Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000693.1 Hibiscus syriacus cultivar Beakdansim tig00001350_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: 116577
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:9184 original size:15 final size:16
Alignment explanation
Indices: 9145--9188 Score: 58
Period size: 14 Copynumber: 2.9 Consensus size: 16
9135 TTATATAAAA
9145 TATATTTTTATTATAAT
1 TATATTTTT-TTATAAT
9162 TATA-TTTTTTAT--T
1 TATATTTTTTTATAAT
9175 TATATTTTTTTATA
1 TATATTTTTTTATA
9189 GTTTTATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 5 0.20
14 8 0.32
15 4 0.16
16 4 0.16
17 4 0.16
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TATATTTTTTTATAAT
Found at i:9247 original size:51 final size:52
Alignment explanation
Indices: 9176--9276 Score: 161
Period size: 51 Copynumber: 2.0 Consensus size: 52
9166 TTTTTTATTT
9176 ATATTTTTTTATAGTTTTATTATAATTTAAATTGATATAATTCATATATAATA
1 ATATTTTTTTATAGTTTTATTATAATTTAAATTGATATAA-TCATATATAATA
* *
9229 ATATTTTTTTA-A-TTTTATTATAGTTTAAATTGATATAATCCTATATAA
1 ATATTTTTTTATAGTTTTATTATAATTTAAATTGATATAATCATATATAA
9277 GTGTAAACAT
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
50 9 0.20
51 25 0.54
52 1 0.02
53 11 0.24
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (52 bp):
ATATTTTTTTATAGTTTTATTATAATTTAAATTGATATAATCATATATAATA
Found at i:14956 original size:5 final size:5
Alignment explanation
Indices: 14948--14979 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
14938 TATGATATAA
14948 AAAAT AAAAT AAAAT AAAAT AAAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT -AAAAT AAAAT A
14980 TGTACAGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:17569 original size:22 final size:22
Alignment explanation
Indices: 17544--17587 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
17534 TTCATTATGA
*
17544 TGAACAAACATTTATGAAAAAT
1 TGAACAAACATTTACGAAAAAT
17566 TGAACAAACATTTACGAAAAAT
1 TGAACAAACATTTACGAAAAAT
17588 CATTAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.55, C:0.11, G:0.09, T:0.25
Consensus pattern (22 bp):
TGAACAAACATTTACGAAAAAT
Found at i:18787 original size:138 final size:136
Alignment explanation
Indices: 18534--18813 Score: 384
Period size: 137 Copynumber: 2.0 Consensus size: 136
18524 TAGAGTGAAG
* *
18534 AAATAAGGAAATTATAAAAAATTGAGGGACTAACTTGAAAAATGGAAAAAAATTATCAAAAAGAG
1 AAATAAGGAAATTATAAAAAATTGAGGGACTAAATTGAAAAATAGAAAAAAATTATCAAAAAGAG
* *
18599 GAATTGAAAGTACATATGTTTTGTACGATGGTTTAGGAACATATAGTTCAAATTTGGTAAAAAAC
66 GAATTCAAAATACATATGTTTTGTACGATGGTTTAGGAACATATAGTTCAAATTTGGT-AAAAAC
18664 ATACTTA
130 ATACTTA
* ***
18671 AGATAAGGAAATTATAAAAAATTGAGGGACTAAATTGAAAAATAGAAAATTTGTTATCAAAAAGA
1 AAATAAGGAAATTATAAAAAATTGAGGGACTAAATTGAAAAATAGAAAA-AAATTATCAAAAAGA
** ** *
18736 GGAATTCAAAATACATATGTATTT-TTTGATGGTTTAGGAGTATGT-GATTCAAATTTGGTAAAA
65 GGAATTCAAAATACATATGT-TTTGTACGATGGTTTAGGAACATATAG-TTCAAATTTGGTAAAA
*
18799 TCATACTTA
128 ACATACTTA
18808 AAATAA
1 AAATAA
18814 AGTAGTAATT
Statistics
Matches: 125, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
137 64 0.51
138 58 0.46
139 3 0.02
ACGTcount: A:0.47, C:0.06, G:0.17, T:0.30
Consensus pattern (136 bp):
AAATAAGGAAATTATAAAAAATTGAGGGACTAAATTGAAAAATAGAAAAAAATTATCAAAAAGAG
GAATTCAAAATACATATGTTTTGTACGATGGTTTAGGAACATATAGTTCAAATTTGGTAAAAACA
TACTTA
Found at i:18985 original size:157 final size:157
Alignment explanation
Indices: 18681--18971 Score: 433
Period size: 157 Copynumber: 1.9 Consensus size: 157
18671 AGATAAGGAA
* *
18681 ATTATAAAAAATTGAGGGACTAAATTGAAAAATAGAAAATTTGTTATCAAAAAGAGGAATTCAAA
1 ATTATAAAAAATTGAGAGACTAAATTGAAAAATAAAAAATTTGTTATCAAAAAGAGGAATTCAAA
* * * * * * * *
18746 ATACATATGTATTTTTTGATGGTTTAGGAGTATGTGATTCAAATTTGGTAAAATCATACTTAAAA
66 ATACATATATATTCTATAATGGTTTAAGAGCATGTAATTCAAATTTGGTAAAAACATACTTAAAA
18811 TAAAGTAGTAATTGAAGAAATAAAAAC
131 TAAAGTAGTAATTGAAGAAATAAAAAC
* *
18838 ATTATAAAAAATTGAGAGACTAAATTGAAAAATAAAAAATTTGTTATC-AAAAGTGGAATTGAAA
1 ATTATAAAAAATTGAGAGACTAAATTGAAAAATAAAAAATTTGTTATCAAAAAGAGGAATTCAAA
*
18902 GTACATATATATTCTATAATGGTTTAAGAGCATGTAATTCAAATTTGGTAAAAAACGA-ACTTAA
