Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001168.1 Hibiscus syriacus cultivar Beakdansim tig00002330_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: 87190
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1510 original size:13 final size:14
Alignment explanation
Indices: 1494--1528 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
1484 ATTGTTTAAT
1494 TGATTTGTAAA-GA
1 TGATTTGTAAATGA
*
1507 TGATTTGTAAATGT
1 TGATTTGTAAATGA
1521 TGATTTGT
1 TGATTTGT
1529 TTAATTGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.29, C:0.00, G:0.23, T:0.49
Consensus pattern (14 bp):
TGATTTGTAAATGA
Found at i:1689 original size:20 final size:19
Alignment explanation
Indices: 1644--1712 Score: 94
Period size: 19 Copynumber: 3.8 Consensus size: 19
1634 ATCGCAACGA
1644 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1663 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1682 GAAAAATCGCAA--CG--A-
1 G-AAAATCGCAATGCGAAAT
1697 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
1713 TTTTCATTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
14 10 0.22
15 1 0.02
16 3 0.07
18 2 0.04
19 20 0.43
20 10 0.22
ACGTcount: A:0.48, C:0.17, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:1782 original size:19 final size:20
Alignment explanation
Indices: 1731--1787 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
1721 TCGCATTGCG
* *
1731 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAGCC
1751 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
1771 ATTTTC-CGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
1788 TCAAATGAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 11 0.31
20 24 0.69
ACGTcount: A:0.18, C:0.23, G:0.21, T:0.39
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:3063 original size:12 final size:12
Alignment explanation
Indices: 3046--3070 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3036 ATATAATCCT
3046 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3058 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3070 G
1 G
3071 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:5393 original size:33 final size:33
Alignment explanation
Indices: 5346--5472 Score: 184
Period size: 33 Copynumber: 3.8 Consensus size: 33
5336 GGAAATTACT
5346 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* **
5379 ATCGCAATGTGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
5411 TTTCGCAATGTGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
5445 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
5473 CGAATTTAAT
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
32 1 0.01
33 81 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.18, G:0.23, T:0.17
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:5426 original size:66 final size:66
Alignment explanation
Indices: 5347--5479 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
5337 GAAATTACTA
* *
5347 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGTGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
5412 T
66 T
* *
5413 TCGCAATGTGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
5478 T
66 T
5479 T
1 T
5480 AATTTCGCGT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.18
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:5494 original size:19 final size:20
Alignment explanation
Indices: 5472--5514 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
5462 AAATCGCAAC
5472 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
5491 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
5511 GCGA
1 GCGA
5515 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:5499 original size:14 final size:14
Alignment explanation
Indices: 5500--5533 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
5490 TGCGATTTTC
5500 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
5514 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
5528 ATTTTC
1 ATTTTC
