGC
* * * * *
23283 ACCTCTGTGCTTGAATTAACGATTGAGCACCTCTGTATTTCAATCAACAAACTGACACCTTTATG
1 ACCTCTGTGCTTG-AGTAACGATTGAGCACCTATGTATTTCAATAAAAAAACTGACACCTCTATG
** * * *
23348 CAATTAAAAATGACTTTGCACCTTTTTGCTTCAGTCTAGAATCTGGA
65 CAATTAAAAATGACTGAGCACCTCTGTGCTTAAGTCTAGAATCTGGA
* * * * *
23395 ACCTCTGTGCTTG-GTAATGATTGAGCACCTATGTGTTTCAATAAAAAAATTGACACCTCTGTGT
1 ACCTCTGTGCTTGAGTAACGATTGAGCACCTATGTATTTCAATAAAAAAACTGACACCTCTATGC
* *
23459 AGTTAGAAATGACTGAGCACCTCTGTGCTTAAGTCTAGAATCT
66 AATTAAAAATGACTGAGCACCTCTGTGCTTAAGTCTAGAATCT
23502 AATACCTCTT
Statistics
Matches: 90, Mismatches: 17, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
110 77 0.86
112 13 0.14
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (111 bp):
ACCTCTGTGCTTGAGTAACGATTGAGCACCTATGTATTTCAATAAAAAAACTGACACCTCTATGC
AATTAAAAATGACTGAGCACCTCTGTGCTTAAGTCTAGAATCTGGA
Found at i:23509 original size:110 final size:110
Alignment explanation
Indices: 23283--23532 Score: 263
Period size: 110 Copynumber: 2.3 Consensus size: 110
23273 AATTCATAGC
* * * * * *
23283 ACCTCTGTGCTTGAATTAACGATTGAGCACCTCTGTATTTCAATCAACAAACTGACACCTTTATG
1 ACCTCTGTGCTTG--GTAATGATTGAGCACCTATGTATTTCAATAAAAAAACTGACACCTCTATG
** * * * *
23348 CAATTAAAAATGACTTTGCACCTTTTTGCTTCAGTCTAGAATCTGGA
64 CAATTAAAAATGACTGAGCACCTCTGTGCTTAAGTCTAGAATCTGAA
* * * *
23395 ACCTCTGTGCTTGGTAATGATTGAGCACCTATGTGTTTCAATAAAAAAATTGACACCTCTGTGTA
1 ACCTCTGTGCTTGGTAATGATTGAGCACCTATGTATTTCAATAAAAAAACTGACACCTCTATGCA
* *
23460 GTTAGAAATGACTGAGCACCTCTGTGCTTAAGTCTAGAATCT-AA
66 ATTAAAAATGACTGAGCACCTCTGTGCTTAAGTCTAGAATCTGAA
*
23504 TACCTCTTTATG-TT-GTAATGATTGAGCAC
1 -ACCTC--TGTGCTTGGTAATGATTGAGCAC
23533 ATTTGTGCTT
Statistics
Matches: 116, Mismatches: 19, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
109 1 0.01
110 97 0.84
111 2 0.02
112 16 0.14
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (110 bp):
ACCTCTGTGCTTGGTAATGATTGAGCACCTATGTATTTCAATAAAAAAACTGACACCTCTATGCA
ATTAAAAATGACTGAGCACCTCTGTGCTTAAGTCTAGAATCTGAA
Found at i:23569 original size:28 final size:28
Alignment explanation
Indices: 23529--23652 Score: 141
Period size: 28 Copynumber: 4.5 Consensus size: 28
23519 TAATGATTGA
23529 GCACATTTGTGCTTATATCTAAAGTTTG
1 GCACATTTGTGCTTATATCTAAAGTTTG
*
23557 GCACCTTTGTGCTTATATCTAAAGTTTG
1 GCACATTTGTGCTTATATCTAAAGTTTG
* * *
23585 GCACCTCTGTGCTT-TA---AAATTGATTG
1 GCACATTTGTGCTTATATCTAAA--GTTTG
*
23611 AGCACATATGTGCTTA-ATCTAAAGTTTG
1 -GCACATTTGTGCTTATATCTAAAGTTTG
23639 GCACATTTGTGCTT
1 GCACATTTGTGCTT
23653 TAAAATTGAT
Statistics
Matches: 82, Mismatches: 7, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
24 3 0.04
26 4 0.05
27 28 0.34
28 44 0.54
30 3 0.04
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.40
Consensus pattern (28 bp):
GCACATTTGTGCTTATATCTAAAGTTTG
Found at i:23622 original size:27 final size:27
Alignment explanation
Indices: 23592--23678 Score: 90
Period size: 27 Copynumber: 3.2 Consensus size: 27
23582 TTGGCACCTC
*
23592 TGTGCTTTAAAATTGATTGAGCACATA
1 TGTGCTTTAAAATTGATTGAGCACATT
* *
23619 TGTGC-TTAATCTAA-AGTTTG-GCACATT
1 TGTGCTTTAA---AATTGATTGAGCACATT
*
23646 TGTGCTTTAAAATTGATTGAGCACCTT
1 TGTGCTTTAAAATTGATTGAGCACATT
23673 TGTGCT
1 TGTGCT
23679 ACAATTCAGC
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
25 2 0.04
26 8 0.17
27 28 0.58
28 8 0.17
29 2 0.04
ACGTcount: A:0.26, C:0.14, G:0.20, T:0.40
Consensus pattern (27 bp):
TGTGCTTTAAAATTGATTGAGCACATT
Found at i:23634 original size:54 final size:55
Alignment explanation
Indices: 23564--23678 Score: 187
Period size: 54 Copynumber: 2.1 Consensus size: 55
23554 TTGGCACCTT
*
23564 TGTGCTTATATCTAAAGTTTGGCACCTCTGTGCTTTAAAATTGATTGAGCACATA