66 ATACATATATATTCTATAATGGTTTAAGAGCATGTAATTCAAATTTGGT-AAAAAC-ATACTTAA
18966 AATAAA
129 AATAAA
18972 TGATGAATTG
Statistics
Matches: 119, Mismatches: 13, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
156 55 0.46
157 63 0.53
158 1 0.01
ACGTcount: A:0.48, C:0.05, G:0.15, T:0.31
Consensus pattern (157 bp):
ATTATAAAAAATTGAGAGACTAAATTGAAAAATAAAAAATTTGTTATCAAAAAGAGGAATTCAAA
ATACATATATATTCTATAATGGTTTAAGAGCATGTAATTCAAATTTGGTAAAAACATACTTAAAA
TAAAGTAGTAATTGAAGAAATAAAAAC
Found at i:19685 original size:23 final size:23
Alignment explanation
Indices: 19653--19703 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
19643 TTTAAATATA
19653 CCTTTATGACACATTTTCTTATG
1 CCTTTATGACACATTTTCTTATG
* *
19676 CCTTTGTGACACGTTTTCTTATG
1 CCTTTATGACACATTTTCTTATG
19699 CCTTT
1 CCTTT
19704 TAACATGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.16, C:0.24, G:0.12, T:0.49
Consensus pattern (23 bp):
CCTTTATGACACATTTTCTTATG
Found at i:19716 original size:23 final size:23
Alignment explanation
Indices: 19661--19714 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
19651 TACCTTTATG
* *
19661 ACACATTTTCTTATGCCTTTGTG
1 ACACGTTTTCTTATGCCTTTGTA
19684 ACACGTTTTCTTATGCCTTT-TA
1 ACACGTTTTCTTATGCCTTTGTA
*
19706 ACATGTTTT
1 ACACGTTTT
19715 TCGATAGTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 9 0.32
23 19 0.68
ACGTcount: A:0.19, C:0.20, G:0.11, T:0.50
Consensus pattern (23 bp):
ACACGTTTTCTTATGCCTTTGTA
Found at i:24807 original size:15 final size:15
Alignment explanation
Indices: 24787--24815 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
24777 TTTATAAAAA
24787 ATTATATGAAACATT
1 ATTATATGAAACATT
24802 ATTATATGAAACAT
1 ATTATATGAAACAT
24816 ATGTACACGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (15 bp):
ATTATATGAAACATT
Found at i:27046 original size:3 final size:3
Alignment explanation
Indices: 27040--27083 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
27030 TGGTATTATT
27040 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
27084 TATTATTATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:27128 original size:3 final size:3
Alignment explanation
Indices: 27082--27109 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
27072 AATAATAATA
27082 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
27110 AGTTTTACCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:27443 original size:33 final size:33
Alignment explanation
Indices: 27405--27471 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
27395 TAATCCATTC
27405 AGCTAAATCAATAGAAAGAAATTCTATTAATTT
1 AGCTAAATCAATAGAAAGAAATTCTATTAATTT
* *
27438 AGCTAAATCAATAGAAATAAATTCTATTGATTT
1 AGCTAAATCAATAGAAAGAAATTCTATTAATTT
27471 A
1 A
27472 ACTTAATCGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.48, C:0.09, G:0.09, T:0.34
Consensus pattern (33 bp):
AGCTAAATCAATAGAAAGAAATTCTATTAATTT
Found at i:28681 original size:3 final size:3
Alignment explanation
Indices: 28675--28716 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
28665 AAGGTAAAAC
28675 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
28717 CAAAACATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:29593 original size:25 final size:26
Alignment explanation
Indices: 29542--29594 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 26
29532 GAAATTTTGG
29542 ATTGAAGTAAAAAGATATATTAGTTT
1 ATTGAAGTAAAAAGATATATTAGTTT
* *
29568 ATTGTAAGTTAAAATATAT-TTA-TTT
1 ATTG-AAGTAAAAAGATATATTAGTTT
29593 AT
1 AT
29595 GAGTTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 5 0.21
26 7 0.29
27 12 0.50
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.45
Consensus pattern (26 bp):
ATTGAAGTAAAAAGATATATTAGTTT
Found at i:31384 original size:22 final size:22
Alignment explanation
Indices: 31353--31423 Score: 108
Period size: 22 Copynumber: 3.2 Consensus size: 22
31343 AAAAAATCCA
*
31353 CAACTCGAATTCGTCAATTTCG
1 CAACTTGAATTCGTCAATTTCG
31375 CAACTTGAATTCGTCAATTTCG
1 CAACTTGAATTCGTCAATTTCG
31397 CAA-TTCGAATTCGTCAATTTCG
1 CAACTT-GAATTCGTCAATTTCG
*
31419 TAACT
1 CAACT
31424 CAATTACCGA