5534 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:5674 original size:14 final size:14
Alignment explanation
Indices: 5655--5691 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
5645 CATCAATTAA
5655 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
5669 ACAAATCACCTTTT
1 ACAAATCAACTTTT
5683 ACAAATCAA
1 ACAAATCAA
5692 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:7114 original size:21 final size:21
Alignment explanation
Indices: 7048--7114 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
7038 GTGAATCGGG
*
7048 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
7068 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
7090 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
7111 CTCT
1 CTCT
7115 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:7133 original size:42 final size:41
Alignment explanation
Indices: 7048--7170 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
7038 GTGAATCGGG
* * * * *
7048 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
7090 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
7132 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
7171 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:9216 original size:20 final size:19
Alignment explanation
Indices: 9171--9355 Score: 165
Period size: 19 Copynumber: 10.1 Consensus size: 19
9161 TCTTTTGGTT
*
9171 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
9190 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
** *
9210 GGAAATGACTATTGCAA--C
1 -GAAATGAAAATCGCAACGC
*
9228 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
9244 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
9262 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
9277 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
9297 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
9316 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
9335 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
9354 GA
1 GA
9356 TTTTGGTTTC
Statistics
Matches: 136, Mismatches: 17, Indels: 26
0.76 0.09 0.15
Matches are distributed among these distances:
14 18 0.13
15 3 0.02
16 2 0.01
17 1 0.01
18 4 0.03
19 62 0.46
20 44 0.32
21 2 0.01
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:9253 original size:33 final size:33
Alignment explanation
Indices: 9196--9294 Score: 135
Period size: 33 Copynumber: 3.0 Consensus size: 33
9186 ACGAGATAAT
* *
9196 GAGAATCGCAACGCGGAAATGACTATTGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
9230 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
9263 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
9295 GCGAAATAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
33 44 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.25, G:0.23, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:9309 original size:39 final size:38
Alignment explanation
Indices: 9266--9355 Score: 153
Period size: 39 Copynumber: 2.3 Consensus size: 38
9256 GCGACCAGAC
9266 AATCGCAACGCGAAATGAAAATCGCAACCGCGAAATAAA
1 AATCGCAACGCGAAATGAAAATCGCAA-CGCGAAATAAA
*
9305 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
*
9343 AATCGCAATGCGA
1 AATCGCAACGCGA
9356 TTTTGGTTTC
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 22 0.45
39 27 0.55
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (38 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
Found at i:9384 original size:19 final size:19
Alignment explanation
Indices: 9351--9417 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
9341 AAAATCGCAA
**
9351 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
9370 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
9389 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
9409 TGCGATTTT
1 TGCGATTTT
9418 CATTCTCGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 29 0.71
20 12 0.29
ACGTcount: A:0.10, C:0.16, G:0.25, T:0.48
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:10021 original size:20 final size:20