1 TGTGCTTATATCTAAAGTTTGGCACATCTGTGCTTTAAAATTGATTGAGCACATA
* * *
23619 TGTGCTTA-ATCTAAAGTTTGGCACATTTGTGCTTTAAAATTGATTGAGCACCTT
1 TGTGCTTATATCTAAAGTTTGGCACATCTGTGCTTTAAAATTGATTGAGCACATA
23673 TGTGCT
1 TGTGCT
23679 ACAATTCAGC
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
54 48 0.86
55 8 0.14
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.40
Consensus pattern (55 bp):
TGTGCTTATATCTAAAGTTTGGCACATCTGTGCTTTAAAATTGATTGAGCACATA
Found at i:25180 original size:24 final size:24
Alignment explanation
Indices: 25148--25196 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
25138 ACTGACATGT
*
25148 AAACATAAAGATCAAAATAGGATG
1 AAACATAAAGATCAAAATAGAATG
25172 AAACATAAAGATCAAAATAGAATG
1 AAACATAAAGATCAAAATAGAATG
25196 A
1 A
25197 TATTGACAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.61, C:0.08, G:0.14, T:0.16
Consensus pattern (24 bp):
AAACATAAAGATCAAAATAGAATG
Found at i:33304 original size:13 final size:13
Alignment explanation
Indices: 33288--33312 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33278 AAAATATTTA
33288 CCCAAATTAAAAC
1 CCCAAATTAAAAC
33301 CCCAAATTAAAA
1 CCCAAATTAAAA
33313 AATACCCTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.28, G:0.00, T:0.16
Consensus pattern (13 bp):
CCCAAATTAAAAC
Found at i:35082 original size:21 final size:19
Alignment explanation
Indices: 35054--35099 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
35044 TCATTGAATC
35054 ATTA-TTCTTAGCTCCTTAAT
1 ATTAGTTCTTAGCT--TTAAT
35074 ATTAGTTCTTAGCTTTAAT
1 ATTAGTTCTTAGCTTTAAT
35093 ACTTAGT
1 A-TTAGT
35100 AGGATTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (19 bp):
ATTAGTTCTTAGCTTTAAT
Found at i:45020 original size:21 final size:19
Alignment explanation
Indices: 44992--45037 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
44982 TCATTGAATC
44992 ATTA-TTCTTAGCTCCTTAAT
1 ATTAGTTCTTAGCT--TTAAT
45012 ATTAGTTCTTAGCTTTAAT
1 ATTAGTTCTTAGCTTTAAT
45031 ACTTAGT
1 A-TTAGT
45038 AGGATTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (19 bp):
ATTAGTTCTTAGCTTTAAT
Found at i:45165 original size:13 final size:13
Alignment explanation
Indices: 45147--45172 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
45137 ACTATATTTA
45147 TAATTTGGGGCAT
1 TAATTTGGGGCAT
45160 TAATTTGGGGCAT
1 TAATTTGGGGCAT
45173 CGATTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.31, T:0.38
Consensus pattern (13 bp):
TAATTTGGGGCAT
Found at i:48516 original size:20 final size:20
Alignment explanation
Indices: 48491--48557 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
48481 TTCGCCTGAC
*
48491 AAGCTTCCAAGCTACCTAGT
1 AAGCTTCCAAGCAACCTAGT
48511 AAGCTTCCAAGCAACCTAGT
1 AAGCTTCCAAGCAACCTAGT
* *
48531 AAGCTTCCAAGCCACATAGT
1 AAGCTTCCAAGCAACCTAGT
*
48551 AGGCTTC
1 AAGCTTC
48558 TCTATCACTA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.22
Consensus pattern (20 bp):
AAGCTTCCAAGCAACCTAGT
Found at i:55984 original size:41 final size:41
Alignment explanation
Indices: 55865--55984 Score: 93
Period size: 41 Copynumber: 2.9 Consensus size: 41
55855 ATAAGCGCCG
* * *
55865 CAACAGAGTAGTACTTTAGTGGCGTTTTTACACAAACGTCG
1 CAACAGATTAGTACTTTAGTGGCGTTTTTATACAAACGTCA
* * * * * ** *
55906 CGATAGGTCCA-T-CTATAGTGGTATTTTT-TCAATAAACGTCA
1 CAACAGAT-TAGTACTTTAGTGGCGTTTTTAT--ACAAACGTCA
55947 CAACAGATTAGTACTTTAGTGGCGTTTTTATACAAACG
1 CAACAGATTAGTACTTTAGTGGCGTTTTTATACAAACG
55985 CCGTAATAGG
Statistics
Matches: 54, Mismatches: 19, Indels: 12
0.64 0.22 0.14
Matches are distributed among these distances:
40 14 0.26
41 25 0.46
42 14 0.26
43 1 0.02
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.33