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
21 2 0.04
22 42 0.93
23 1 0.02
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.35
Consensus pattern (22 bp):
CAACTTGAATTCGTCAATTTCG
Found at i:31489 original size:49 final size:50
Alignment explanation
Indices: 31413--31507 Score: 156
Period size: 49 Copynumber: 1.9 Consensus size: 50
31403 GAATTCGTCA
*
31413 ATTTCGTAACTCAATTACCGATATAGGTAAACACGGTATAAAAAATCCGC
1 ATTTCGTAACTCAATTACCGATATAGGTAAACACGGTAGAAAAAATCCGC
* *
31463 ATTTCG-AATTCAATTACCGATGTAGGTAAACACGGTAGAAAAAAT
1 ATTTCGTAACTCAATTACCGATATAGGTAAACACGGTAGAAAAAAT
31508 ACACAACTCT
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
49 36 0.86
50 6 0.14
ACGTcount: A:0.41, C:0.17, G:0.16, T:0.26
Consensus pattern (50 bp):
ATTTCGTAACTCAATTACCGATATAGGTAAACACGGTAGAAAAAATCCGC
Found at i:31522 original size:49 final size:49
Alignment explanation
Indices: 31423--31522 Score: 137
Period size: 49 Copynumber: 2.0 Consensus size: 49
31413 ATTTCGTAAC
* * * **
31423 TCAATTACCGATATAGGTAAACACGGTATAAAAAATCCGCATTTCGAAT
1 TCAATTACCGATATAGGTAAACACGGTAGAAAAAATACACAACTCGAAT
* *
31472 TCAATTACCGATGTAGGTAAACACGGTAGAAAAAATACACAACTCTAAT
1 TCAATTACCGATATAGGTAAACACGGTAGAAAAAATACACAACTCGAAT
31521 TC
1 TC
31523 GCGTTGCAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.25
Consensus pattern (49 bp):
TCAATTACCGATATAGGTAAACACGGTAGAAAAAATACACAACTCGAAT
Found at i:31682 original size:22 final size:22
Alignment explanation
Indices: 31657--31698 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
31647 GCGAAATCCG
31657 AATTCGAATTACGAATTTGGGA
1 AATTCGAATTACGAATTTGGGA
** *
31679 AATTCGTGTTGCGAATTTGG
1 AATTCGAATTACGAATTTGG
31699 AAACTGTGTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.29, C:0.10, G:0.26, T:0.36
Consensus pattern (22 bp):
AATTCGAATTACGAATTTGGGA
Found at i:32792 original size:22 final size:22
Alignment explanation
Indices: 32767--32808 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
32757 TTTATTGTCC
* *
32767 TTTTCTTATAAAATAATTTTTT
1 TTTTATTATAAAAGAATTTTTT
*
32789 TTTTATTTTAAAAGAATTTT
1 TTTTATTATAAAAGAATTTT
32809 ATCTATTGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (22 bp):
TTTTATTATAAAAGAATTTTTT
Found at i:35334 original size:17 final size:17
Alignment explanation
Indices: 35309--35354 Score: 83
Period size: 17 Copynumber: 2.6 Consensus size: 17
35299 TCTTACATGA
35309 GTTTGGGTCTTGTTTCAT
1 GTTT-GGTCTTGTTTCAT
35327 GTTTGGTCTTGTTTCAT
1 GTTTGGTCTTGTTTCAT
35344 GTTTGGTCTTG
1 GTTTGGTCTTG
35355 GACAGAAAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 24 0.86
18 4 0.14
ACGTcount: A:0.04, C:0.11, G:0.28, T:0.57
Consensus pattern (17 bp):
GTTTGGTCTTGTTTCAT
Found at i:43369 original size:18 final size:18
Alignment explanation
Indices: 43339--43380 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
43329 GAGATAATTA
43339 TTTT-GGATCTTTGTAAC
1 TTTTGGGATCTTTGTAAC
*
43356 TTTTGGGATTTTTGTAAC
1 TTTTGGGATCTTTGTAAC
43374 TTTTGGG
1 TTTTGGG
43381 GTTTATGATG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.14, C:0.07, G:0.24, T:0.55
Consensus pattern (18 bp):
TTTTGGGATCTTTGTAAC
Found at i:47589 original size:55 final size:55
Alignment explanation
Indices: 47244--47590 Score: 363
Period size: 55 Copynumber: 6.3 Consensus size: 55
47234 GAACACCTTC
* * * * ** **
47244 AACAATCGTATCTGCTCCCTATTTCTTCAGAGAGTATAAGATTTAAATTATCTTT
1 AACAATCGTGTCTGCTCCCTATATCTTCAGAGAGTAAAAGACTCGAACAATCTTT
* * * * * * *
47299 AACAATCGTTTCTGCCCCCTATTTCTTTACAGAGTATAAGACTCGAACAATCTTC
1 AACAATCGTGTCTGCTCCCTATATCTTCAGAGAGTAAAAGACTCGAACAATCTTT
** * * * * * * *
47354 AACAATCGCATATGCCCCCTATTTCTTCAGAGAGTAAAAGGCTAGAATAATATTT
1 AACAATCGTGTCTGCTCCCTATATCTTCAGAGAGTAAAAGACTCGAACAATCTTT
* ** * *
47409 AACAATCGCGTCTGCTCCCTATATCTTCAGAGAGTATGAGACTCGAACAGTCTTC
1 AACAATCGTGTCTGCTCCCTATATCTTCAGAGAGTAAAAGACTCGAACAATCTTT
** * *
47464 AATGATCGCGCCTGCTCCCTATATCTTCAGAGAGTAAAAGACTCGAACAAT-TTT
1 AACAATCGTGTCTGCTCCCTATATCTTCAGAGAGTAAAAGACTCGAACAATCTTT
*
47518 CAACAATCGTGCCTGCTCCCTATATCTTCAGAGAGTAAAAGACTCGAACAATCTTT
1 -AACAATCGTGTCTGCTCCCTATATCTTCAGAGAGTAAAAGACTCGAACAATCTTT