Alignment explanation
Indices: 9936--10049 Score: 122
Period size: 20 Copynumber: 5.7 Consensus size: 20
9926 CGCTATGTAA
* * *
9936 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
9956 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
9976 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
9997 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
10017 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
10037 ATCGCATTGCGAT
1 ATCGCATTGCGAT
10050 TTTCCCAATT
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
19 3 0.04
20 65 0.79
21 12 0.15
22 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:10034 original size:61 final size:61
Alignment explanation
Indices: 9936--10052 Score: 171
Period size: 61 Copynumber: 1.9 Consensus size: 61
9926 CGCTATGTAA
* * * *
9936 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
9997 ATCGCATTGCGATAGTCAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
10053 CCCAATTCGC
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 49 1.00
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:10068 original size:61 final size:61
Alignment explanation
Indices: 9936--10070 Score: 164
Period size: 61 Copynumber: 2.2 Consensus size: 61
9926 CGCTATGTAA
* * * * ** *
9936 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTCAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * *
9997 ATCGCATTGCGATAGTCAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTCAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
10059 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
10071 TTACTTATTC
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
61 60 0.97
62 2 0.03
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTCAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:10160 original size:21 final size:21
Alignment explanation
Indices: 10120--10160 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
10110 ATTGTAGACC
**
10120 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
10141 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
10161 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:17554 original size:33 final size:34
Alignment explanation
Indices: 17511--17580 Score: 124
Period size: 33 Copynumber: 2.1 Consensus size: 34
17501 AATAATCCCC
17511 TAAACCCTACAATTTAAAGCTAAGCTTATCTTCT
1 TAAACCCTACAATTTAAAGCTAAGCTTATCTTCT
*
17545 TAAA-CCTACAATTTAAGGCTAAGCTTATCTTCT
1 TAAACCCTACAATTTAAAGCTAAGCTTATCTTCT
17578 TAA
1 TAA
17581 TAAAAATTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
33 31 0.89
34 4 0.11
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (34 bp):
TAAACCCTACAATTTAAAGCTAAGCTTATCTTCT
Found at i:18140 original size:2 final size:2
Alignment explanation
Indices: 18135--18166 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
18125 TATTTGAAGA
18135 AT 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 AT
18167 GAGTAAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19028 original size:19 final size:19
Alignment explanation
Indices: 19004--19042 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
18994 TATCTCACCA
19004 ACCAAAGTGATTAAAAATG
1 ACCAAAGTGATTAAAAATG
19023 ACCAAAGTGATTAAAAATG
1 ACCAAAGTGATTAAAAATG
19042 A
1 A
19043 AGATAAATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.54, C:0.10, G:0.15, T:0.21
Consensus pattern (19 bp):
ACCAAAGTGATTAAAAATG
Found at i:19895 original size:14 final size:14
Alignment explanation
Indices: 19856--19886 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
19846 TCCAATGTAT
19856 ATACACACACACAC
1 ATACACACACACAC
19870 ATACACACACACAC
1 ATACACACACACAC
19884 ATA
1 ATA
19887 TATATACACG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.52, C:0.39, G:0.00, T:0.10
Consensus pattern (14 bp):
ATACACACACACAC
Found at i:36174 original size:2 final size:2
Alignment explanation
Indices: 36167--36194 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