Consensus pattern (41 bp):
CAACAGATTAGTACTTTAGTGGCGTTTTTATACAAACGTCA
Found at i:56143 original size:84 final size:83
Alignment explanation
Indices: 55847--56161 Score: 303
Period size: 83 Copynumber: 3.8 Consensus size: 83
55837 TTTAGCGGCG
* * * * * * * *
55847 TTTTTTCGATAAGCGCCGCAACAGAGTAGTACTTTAGTGGCGTTTTTACACAAACGTCGCGAT-A
1 TTTTTTCAATAAACACCGCAACAGATTAATACTTTAGAGGCGTTTTTATACAAACGTCGCAATAA
* * *
55911 GGTCCATCTATAGTGGTA
66 GGTTCACCTATAGTGGCA
** * * * * * *
55929 TTTTTTCAATAAACGTCACAACAGATTAGTACTTTAGTGGCGTTTTTATACAAACGCCGTAATAG
1 TTTTTTCAATAAACACCGCAACAGATTAATACTTTAGAGGCGTTTTTATACAAACGTCGCAATAA
*
55994 GGTTCACCTATAGTGGCG
66 GGTTCACCTATAGTGGCA
* * ** * * *
56012 TTTTTTCAATAAACACCGTAATAGATTAGA-ACTTTAGCA-ATGATTTTATACAAATGTAGCAAT
1 TTTTTTCAATAAACACCGCAACAGATTA-ATACTTTAG-AGGCGTTTTTATACAAACGTCGCAAT
*
56075 AAGGTTCACCCATAGTGGCA
64 AAGGTTCACCTATAGTGGCA
* * *
56095 TTTTGTTCAATAAACACCGCAAAAGATTAATACTTTTGAGGCGTTTTTATACAAACGCCGCAATA
1 TTTT-TTCAATAAACACCGCAACAGATTAATACTTTAGAGGCGTTTTTATACAAACGTCGCAATA
56160 AG
65 AG
56162 TTTTATCTGT
Statistics
Matches: 187, Mismatches: 40, Indels: 10
0.79 0.17 0.04
Matches are distributed among these distances:
82 54 0.29
83 84 0.45
84 49 0.26
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (83 bp):
TTTTTTCAATAAACACCGCAACAGATTAATACTTTAGAGGCGTTTTTATACAAACGTCGCAATAA
GGTTCACCTATAGTGGCA
Found at i:60231 original size:30 final size:30
Alignment explanation
Indices: 60197--60264 Score: 109
Period size: 30 Copynumber: 2.3 Consensus size: 30
60187 TGGCAGATGT
* *
60197 GTTGATGGAGCAGGTACTGGTGGAACACAC
1 GTTGATGGAGCAGGCACTGATGGAACACAC
*
60227 GTTGATGGAGCAGGCACTGATGGAACGCAC
1 GTTGATGGAGCAGGCACTGATGGAACACAC
60257 GTTGATGG
1 GTTGATGG
60265 GACTTGCAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.25, C:0.16, G:0.38, T:0.21
Consensus pattern (30 bp):
GTTGATGGAGCAGGCACTGATGGAACACAC
Found at i:64778 original size:43 final size:41
Alignment explanation
Indices: 64730--64908 Score: 155
Period size: 42 Copynumber: 4.2 Consensus size: 41
64720 AAGGTAATTA
*
64730 GCGGCGTTTGTATCAAAAAACGCCGCTATAGATCTAACCTTTT
1 GCGGCGTTTGT-TC-AAAAACGCCGCTATAGATCTGACCTTTT
* * * * *
64773 GCGGCGTTTATTCCAAAACGCCGCTATATATATCGACATTTT
1 GCGGCGTTTGTTCAAAAACGCCGCTATAGATCT-GACCTTTT
* * **
64815 GCGGCGTTTGTTCCAAAACGCCCCTATAGATATCT-TTCTTTT
1 GCGGCGTTTGTTCAAAAACGCCGCTATAG--ATCTGACCTTTT
* * *
64857 GCGGCGTTTGTTCCAAAAACACC-ATGATAGATCTTGACCTATT
1 GCGGCGTTTGTT-CAAAAACGCCGCT-ATAGATC-TGACCTTTT
64900 GCGGCGTTT
1 GCGGCGTTT
64909 TTTGTTCTCA
Statistics
Matches: 110, Mismatches: 19, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
41 20 0.18
42 52 0.47
43 35 0.32
44 3 0.03
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (41 bp):
GCGGCGTTTGTTCAAAAACGCCGCTATAGATCTGACCTTTT
Found at i:64829 original size:42 final size:41
Alignment explanation
Indices: 64730--64874 Score: 166
Period size: 42 Copynumber: 3.4 Consensus size: 41
64720 AAGGTAATTA
* *
64730 GCGGCGTTTGTATCAAAAAACGCCGCTATAGATCT-AACCTTTT
1 GCGGCGTTTGT-TC-CAAAACGCCGCTATAGATATCAA-CTTTT
* * *
64773 GCGGCGTTTATTCCAAAACGCCGCTATATATATCGACATTTT
1 GCGGCGTTTGTTCCAAAACGCCGCTATAGATATCAAC-TTTT
* **
64815 GCGGCGTTTGTTCCAAAACGCCCCTATAGATATCTTTCTTTT
1 GCGGCGTTTGTTCCAAAACGCCGCTATAGATATC-AACTTTT
64857 GCGGCGTTTGTTCCAAAA
1 GCGGCGTTTGTTCCAAAA
64875 ACACCATGAT
Statistics
Matches: 89, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
41 18 0.20
42 60 0.67
43 11 0.12
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (41 bp):
GCGGCGTTTGTTCCAAAACGCCGCTATAGATATCAACTTTT
Found at i:65497 original size:16 final size:17
Alignment explanation