*
47574 AACAATAGTGTCTGCTC
1 AACAATCGTGTCTGCTC
47591 TATTCTTTCA
Statistics
Matches: 245, Mismatches: 45, Indels: 4
0.83 0.15 0.01
Matches are distributed among these distances:
54 2 0.01
55 240 0.98
56 3 0.01
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (55 bp):
AACAATCGTGTCTGCTCCCTATATCTTCAGAGAGTAAAAGACTCGAACAATCTTT
Found at i:47590 original size:110 final size:110
Alignment explanation
Indices: 47240--47579 Score: 414
Period size: 110 Copynumber: 3.1 Consensus size: 110
47230 ACTTGAACAC
* * * * *
47240 CTTCAACAATCGTATCTGCTCCCTATTTCTTCAGAGAGTATAAGATTTA-AATTATCTTTAACAA
1 CTTCAACAATCGCATCTGCTCCCTATTTCTTCAGAGAGTAAAAGA-CTAGAATAATATTTAACAA
* * * * *
47304 TCGTTTCTGCCCCCTATTTCTTTACAGAGTATAAGACTCGAACAAT
65 TCGTGTCTGCTCCCTATATCTTCAGAGAGTATAAGACTCGAACAAT
* * *
47350 CTTCAACAATCGCATATGCCCCCTATTTCTTCAGAGAGTAAAAGGCTAGAATAATATTTAACAAT
1 CTTCAACAATCGCATCTGCTCCCTATTTCTTCAGAGAGTAAAAGACTAGAATAATATTTAACAAT
* * *
47415 CGCGTCTGCTCCCTATATCTTCAGAGAGTATGAGACTCGAACAGT
66 CGTGTCTGCTCCCTATATCTTCAGAGAGTATAAGACTCGAACAAT
** ** * * *
47460 CTTCAATGATCGCGCCTGCTCCCTATATCTTCAGAGAGTAAAAGACTCGAACAAT-TTTCAACAA
1 CTTCAACAATCGCATCTGCTCCCTATTTCTTCAGAGAGTAAAAGACTAGAATAATATTT-AACAA
* *
47524 TCGTGCCTGCTCCCTATATCTTCAGAGAGTAAAAGACTCGAACAAT
65 TCGTGTCTGCTCCCTATATCTTCAGAGAGTATAAGACTCGAACAAT
*
47570 CTTTAACAAT
1 CTTCAACAAT
47580 AGTGTCTGCT
Statistics
Matches: 194, Mismatches: 34, Indels: 4
0.84 0.15 0.02
Matches are distributed among these distances:
109 5 0.03
110 189 0.97
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (110 bp):
CTTCAACAATCGCATCTGCTCCCTATTTCTTCAGAGAGTAAAAGACTAGAATAATATTTAACAAT
CGTGTCTGCTCCCTATATCTTCAGAGAGTATAAGACTCGAACAAT
Found at i:47685 original size:51 final size:51
Alignment explanation
Indices: 47601--48391 Score: 705
Period size: 51 Copynumber: 15.5 Consensus size: 51
47591 TATTCTTTCA
* * * *
47601 GGAAGTATAGAACTCCAATAACTTCACACGGGTTCGCTCCCTCTTTCTCTAG
1 GGAA-TATAGAACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAG
* * * *
47653 GGAATATGGAACTCGAACATCTTTAAATGGGTTTGCTCCCTCTTTCTCTAG
1 GGAATATAGAACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAG
* * * *
47704 GGAGTATGGAACTCGAAAATCTTCAAATGGGTTCGCTCCCTCTTTCTCTAG
1 GGAATATAGAACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAG
* * * *
47755 GGAGTATGGAACTCAAAAATCTTC-AA--------CT---TCTTTCTCTAG
1 GGAATATAGAACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAG
* * * *
47794 GGAGTATGA-AACTCGAAAATCTTTAAACGGGTTCACTCCCTCTTTCT-TCA-
1 GGAATAT-AGAACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AG
*
47844 GGAAGTATAGAACTCGGAAATCTTCTTCAAACGGGTTCGCTCCCTCTTTCT-TCA-
1 GGAA-TATAGAACTC-G-AA-CATCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AG
* *
47898 GAAAGTATAGAACTCGAACATCTTCTTCAAACGTGTTCGCTCCCTCTTTCT-TCA-
1 GGAA-TATAGAACTCGAACA---TCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AG
*
47952 GGAAGTATAGAACTCGAACATCTTCAAATGGGTTCGCTCCCTCTTTCT-TCA-
1 GGAA-TATAGAACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AG
*
48003 GGAAGTATAGAACTCAAACATCTTCAAACGGGTTCGCTCCCTCTTTCT-TCA-
1 GGAA-TATAGAACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AG
* * * * *
48054 GGAAGTATAGAACTCCAATAACTTCACACGGGTTTGCTCCCTCTTTCTCTAG
1 GGAA-TATAGAACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAG
* * *
48106 GGAGTATGGAACTCGAACATCCTCAAACGGGTTCGCTCCCTCTTTCTCTAG
1 GGAATATAGAACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAG
* * *
48157 GGAGTAT-GAAACTCGGACATCTTCTTCAAACGGGTTCTCTCCCTCTTTCTCTAG
1 GGAATATAG-AACTC-GA-A-CATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAG
* * *
48211 GGAATATGGAACTCAAACATCTTCAAATGGGTTCGCTCCCTCTTTCTCTAG
1 GGAATATAGAACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAG
* * * * ** *
48262 GGAGTATTGAACTCAAAAAATCGTCTTCTTACGGGTTCGCTCTCTCTTTCT-TCAG
1 GGAATATAGAACTC---GAA-CATCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AG
* * *
48317 GAAATATAGAACTCGAACATCTTCAAATGGGTTCGCTGCCTCTTTCTCTAG
1 GGAATATAGAACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAG
* *
48368 GGAGTATAGAACTCGAATATCTTC