36157 CCATTATTTC
36167 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
36195 TAAATTGTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36443 original size:2 final size:2
Alignment explanation
Indices: 36436--36494 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
36426 TTTTAATAAT
36436 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
36478 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
36495 GTATGTATGT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:36706 original size:16 final size:17
Alignment explanation
Indices: 36685--36721 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
36675 TGATTGGTGA
36685 AAAATATT-ATTTAATT
1 AAAATATTAATTTAATT
36701 AAAATATTAAATTTAATT
1 AAAATATT-AATTTAATT
36719 AAA
1 AAA
36722 TTAATCCTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.42
18 11 0.58
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AAAATATTAATTTAATT
Found at i:39005 original size:16 final size:16
Alignment explanation
Indices: 38986--39021 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
38976 TTTGTTCTAA
38986 GTGAAAAATATCCTAC
1 GTGAAAAATATCCTAC
*
39002 GTG-AAAATATCCTAT
1 GTGAAAAATATCCTAC
39017 GTGAA
1 GTGAA
39022 TAAGATGAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.28
Consensus pattern (16 bp):
GTGAAAAATATCCTAC
Found at i:39151 original size:23 final size:23
Alignment explanation
Indices: 39125--39226 Score: 161
Period size: 23 Copynumber: 4.4 Consensus size: 23
39115 ATTGTTGAGG
*
39125 TTCTATGTGATCATTCAGGACAA
1 TTCTATGTGGTCATTCAGGACAA
*
39148 TTCTATGTGGTCTTTCAGGACAA
1 TTCTATGTGGTCATTCAGGACAA
39171 TTCTATGTGGTCATTCAGGACAA
1 TTCTATGTGGTCATTCAGGACAA
*
39194 TTCTATGTGGTCCTTCAGGAC-A
1 TTCTATGTGGTCATTCAGGACAA
39216 TATCTATGTGG
1 T-TCTATGTGG
39227 CAGTTCAATG
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
22 2 0.03
23 72 0.97
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.37
Consensus pattern (23 bp):
TTCTATGTGGTCATTCAGGACAA
Found at i:39371 original size:19 final size:19
Alignment explanation
Indices: 39347--39383 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
39337 ACTTTGGGCT
*
39347 AATTAAATAAATGGATATA
1 AATTAAACAAATGGATATA
*
39366 AATTAAACAAATTGATAT
1 AATTAAACAAATGGATAT
39384 TGATTGAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.03, G:0.08, T:0.32
Consensus pattern (19 bp):
AATTAAACAAATGGATATA
Found at i:40355 original size:8 final size:8
Alignment explanation
Indices: 40343--40383 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
40333 TAATTTTCCT
*
40343 TTAAAATT
1 TTAAAATA
40351 TTAAAATA
1 TTAAAATA
40359 TTAAAATA
1 TTAAAATA
40367 TT--AATA
1 TTAAAATA
*
40373 GTAAAATA
1 TTAAAATA
40381 TTA
1 TTA
40384 CAAAATAGGT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
6 5 0.18
8 23 0.82
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (8 bp):
TTAAAATA
Found at i:41257 original size:7 final size:7
Alignment explanation
Indices: 41245--41320 Score: 152
Period size: 7 Copynumber: 10.9 Consensus size: 7
41235 AAAAGACAGT
41245 TGAAGGA
1 TGAAGGA
41252 TGAAGGA
1 TGAAGGA
41259 TGAAGGA
1 TGAAGGA
41266 TGAAGGA
1 TGAAGGA
41273 TGAAGGA
1 TGAAGGA
41280 TGAAGGA
1 TGAAGGA
41287 TGAAGGA
1 TGAAGGA
41294 TGAAGGA
1 TGAAGGA
41301 TGAAGGA
1 TGAAGGA
41308 TGAAGGA
1 TGAAGGA
41315 TGAAGG
1 TGAAGG
41321 GGATTTACCG
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 69 1.00
ACGTcount: A:0.42, C:0.00, G:0.43, T:0.14
Consensus pattern (7 bp):
TGAAGGA
Found at i:45473 original size:26 final size:26
Alignment explanation
Indices: 45437--45497 Score: 104
Period size: 26 Copynumber: 2.3 Consensus size: 26
45427 TTGTTCTCCA
* *
45437 TTCTTTCTCCTCCATATCTACGGGTT
1 TTCTTCCTCCTCAATATCTACGGGTT
45463 TTCTTCCTCCTCAATATCTACGGGTT
1 TTCTTCCTCCTCAATATCTACGGGTT
45489 TTCTTCCTC
1 TTCTTCCTC
45498 AATGGTGATG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.11, C:0.33, G:0.10, T:0.46
Consensus pattern (26 bp):
TTCTTCCTCCTCAATATCTACGGGTT