Indices: 65470--65505 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
65460 AATATGAAAA
65470 AAATTCAATTTAAATTT
1 AAATTCAATTTAAATTT
*
65487 AAATT-AATTTAATTTT
1 AAATTCAATTTAAATTT
65503 AAA
1 AAA
65506 ATACTATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
AAATTCAATTTAAATTT
Found at i:71510 original size:87 final size:87
Alignment explanation
Indices: 71364--71613 Score: 446
Period size: 87 Copynumber: 2.9 Consensus size: 87
71354 TATATTATAT
*
71364 TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
1 TATTTAACAGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
71429 AGCGCTTATATAATAAAATAGG
66 AGCGCTTATATAATAAAATAGG
* *
71451 TATTTAACGGGAAATATTATCAAGTACAATAATATATTAGGTAACGCTTATATAATGTAATAGAT
1 TATTTAACAGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
71516 AGCGCTTATATAATAAAATAGG
66 AGCGCTTATATAATAAAATAGG
* *
71538 TATTTAACAGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
1 TATTTAACAGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
*
71603 AGCGATTATAT
66 AGCGCTTATAT
71614 TGACCTATTT
Statistics
Matches: 156, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
87 156 1.00
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.33
Consensus pattern (87 bp):
TATTTAACAGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
AGCGCTTATATAATAAAATAGG
Found at i:75344 original size:120 final size:120
Alignment explanation
Indices: 75131--75369 Score: 433
Period size: 120 Copynumber: 2.0 Consensus size: 120
75121 TCTTCCATTC
*
75131 TGGACATAAAGTACCGACACAATATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATA
1 TGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATA
75196 AAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATAATTA
66 AAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATAATTA
* *
75251 TGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATA
1 TGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATA
* *
75316 AAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATT
66 AAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATAATT
75370 CTGGGTTCCG
Statistics
Matches: 114, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
120 114 1.00
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (120 bp):
TGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATA
AAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATAATTA
Found at i:75509 original size:303 final size:303
Alignment explanation
Indices: 74962--75556 Score: 1109
Period size: 303 Copynumber: 2.0 Consensus size: 303
74952 TTAAAATTAG
*
74962 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
1 CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
*
75027 ATACCGGTTATATTACAAAATTATCTATTATATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
66 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
75092 CACATTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
131 CACATTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
*
75157 AAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATAAAACCGGTATACTTATACCGGTTATA
196 AAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATAAAACCGGTATACTTATACCGATTATA
75222 TTACAAAATTATCTAGTACATTATAATTATGGACATAAAGTAC
261 TTACAAAATTATCTAGTACATTATAATTATGGACATAAAGTAC
75265 CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
1 CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
75330 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
66 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
* *
75395 CACTTTTTGACAATGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
131 CACATTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
* * *