1 GGAATATAGAACTCGAACATCTTC
48392 TTCCTCTTCA
Statistics
Matches: 634, Mismatches: 70, Indels: 71
0.82 0.09 0.09
Matches are distributed among these distances:
39 31 0.05
40 2 0.00
42 2 0.00
48 2 0.00
50 8 0.01
51 390 0.62
52 17 0.03
53 5 0.01
54 138 0.22
55 39 0.06
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (51 bp):
GGAATATAGAACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAG
Found at i:47851 original size:90 final size:90
Alignment explanation
Indices: 47693--47868 Score: 264
Period size: 90 Copynumber: 2.0 Consensus size: 90
47683 GTTTGCTCCC
* * * *
47693 TCTTTCTCTAGGGAGTATGGAACTCGAAAATCTTCAAATGGGTTCGCTCCCTCTTTCTCTAGGGA
1 TCTTTCTCTAGGGAGTATGAAACTCGAAAATCTTCAAACGGGTTCACTCCCTCTTTCTCTAGGAA
*
47758 GTATGGAACTCAAAAATCTTCAACT
66 GTATAGAACTCAAAAATCTTCAACT
*
47783 TCTTTCTCTAGGGAGTATGAAACTCGAAAATCTTTAAACGGGTTCACTCCCTCTTTCT-TCAGGA
1 TCTTTCTCTAGGGAGTATGAAACTCGAAAATCTTCAAACGGGTTCACTCCCTCTTTCTCT-AGGA
**
47847 AGTATAGAACTCGGAAATCTTC
65 AGTATAGAACTCAAAAATCTTC
47869 TTCAAACGGG
Statistics
Matches: 77, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
89 1 0.01
90 76 0.99
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.32
Consensus pattern (90 bp):
TCTTTCTCTAGGGAGTATGAAACTCGAAAATCTTCAAACGGGTTCACTCCCTCTTTCTCTAGGAA
GTATAGAACTCAAAAATCTTCAACT
Found at i:47988 original size:105 final size:105
Alignment explanation
Indices: 47803--48391 Score: 629
Period size: 105 Copynumber: 5.7 Consensus size: 105
47793 GGGAGTATGA
* * * *
47803 AACTCGAA-AATCTTTAAACGGGTTCACTCCCTCTTTCT-TCAGGAAGTATAGAACTCGGAAATC
1 AACTCGAACACTCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGGAAGTATAGAACTCAG-AATC
* *
47866 TTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGAAAGTATAG
64 ATCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAG
*
47908 AACTCGAACATCTTCTTCAAACGTGTTCGCTCCCTCTTTCT-TCAGGAAGTATAGAACTC-GAA-
1 AACTCGAACA-C-TCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGGAAGTATAGAACTCAGAAT
*
47970 CATCTTCAAATGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAG
63 CATCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAG
* *
48013 AACTCAAACA-TCTTCAAACGGGTTCGCTCCCTCTTTCT-TCAGGAAGTATAGAACTC-CAAT-A
1 AACTCGAACACTCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGGAAGTATAGAACTCAGAATCA
* * * * *
48074 ACTTCACACGGGTTTGCTCCCTCTTTC-TCTAGGGAGTATGG
65 TCTTCAAACGGGTTCGCTCCCTCTTTCTTC-AGGAAGTATAG
* * *
48115 AACTCGAACA-TCCTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTAT-GAAACTCGGACATC
1 AACTCGAACACTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGAAGTATAG-AACTCAGA-ATC
* * *
48178 TTCTTCAAACGGGTTCTCTCCCTCTTTC-TCTAGGGAA-TATGG
64 ATCTTCAAACGGGTTCGCTCCCTCTTTCTTC-A-GGAAGTATAG
* * * * *
48220 AACTCAAACA-TCTTCAAATGGGTTCGCTCCCTCTTTCTCTAGGGAGTATTGAACTCAAAAAATC
1 AACTCGAACACTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGAAGTATAGAACTC--AGAATC
* ** * *
48284 GTCTTCTTACGGGTTCGCTCTCTCTTTCTTCAGGAAATATAG
64 ATCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAG
* * *
48326 AACTCGAACA-TCTTCAAATGGGTTCGCTGCCTCTTTCTCTAGGGAGTATAGAACTC-GAAT-AT
1 AACTCGAACACTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGAAGTATAGAACTCAGAATCAT
48388 CTTC
66 CTTC
48392 TTCCTCTTCA
Statistics
Matches: 426, Mismatches: 42, Indels: 35
0.85 0.08 0.07
Matches are distributed among these distances:
101 3 0.01
102 134 0.31
103 5 0.01
104 2 0.00
105 144 0.34
106 91 0.21
107 4 0.01
108 43 0.10
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (105 bp):
AACTCGAACACTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGAAGTATAGAACTCAGAATCAT
CTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAG
Found at i:59405 original size:25 final size:25
Alignment explanation
Indices: 59374--59421 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
59364 CATTAAAACC
59374 CTAACCACATGATAACTAGTTCAAA
1 CTAACCACATGATAACTAGTTCAAA
**
59399 CTAACCACATGATCTCTAGTTCA
1 CTAACCACATGATAACTAGTTCA
59422 CATGCATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.38, C:0.27, G:0.08, T:0.27
Consensus pattern (25 bp):
CTAACCACATGATAACTAGTTCAAA