Found at i:46245 original size:40 final size:38
Alignment explanation
Indices: 46163--46245 Score: 94
Period size: 40 Copynumber: 2.1 Consensus size: 38
46153 CTATTTAGGG
* *
46163 ACCAAAGATGAAATTCCCATGTGCAAAGTTGACCACCT
1 ACCAAAGATGAAATTCCCATATGCAAAGTTGACCACCA
* * * *
46201 ACCAAAGATGAATTTTCTCATATGTATAAGTTGGCCACCA
1 ACCAAAGATGAA-ATTCCCATATGCA-AAGTTGACCACCA
46241 ACCAA
1 ACCAA
46246 CTTGTCAACT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
38 12 0.32
39 9 0.24
40 16 0.43
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.24
Consensus pattern (38 bp):
ACCAAAGATGAAATTCCCATATGCAAAGTTGACCACCA
Found at i:46275 original size:17 final size:17
Alignment explanation
Indices: 46242--46275 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
46232 TGGCCACCAA
* *
46242 CCAACTTGTCAACTTTG
1 CCAACTTGCCAAATTTG
46259 CCAACTTGCCAAATTTG
1 CCAACTTGCCAAATTTG
46276 ACAATTTACA
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:0.26, C:0.29, G:0.12, T:0.32
Consensus pattern (17 bp):
CCAACTTGCCAAATTTG
Found at i:48236 original size:16 final size:16
Alignment explanation
Indices: 48215--48245 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
48205 TTGATACTAA
*
48215 CATTTTATTTTTATTG
1 CATTTTATTTCTATTG
48231 CATTTTATTTCTATT
1 CATTTTATTTCTATT
48246 ATTTAACTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.10, G:0.03, T:0.68
Consensus pattern (16 bp):
CATTTTATTTCTATTG
Found at i:48272 original size:16 final size:16
Alignment explanation
Indices: 48247--48282 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
48237 ATTTCTATTA
*
48247 TTTAACTTTATGCACT
1 TTTAAATTTATGCACT
*
48263 TTTAAATTTATGCCCT
1 TTTAAATTTATGCACT
48279 TTTA
1 TTTA
48283 TTTTCTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.25, C:0.17, G:0.06, T:0.53
Consensus pattern (16 bp):
TTTAAATTTATGCACT
Found at i:52255 original size:14 final size:14
Alignment explanation
Indices: 52217--52267 Score: 68
Period size: 15 Copynumber: 3.6 Consensus size: 14
52207 AATAAAAAAT
52217 AAGCAAAGAGGAAA
1 AAGCAAAGAGGAAA
52231 GAAGCAAAGAGGAAA
1 -AAGCAAAGAGGAAA
*
52246 AAGCAGAGA-GAAA
1 AAGCAAAGAGGAAA
*
52259 AAACAAAGA
1 AAGCAAAGA
52268 AAGAAAAGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
13 11 0.33
14 8 0.24
15 14 0.42
ACGTcount: A:0.65, C:0.08, G:0.27, T:0.00
Consensus pattern (14 bp):
AAGCAAAGAGGAAA
Found at i:55108 original size:103 final size:104
Alignment explanation
Indices: 54942--55219 Score: 341
Period size: 103 Copynumber: 2.7 Consensus size: 104
54932 TTTGAAATTT
** * * *
54942 TTGAAACAAAATTAATCTCACTTGAGATTG-TTTTCTTAAAAACAAATTTTGTCTTGTTTGAGAC
1 TTGAAACAAAATTAATAACATTTGAGATTGTTTTTCTTAAAAACAAATTTTGTCTCGCTTGAGAC
55006 AGTTTCCCCTAAAAACAC-AAATTCT-GAAATTGTTTCAC
66 AGTTTCCCCTAAAAACACAAAATT-TGGAAATTGTTTCAC
* **
55044 TTGAAACAAAATTGATAACATTTGAGATTGTTTTTCTTAAAAACAAATTTCATCTCGCTTGAGAC
1 TTGAAACAAAATTAATAACATTTGAGATTGTTTTTCTTAAAAACAAATTTTGTCTCGCTTGAGAC
* * * *
55109 AATTTTCCCTCAAAACACAAAATTTGGAAGTTGTTTCAC
66 AGTTTCCCCTAAAAACACAAAATTTGGAAATTGTTTCAC
* * **
55148 TTGAAACAAAATTAATAA-ATCTTTGAGATTATTTCTC-TCGAAACAAAGTTTTGTCTCGCTTGA
1 TTGAAACAAAATTAATAACA--TTTGAGATTGTTTTTCTTAAAAACAAA-TTTTGTCTCGCTTGA
55211 GACAGTTTC
63 GACAGTTTC
55220 TCTTGAAACA
Statistics
Matches: 149, Mismatches: 21, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
102 26 0.17
103 47 0.32
104 42 0.28
105 34 0.23
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (104 bp):
TTGAAACAAAATTAATAACATTTGAGATTGTTTTTCTTAAAAACAAATTTTGTCTCGCTTGAGAC
AGTTTCCCCTAAAAACACAAAATTTGGAAATTGTTTCAC
Found at i:55229 original size:104 final size:103
Alignment explanation
Indices: 54942--55261 Score: 310
Period size: 104 Copynumber: 3.1 Consensus size: 103
54932 TTTGAAATTT
** * * * *
54942 TTGAAACAAAATTAATCTCACTTGAGATTGTTT-TCTTAAAAACAAATTTTGTCTTGTTTGAGAC
1 TTGAAACAAAATTAATAACATTTGAGATTATTTCTCTTAAAAACAAATTTTGTCTCGCTTGAGAC
* *
55006 AGTTTCCCCTAAAAACACAAATTCTGAAATTGTTTCAC