75460 AAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTTATAAAACCGGTATATTTATACCGATTATA
196 AAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATAAAACCGGTATACTTATACCGATTATA
*
75525 TTACAAAATTATCTATTACATTATAATTATGG
261 TTACAAAATTATCTAGTACATTATAATTATGG
75557 GTTCCGATGT
Statistics
Matches: 283, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
303 283 1.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.34
Consensus pattern (303 bp):
CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
CACATTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
AAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATAAAACCGGTATACTTATACCGATTATA
TTACAAAATTATCTAGTACATTATAATTATGGACATAAAGTAC
Found at i:75560 original size:183 final size:182
Alignment explanation
Indices: 75247--75652 Score: 688
Period size: 183 Copynumber: 2.2 Consensus size: 182
75237 GTACATTATA
*
75247 ATTATGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
* *
75312 CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
66 CATAAAACCGGTATATTTATACCGATTATATTACAAAATTATCTATTACATTATAATTATGGGTT
* *
75377 CCGATG-TGTAAATGTCGACACTTTTTGACAATGTATCGACACATTTTTCTTCC
131 CCGATGTTGTAAA--TCGACACTTTTTGAAAAGGTATCGACACATTTTTCTTCC
*
75430 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
*
75495 TATAAAACCGGTATATTTATACCGATTATATTACAAAATTATCTATTACATTATAATTATGGGTT
66 CATAAAACCGGTATATTTATACCGATTATATTACAAAATTATCTATTACATTATAATTATGGGTT
* *
75560 CCGATGTTTTTTCAATCGACACTTTTTGAAAAGGTATCGACACATTTTTCTTCC
131 CCGATG--TTGTAAATCGACACTTTTTGAAAAGGTATCGACACATTTTTCTTCC
75614 ATTATGGACATAAAGTACCGACACAATATTAAAAAGTGT
1 ATTATGGACATAAAGTACCGACACAATATTAAAAAGTGT
75653 GAAAACTTTG
Statistics
Matches: 210, Mismatches: 10, Indels: 5
0.93 0.04 0.02
Matches are distributed among these distances:
183 131 0.62
184 75 0.36
186 4 0.02
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.35
Consensus pattern (182 bp):
ATTATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
CATAAAACCGGTATATTTATACCGATTATATTACAAAATTATCTATTACATTATAATTATGGGTT
CCGATGTTGTAAATCGACACTTTTTGAAAAGGTATCGACACATTTTTCTTCC
Found at i:76613 original size:200 final size:200
Alignment explanation
Indices: 76257--76909 Score: 1191
Period size: 200 Copynumber: 3.3 Consensus size: 200
76247 CCGCTGAATC
76257 ATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGAC
1 ATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGAC
* *
76322 CAAAAATATCGACACAAACTATAAAAGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACC
66 CAAAAATATCGACACAAACTACAAAAGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACC
* * *
76387 GGTATACTTGTACCAGTTAAATTGAAAAATTACCTATTATATTATACTTATGGGTTTCGATGTTT
131 GGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTT
76452 ATGGG
196 ATGGG
* *
76457 ATCGACACTTTTTATATATGGTTCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGAC
1 ATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGAC
76522 CAAAAATATCGACACAAACTACAAAAGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACC
66 CAAAAATATCGACACAAACTACAAAAGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACC
*
76587 GGTATACTTTTACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTT
131 GGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTT
*
76652 ATCGG
196 ATGGG
*
76657 ATCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGAC
1 ATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGAC
76722 CAAAAATATCGACACAAACTACAAAAGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACC
66 CAAAAATATCGACACAAACTACAAAAGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACC
* *
76787 GGTATACTTGTACCGATTAGATTGAAAAATTACCTATTACATTATACTTTTGGGTTTCGATGTTT