Found at i:65575 original size:21 final size:22
Alignment explanation
Indices: 65540--65585 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
65530 AATAAAATGT
65540 TTAATGAAAAAGATACCAATTG
1 TTAATGAAAAAGATACCAATTG
* *
65562 TTAAT-AAAATGATATCAATTG
1 TTAATGAAAAAGATACCAATTG
65583 TTA
1 TTA
65586 CCAATTGTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.48, C:0.07, G:0.11, T:0.35
Consensus pattern (22 bp):
TTAATGAAAAAGATACCAATTG
Found at i:66747 original size:19 final size:20
Alignment explanation
Indices: 66704--66751 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
66694 TCTGAATCAT
*
66704 TTTTCAAAATTTCATTTTAG
1 TTTTCAAAATCTCATTTTAG
* *
66724 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTAG
66743 TTTTCAAAA
1 TTTTCAAAA
66752 GAAAATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.31, C:0.12, G:0.04, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTAG
Found at i:67538 original size:33 final size:34
Alignment explanation
Indices: 67501--67571 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
67491 CCTTTACAAC
*
67501 TCCCTAG-TTTTTCACCGGATAAACTAGAACATT
1 TCCCTAGCTTTTACACCGGATAAACTAGAACATT
* * * *
67534 TCCCTAGCTTTTACACGGGCTTAGCTAGAACATT
1 TCCCTAGCTTTTACACCGGATAAACTAGAACATT
67568 TCCC
1 TCCC
67572 CTTTACAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 7 0.22
34 25 0.78
ACGTcount: A:0.25, C:0.28, G:0.14, T:0.32
Consensus pattern (34 bp):
TCCCTAGCTTTTACACCGGATAAACTAGAACATT
Found at i:75734 original size:16 final size:17
Alignment explanation
Indices: 75692--75748 Score: 98
Period size: 17 Copynumber: 3.4 Consensus size: 17
75682 GCTAGGGTAG
75692 CGATACTCTTTGAGTAC
1 CGATACTCTTTGAGTAC
75709 CGATACTCTTTGAGTAC
1 CGATACTCTTTGAGTAC
*
75726 TGA-ACTCTTTGAGTAC
1 CGATACTCTTTGAGTAC
75742 CGATACT
1 CGATACT
75749 AGAATTGGCT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
16 15 0.41
17 22 0.59
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.35
Consensus pattern (17 bp):
CGATACTCTTTGAGTAC
Found at i:76563 original size:17 final size:17
Alignment explanation
Indices: 76530--76563 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
76520 TTGGAGAGAA
*
76530 AGAAGAAGATGAAAAAG
1 AGAAGAAGAAGAAAAAG
*
76547 AGAAGAAGAAGACAAAG
1 AGAAGAAGAAGAAAAAG
76564 GTGAGTATGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.03, G:0.29, T:0.03
Consensus pattern (17 bp):
AGAAGAAGAAGAAAAAG
Found at i:85835 original size:41 final size:38
Alignment explanation
Indices: 85790--85866 Score: 109
Period size: 39 Copynumber: 1.9 Consensus size: 38
85780 TTGTTTTGTT
*
85790 TTTTTCGAACAACATCTTTTTTCTTTCTTTCTTTTTTTCTC
1 TTTTTCGAACAAC-T-GTTTTTCTTTCTTT-TTTTTTTCTC
*
85831 TTTTTCGAACTACTGTTTTTCTTTCTTTTTTTTTTC
1 TTTTTCGAACAACTGTTTTTCTTTCTTTTTTTTTTC
85867 GATGGAGCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
38 8 0.24
39 13 0.38
40 1 0.03
41 12 0.35
ACGTcount: A:0.10, C:0.19, G:0.04, T:0.66
Consensus pattern (38 bp):
TTTTTCGAACAACTGTTTTTCTTTCTTTTTTTTTTCTC
Found at i:94695 original size:21 final size:20
Alignment explanation
Indices: 94670--94709 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
94660 AAAAACAAAG
94670 CTTGAAAAGAAAAATGAAAAA
1 CTTGAAAAGAAAAAT-AAAAA
*
94691 CTTGAAAAGTAAAATAAAA
1 CTTGAAAAGAAAAATAAAA
94710 GAGAAAACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.65, C:0.05, G:0.12, T:0.17
Consensus pattern (20 bp):
CTTGAAAAGAAAAATAAAAA
Found at i:97781 original size:90 final size:91
Alignment explanation
Indices: 97635--97808 Score: 269
Period size: 90 Copynumber: 1.9 Consensus size: 91
97625 ACCCATGTGC
* * * *
97635 TTTGCATATGACCAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATGAAGAGTTC
1 TTTGCATATGAACAGCCCCCATGTACCTTGCATGAGGATCATTTAGGCGCCAAGATGAAGAGCTA
97700 TCTCCCTATTCGGCCAAGCCATGTAT
66 TCTCCCTATTCGGCCAAGCCATGTAT
* * * *
97726 TTTGCATGTGAACAG-CCCCATGTACCTTGCATGTGGTTTATTTAGGCGCCAAGATGAAGAGCTA
1 TTTGCATATGAACAGCCCCCATGTACCTTGCATGAGGATCATTTAGGCGCCAAGATGAAGAGCTA
97790 TCTCCCTATTCGGCCAAGC
66 TCTCCCTATTCGGCCAAGC
97809 ATCATTTCCC
Statistics