131 GGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTT
76852 ATGGG
196 ATGGG
76857 ATCGACAC-TTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCAT
1 ATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCAT
76910 ATTATAAATT
Statistics
Matches: 438, Mismatches: 15, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
199 44 0.10
200 394 0.90
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (200 bp):
ATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGAC
CAAAAATATCGACACAAACTACAAAAGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACC
GGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTT
ATGGG
Found at i:77154 original size:18 final size:18
Alignment explanation
Indices: 77131--77191 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
77121 TTTCATTCAT
*
77131 AATTATATTCACATACAA
1 AATTATAATCACATACAA
**
77149 AATTATAAATCGTATACAA
1 AATTAT-AATCACATACAA
**
77168 AATTATAAATCTTATACAA
1 AATTAT-AATCACATACAA
77187 AATTA
1 AATTA
77192 ACCCTACATT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
18 6 0.16
19 32 0.84
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.34
Consensus pattern (18 bp):
AATTATAATCACATACAA
Found at i:77167 original size:19 final size:19
Alignment explanation
Indices: 77143--77191 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
77133 TTATATTCAC
77143 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
77162 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
77181 ATACAAAATTA
1 ATACAAAATTA
77192 ACCCTACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:78771 original size:18 final size:17
Alignment explanation
Indices: 78738--78791 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 17
78728 CATCGACTTC
*
78738 CTTCCTCCTCATTTCTT
1 CTTCCTCCTCTTTTCTT
*
78755 C--CAT-CTCTTCTTCTT
1 CTTCCTCCTCTT-TTCTT
78770 CTTCCTCCCTCTTTTCTT
1 CTTCCT-CCTCTTTTCTT
78788 CTTC
1 CTTC
78792 ATATTTTTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 9
0.71 0.07 0.22
Matches are distributed among these distances:
14 4 0.14
15 8 0.28
17 3 0.10
18 9 0.31
19 5 0.17
ACGTcount: A:0.04, C:0.43, G:0.00, T:0.54
Consensus pattern (17 bp):
CTTCCTCCTCTTTTCTT
Found at i:78786 original size:15 final size:15
Alignment explanation
Indices: 78738--78788 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
78728 CATCGACTTC
*
78738 CTTCCT-CCTCATTT
1 CTTCCTCCCTCTTTT
*
78752 CTTCCATCTCTTCTTCTT
1 CTTCC-TC-CCTCTT-TT
78770 CTTCCTCCCTCTTTT
1 CTTCCTCCCTCTTTT
78785 CTTC
1 CTTC
78789 TTCATATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
14 5 0.17
15 7 0.23
16 5 0.17
17 6 0.20
18 7 0.23
ACGTcount: A:0.04, C:0.43, G:0.00, T:0.53
Consensus pattern (15 bp):
CTTCCTCCCTCTTTT
Found at i:79097 original size:21 final size:21
Alignment explanation
Indices: 79073--79113 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
79063 TTTATGCCTC
79073 TCAAGTGTATCTTCGACTCTA
1 TCAAGTGTATCTTCGACTCTA
* *
79094 TCAAGTTTCTCTTCGACTCT
1 TCAAGTGTATCTTCGACTCT
79114 TGATTGTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.27, G:0.12, T:0.41
Consensus pattern (21 bp):
TCAAGTGTATCTTCGACTCTA
Found at i:81372 original size:19 final size:19
Alignment explanation
Indices: 81327--81372 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
81317 TCCGGTATCG
81327 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
81346 TTGATACCGG-TTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
81366 TTTTACC
1 TTTTACC
81373 TGTTATATCG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.20, C:0.17, G:0.11, T:0.52
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:81553 original size:20 final size:19