Matches: 75, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
90 62 0.83
91 13 0.17
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.28
Consensus pattern (91 bp):
TTTGCATATGAACAGCCCCCATGTACCTTGCATGAGGATCATTTAGGCGCCAAGATGAAGAGCTA
TCTCCCTATTCGGCCAAGCCATGTAT
Found at i:99752 original size:94 final size:95
Alignment explanation
Indices: 99582--99786 Score: 288
Period size: 94 Copynumber: 2.2 Consensus size: 95
99572 TCGATAATAC
* * * **
99582 TACCCTGGTACCGATACTTCTATACTATGGTACCGATACCCCCTTCAAGTATCGATACCAAAATT
1 TACCATGGTATCGATACTACTATACTATGACACCGATACCCCCTTCAAGTATCGATACCAAAATT
* * *
99647 AGCTTCGATGTTGCA-TGGTAT-GATACCCT
66 AGATTCAATGTT-CACTGGTATCGACACCCT
*
99676 TACCATGGTATCGATACTACTATACTATGACACCGATACCCCCTTCAGGTATCGATACCAAAATT
1 TACCATGGTATCGATACTACTATACTATGACACCGATACCCCCTTCAAGTATCGATACCAAAATT
* *
99741 AGATTCAATGTTTACTGGTATCGACACTCT
66 AGATTCAATGTTCACTGGTATCGACACCCT
99771 TACCATGGTATCGATA
1 TACCATGGTATCGATA
99787 ATACCTCATC
Statistics
Matches: 98, Mismatches: 11, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
93 1 0.01
94 75 0.77
95 22 0.22
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (95 bp):
TACCATGGTATCGATACTACTATACTATGACACCGATACCCCCTTCAAGTATCGATACCAAAATT
AGATTCAATGTTCACTGGTATCGACACCCT
Found at i:110312 original size:15 final size:16
Alignment explanation
Indices: 110292--110321 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
110282 CGATCATCAT
110292 TCCTAAT-AGAAGAAG
1 TCCTAATGAGAAGAAG
110307 TCCTAATGAGAAGAA
1 TCCTAATGAGAAGAA
110322 CTTTCTTAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.47, C:0.13, G:0.20, T:0.20
Consensus pattern (16 bp):
TCCTAATGAGAAGAAG
Found at i:110314 original size:79 final size:80
Alignment explanation
Indices: 110152--110339 Score: 220
Period size: 79 Copynumber: 2.4 Consensus size: 80
110142 GGAGAGTTTG
* ** * * *
110152 TAATGAGAAGAACTTGCTCAACATTT-TTTGATTCCCTCACGGAAGGAGTTGGATCAACATTCCC
1 TAATGAGAAGAACTTGCTCAACATTTGCTCAATTCCATCACGGAAAGAGTTCGATCAACATTCCC
*
110216 AAGAGAATGAGTTTA
66 AAGAGAATGAGTTCA
* * *
110231 TAATGAGAAGAACTTGCTCAACATTTGCTCAATTCCATCGCGGAAAGAGTTCGATCATCATTCCT
1 TAATGAGAAGAACTTGCTCAACATTTGCTCAATTCCATCACGGAAAGAGTTCGATCAACATTCCC
* *
110296 AATAGAA-GAAG-TCC
66 AAGAGAATG-AGTTCA
* *
110310 TAATGAGAAGAACTTTCTTAACATTTGCTC
1 TAATGAGAAGAACTTGCTCAACATTTGCTC
110340 GATTGAGTTG
Statistics
Matches: 93, Mismatches: 14, Indels: 4
0.84 0.13 0.04
Matches are distributed among these distances:
79 56 0.60
80 37 0.40
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (80 bp):
TAATGAGAAGAACTTGCTCAACATTTGCTCAATTCCATCACGGAAAGAGTTCGATCAACATTCCC
AAGAGAATGAGTTCA
Found at i:110459 original size:44 final size:44
Alignment explanation
Indices: 110409--110556 Score: 126
Period size: 44 Copynumber: 3.4 Consensus size: 44
110399 CCTTAGTTCA
*
110409 TCCATCACATAAGGAGTTGGATCAACACTAACACTACGCTTTAT
1 TCCATCACATAAGGAGTTGGATCAACACTAACACTACGCTTAAT
* * * * * * *
110453 TCCATCACGTAATGAGTTAGATCAGC-GT--CAC-CCG-TGAAT
1 TCCATCACATAAGGAGTTGGATCAACACTAACACTACGCTTAAT
* * * *
110492 TACCCTTCACAGAAGGAGTTGAATCAACACTAACACTACGCTTGAT
1 T--CCATCACATAAGGAGTTGGATCAACACTAACACTACGCTTAAT
*
110538 TCCATCATATAAGGAGTTG
1 TCCATCACATAAGGAGTTG
110557 ATCCAGTGTC
Statistics
Matches: 75, Mismatches: 22, Indels: 14
0.68 0.20 0.13
Matches are distributed among these distances:
39 4 0.05
40 2 0.03
41 21 0.28
42 1 0.01
43 1 0.01
44 40 0.53
45 2 0.03
46 4 0.05
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.26
Consensus pattern (44 bp):
TCCATCACATAAGGAGTTGGATCAACACTAACACTACGCTTAAT
Found at i:110568 original size:85 final size:85
Alignment explanation
Indices: 110412--110607 Score: 268
Period size: 85 Copynumber: 2.3 Consensus size: 85
110402 TAGTTCATCC
* * * *
110412 ATCACATAAGGAGTTGGATCAACACTAACACTACGCTTTATTCCATCACGTAATGAGTTAGATCA
1 ATCACAAAAGGAGTTGGATCAACACTAACACTACGCTTGATTCCATCACATAAGGAGTTAGATCA
* *
110477 GCGTCACCCGTGAATTACCC
66 GCGTCACCCGCGAATTACCA
* * * *
110497 TTCACAGAAGGAGTTGAATCAACACTAACACTACGCTTGATTCCATCATATAAGGAGTT-GATCC
1 ATCACAAAAGGAGTTGGATCAACACTAACACTACGCTTGATTCCATCACATAAGGAGTTAGAT-C
* *
110561 AGTGTCACCCGCGAATTACGA