Alignment explanation
Indices: 81507--81553 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
81497 TCCGGTAACG
*
81507 TTTTACTGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
81526 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
81547 TTTTACC
1 TTTTACC
81554 TGGTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.19, C:0.15, G:0.11, T:0.55
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:81619 original size:181 final size:182
Alignment explanation
Indices: 81294--81765 Score: 698
Period size: 181 Copynumber: 2.6 Consensus size: 182
81284 CGTACTTACG
*
81294 AAAGTATCGACACTTTCAATATATCCGGTATCGTTTTACCGGTTTTATCATTTTGATACCGG-TT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
81358 TATCATATTTTTACCTGTTATATCGTTGTAGATCGATATATTTTTTTAAAGTATCGACACATTAT
66 TATCATATTTTTACCTGTTATATCGTTTTAGATCGATACATTTTTTAAAAGTATCGACACATTAT
*
81423 AGGCGCTAAAACTGCTTCTCTTTTAAATTCAC-AAAGTGTCAATCCTTATA-T
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACGAAA-TGTCAATCCTTATATT
*
81474 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACTGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * * *
81539 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATGCATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTAGATCGATACATTTTTTAAAAGTATCGACACATTAT
** *
81604 AGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAATGTCGATCCTTATATT
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACGAAATGTCAATCCTTATATT
* * * * * * **
81656 AAAGTACCGACACTTTAAATGTATCCGATAGCGCTTTACCGGTTTTATCATTTCAATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
81721 TGTCATAGTTTTACCTGTTATATCGTTTTAGATCGACACATTTTT
66 TATCATATTTTTACCTGTTATATCGTTTTAGATCGATACATTTTT
81766 AATTTGGATC
Statistics
Matches: 261, Mismatches: 28, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
180 60 0.23
181 102 0.39
182 99 0.38
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (182 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTAGATCGATACATTTTTTAAAAGTATCGACACATTAT
AGGAGCTAAAACTGCTTCTCTTTTAAATTCACGAAATGTCAATCCTTATATT
Found at i:81779 original size:182 final size:181
Alignment explanation
Indices: 81294--81780 Score: 660
Period size: 182 Copynumber: 2.7 Consensus size: 181
81284 CGTACTTACG
*
81294 AAAGTATCGACACTTTCAATATATCCGGTATCGTTTTACCGGTTTTATCATTTTGATACCGG-TT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
81358 TATCATATTTTTACCTGTTATATCGTTGTAGATCGATATATTTTT--TTAAAGTATCGACACATT
66 TATCATATTTTTACCTGTTATATCGTTTTAGATCGATACATTTTTAATT--AGTATCGACACATT
*
81421 ATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCAATCCTTATAT
129 ATAGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCAATCCTTATAT
*
81474 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACTGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * * * *
81539 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATGCATTTTTTAA-AAGTATCGACACTTTA
66 TATCATATTTTTACCTGTTATATCGTTTTAGATCGATACA-TTTTTAATTAGTATCGACACATTA
** *
81603 TAGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAA-TGTCGATCCTTATATT
130 TAGGAGCTAAAACTGCTTCTCTTTTAAATTCAC-AAAGTGTCAATCCTTATA-T
* * * * * * **
81656 AAAGTACCGACACTTTAAATGTATCCGATAGCGCTTTACCGGTTTTATCATTTCAATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * * * *
81721 TGTCATAGTTTTACCTGTTATATCGTTTTAGATCGACACATTTTTAATTTGGATCGACAC
66 TATCATATTTTTACCTGTTATATCGTTTTAGATCGATACATTTTTAATTAGTATCGACAC
81781 GAACCGACAT
Statistics
Matches: 269, Mismatches: 31, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
180 60 0.22
181 101 0.38
182 108 0.40
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (181 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTAGATCGATACATTTTTAATTAGTATCGACACATTAT
AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCAATCCTTATAT
Found at i:82292 original size:15 final size:15
Alignment explanation
Indices: 82272--82307 Score: 58
Period size: 13 Copynumber: 2.5 Consensus size: 15
82262 ATATTTATAT
82272 TTTTTAAAAAGAATA
1 TTTTTAAAAAGAATA
82287 TTTTT--AAAGAATA
1 TTTTTAAAAAGAATA
82300 TTTTTAAA
1 TTTTTAAA
82308 TTTAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 13 0.68
15 6 0.32
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (15 bp):
TTTTTAAAAAGAATA
Found at i:82421 original size:17 final size:17
Alignment explanation
Indices: 82399--82450 Score: 56
Period size: 16 Copynumber: 3.1 Consensus size: 17
82389 TTTTTAATGA
82399 ATTTTTTTAAAAATAAT
1 ATTTTTTTAAAAATAAT
82416 A-TTTTTTAAATAAT-AT
1 ATTTTTTTAAA-AATAAT
*
82432 TTTTATTTTAAAAA-AAT
1 ATTT-TTTTAAAAATAAT
82449 AT
1 AT
82451 AAACGTGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
16 11 0.38
17 11 0.38
18 7 0.24
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTTTTAAAAATAAT
Found at i:82435 original size:14 final size:14
Alignment explanation
Indices: 82409--82435 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
82399 ATTTTTTTAA
82409 AAATAATATTTTTT
1 AAATAATATTTTTT
82423 AAATAATATTTTT
1 AAATAATATTTTT
82436 ATTTTAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
AAATAATATTTTTT
Found at i:84927 original size:76 final size:75
Alignment explanation
Indices: 84751--85022 Score: 297
Period size: 75 Copynumber: 3.6 Consensus size: 75
84741 TAGGGTGTAC
* ** * * *
84751 ATTAACATTCCA-ATCACAACCTAGATCTTAGTGAACCATGACATTTTT-ACGCACCCCATTTTA
1 ATTAACATTCCATATC-CAACATATTTCTTAGTGAACCATGACATTTTTGGCGCAACTCATTTTA
84814 TTAATAAAACT
65 TTAATAAAACT
* *
84825 ATTAAACATTCCATAT-CAATCCTATTTCTTAGTGAACCATGATATTTTTGGCGCAACTCATTTT
1 ATT-AACATTCCATATCCAA-CATATTTCTTAGTGAACCATGACATTTTTGGCGCAACTCATTTT
84889 ATTAATAAAACT
64 ATTAATAAAACT
* * * * * *
84901 ATTAACATTTCAAATCGCAACATATTTCTGAG-GAACTATGACTTTCTTTGGCGTAA-T-ATTTT
1 ATTAACATTCCATATC-CAACATATTTCTTAGTGAACCATGACATT-TTTGGCGCAACTCATTTT
84963 ATTAATAAAA-T
64 ATTAATAAAACT
* *
84974 ATTAACATTCCATATCACAACTTATTTCTCAGTGAACCATGACATTTTT
1 ATTAACATTCCATATC-CAACATATTTCTTAGTGAACCATGACATTTTT
85023 AAGTACAATT
Statistics
Matches: 169, Mismatches: 21, Indels: 17
0.82 0.10 0.08
Matches are distributed among these distances:
73 31 0.18
74 32 0.19
75 56 0.33
76 47 0.28
77 3 0.02
ACGTcount: A:0.35, C:0.19, G:0.08, T:0.38
Consensus pattern (75 bp):
ATTAACATTCCATATCCAACATATTTCTTAGTGAACCATGACATTTTTGGCGCAACTCATTTTAT
TAATAAAACT
Found at i:85917 original size:23 final size:22
Alignment explanation
Indices: 85870--85918 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
85860 TTGTGTTGTC
* *
85870 AAAATTATATCTAAGAATTACT
1 AAAATTATATCAAAGAATTAAT
85892 AAAATTAT-TCAAATGATATTAAT
1 AAAATTATATCAAA-GA-ATTAAT
85915 AAAA
1 AAAA
85919 ATCCATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 4 0.17
22 10 0.43
23 9 0.39
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.35
Consensus pattern (22 bp):
AAAATTATATCAAAGAATTAAT
Found at i:86801 original size:23 final size:23
Alignment explanation
Indices: 86771--86826 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
86761 CATAGATGCC
86771 AGAGGTATGAGCGTTCAATGTCA
1 AGAGGTATGAGCGTTCAATGTCA
86794 AGAGGTATGAGCGTTCAATGTCA
1 AGAGGTATGAGCGTTCAATGTCA
86817 AGAGGT-TGAG
1 AGAGGTATGAG
86827 AGTTATCTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 4 0.12
23 29 0.88
ACGTcount: A:0.30, C:0.11, G:0.34, T:0.25
Consensus pattern (23 bp):
AGAGGTATGAGCGTTCAATGTCA
Done.