65 AGCGTCACCCGCGAATTACCA
110582 ATCACAAAAGGAGTTGGATCAACACT
1 ATCACAAAAGGAGTTGGATCAACACT
110608 TCCAAGAGAA
Statistics
Matches: 96, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
84 3 0.03
85 93 0.97
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (85 bp):
ATCACAAAAGGAGTTGGATCAACACTAACACTACGCTTGATTCCATCACATAAGGAGTTAGATCA
GCGTCACCCGCGAATTACCA
Found at i:113470 original size:21 final size:21
Alignment explanation
Indices: 113444--113485 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
113434 CCAGAATGGG
*
113444 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
113465 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
113486 ATATTCAAAT
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:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:113584 original size:19 final size:19
Alignment explanation
Indices: 113560--113608 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
113550 TGGTTCCCCT
113560 TTTACTGTTCAAATAGTAA
1 TTTACTGTTCAAATAGTAA
113579 TTTACTGTTCAAATAGTAA
1 TTTACTGTTCAAATAGTAA
* *
113598 ATTACTATTCA
1 TTTACTGTTCA
113609 TAAAAACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.37, C:0.12, G:0.08, T:0.43
Consensus pattern (19 bp):
TTTACTGTTCAAATAGTAA
Found at i:113705 original size:29 final size:31
Alignment explanation
Indices: 113673--113732 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
113663 AATTTTGAAT
*
113673 AAATTCAATT-AAGTCCAAATA-CATTTTGC
1 AAATTCAATTCAAGTCCAAAAACCATTTTGC
113702 AAATTCAATTCAAGTCCAAAAACCATTTTGC
1 AAATTCAATTCAAGTCCAAAAACCATTTTGC
113733 CTTAAATTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 10 0.36
30 10 0.36
31 8 0.29
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.32
Consensus pattern (31 bp):
AAATTCAATTCAAGTCCAAAAACCATTTTGC
Found at i:114091 original size:23 final size:23
Alignment explanation
Indices: 114060--114111 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
114050 CCAAACAAAA
*
114060 TTAAGCTTTTAAGATCTTGACAC
1 TTAAACTTTTAAGATCTTGACAC
114083 TTAAACTTTTAAGATCTTGACAC
1 TTAAACTTTTAAGATCTTGACAC
114106 TTAAAC
1 TTAAAC
114112 AAAATATTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (23 bp):
TTAAACTTTTAAGATCTTGACAC
Found at i:115024 original size:19 final size:20
Alignment explanation
Indices: 114981--115028 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
114971 TCTAAATCAT
*
114981 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
115001 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
115020 TTTTCAAAA
1 TTTTCAAAA
115029 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:116240 original size:21 final size:21
Alignment explanation
Indices: 116214--116255 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
116204 CCCAGAATGG
**
116214 GGGAATCGGTACCCCTTCATA
1 GGGAATCAATACCCCTTCATA
116235 GGGAATCAATACCCCTTCATA
1 GGGAATCAATACCCCTTCATA
116256 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:0.29, C:0.29, G:0.19, T:0.24
Consensus pattern (21 bp):
GGGAATCAATACCCCTTCATA
Found at i:116382 original size:19 final size:19
Alignment explanation
Indices: 116358--116423 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
116348 AGCCTTGGGG
*
116358 TACTGTTCAAACAGTGATT
1 TACTGTTCAAACAGTAATT
* *
116377 TACTGTTCAGATAGTAATT
1 TACTGTTCAAACAGTAATT
* * *
116396 TATTGTTCAAATAGTAAAT
1 TACTGTTCAAACAGTAATT
*
116415 TACTATTCA
1 TACTGTTCA
116424 TAAAAACATT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 39 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (19 bp):
TACTGTTCAAACAGTAATT
Found at i:116545 original size:32 final size:30
Alignment explanation
Indices: 116486--116547 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
116476 AAATTTTGAA
* * *
116486 TAAATTCAATTAATTCCAAAATACATTTTG
1 TAAATTCAATTAAGTACAAAAAACATTTTG
116516 TAAATTCAATTCAAGTACAAAAAACCATTTTG
1 TAAATTCAATT-AAGTACAAAAAA-CATTTTG
116548 CCTTAAATTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 11 0.41
31 9 0.33
32 7 0.26
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (30 bp):
TAAATTCAATTAAGTACAAAAAACATTTTG
Done.