66 AGTTTCCCTTAAACACACAAATTCTGAAATTGTTTCAC
* * * **
55044 TTGAAACAAAATTGATAACATTTGAGATTGTTTTTCTTAAAAACAAATTTCATCTCGCTTGAGAC
1 TTGAAACAAAATTAATAACATTTGAGATTATTTCTCTTAAAAACAAATTTTGTCTCGCTTGAGAC
* * *
55109 AATTTTCCCTCAAA-ACACAAAATT-TGGAAGTTGTTTCAC
66 -AGTTTCCCTTAAACACAC-AAATTCT-GAAATTGTTTCAC
**
55148 TTGAAACAAAATTAATAA-ATCTTTGAGATTATTTCTC-TCGAAACAAAGTTTTGTCTCGCTTGA
1 TTGAAACAAAATTAATAACA--TTTGAGATTATTTCTCTTAAAAACAAA-TTTTGTCTCGCTTGA
* * * ** * *
55211 GACAGTTTCTCTTGAAACATATACCTT-TGAGATTGTTTCTC
63 GACAGTTTCCCTT-AAACACACAAATTCTGAAATTGTTTCAC
55252 TTGAAACAAA
1 TTGAAACAAA
55262 TTTTGTCTCA
Statistics
Matches: 180, Mismatches: 29, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
102 29 0.16
103 33 0.18
104 79 0.44
105 37 0.21
106 2 0.01
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (103 bp):
TTGAAACAAAATTAATAACATTTGAGATTATTTCTCTTAAAAACAAATTTTGTCTCGCTTGAGAC
AGTTTCCCTTAAACACACAAATTCTGAAATTGTTTCAC
Found at i:55241 original size:67 final size:67
Alignment explanation
Indices: 55168--55362 Score: 275
Period size: 66 Copynumber: 2.9 Consensus size: 67
55158 ATTAATAAAT
* *
55168 CTTTGAGATTATTTCTCTCGAAACAAAGTTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAT
1 CTTTGAGATTATTTCTCTCGAAACAAAGTTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACACAA
55233 AC
66 AC
* * ** *
55235 CTTTGAGATTGTTTCTCTTGAAACAAA-TTTTGTCTCATTTGAAACAGTTTCTCTTGAAACACAA
1 CTTTGAGATTATTTCTCTCGAAACAAAGTTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACACAA
55299 AC
66 AC
** * * *
55301 CTTTGAGATTATTTCTCTCGAAACAAAGTTTCATCTAGCTTGAGATAGTTTCTATTGAAACA
1 CTTTGAGATTATTTCTCTCGAAACAAAGTTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACA
55363 AAGTTTGTCT
Statistics
Matches: 110, Mismatches: 17, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
66 59 0.54
67 51 0.46
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (67 bp):
CTTTGAGATTATTTCTCTCGAAACAAAGTTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACACAA
AC
Found at i:55285 original size:36 final size:35
Alignment explanation
Indices: 55179--55295 Score: 109
Period size: 36 Copynumber: 3.4 Consensus size: 35
55169 TTTGAGATTA
* *
55179 TTTCTCTCGAAACAAAGTTTTGTCTCGCTTGAGACAG
1 TTTCTCTTGAAACAAA-TTTTGTCTC-TTTGAGACAG
* * **
55216 TTTCTCTTGAAAC--A-TAT-AC-CTTTGAGATTG
1 TTTCTCTTGAAACAAATTTTGTCTCTTTGAGACAG
*
55246 TTTCTCTTGAAACAAATTTTGTCTCATTTGAAACAG
1 TTTCTCTTGAAACAAATTTTGTCTC-TTTGAGACAG
55282 TTTCTCTTGAAACA
1 TTTCTCTTGAAACA
55296 CAAACCTTTG
Statistics
Matches: 63, Mismatches: 11, Indels: 13
0.72 0.13 0.15
Matches are distributed among these distances:
30 20 0.32
31 1 0.02
32 2 0.03
33 4 0.06
34 1 0.02
35 2 0.03
36 21 0.33
37 12 0.19
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (35 bp):
TTTCTCTTGAAACAAATTTTGTCTCTTTGAGACAG
Found at i:55389 original size:88 final size:87
Alignment explanation
Indices: 55284--55449 Score: 242
Period size: 88 Copynumber: 1.9 Consensus size: 87
55274 TGAAACAGTT
*
55284 TCTCTTGAAACACAAACCTTTGAGATTATTTCTCTCGAAACAAAGTTTCATCTAGCTTGAGATAG
1 TCTCCTGAAACACAAACCTTTGAGATTATTTCTCTCGAAACAAA-TTTCATCTAGCTTGAGATAG
55349 TTTCTATTGAAACAAAGTTTGTC
65 TTTCTATTGAAACAAAGTTTGTC
* * * ** * *
55372 TCTCCTGAAACATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCGCTTGAGCTAGT
1 TCTCCTGAAACACAAACCTTTGAGATTATTTCTCTCGAAACAAATTTCATCTAGCTTGAGATAGT
*
55437 TTCTCTTGAAACA
66 TTCTATTGAAACA
55450 TAAACTATTG
Statistics
Matches: 69, Mismatches: 9, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
87 29 0.42
88 40 0.58
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (87 bp):
TCTCCTGAAACACAAACCTTTGAGATTATTTCTCTCGAAACAAATTTCATCTAGCTTGAGATAGT
TTCTATTGAAACAAAGTTTGTC
Found at i:55411 original size:30 final size:30
Alignment explanation
Indices: 55367--55479 Score: 77
Period size: 30 Copynumber: 3.6 Consensus size: 30
55357 GAAACAAAGT
* *
55367 TTGTCTCTCCTGAAACATAAACCTTTGAGA
1 TTGTTTCTCTTGAAACATAAACCTTTGAGA
* * *
55397 TTGTTTCTCTTGAAACA-AATTTTGTCTCGCTTGAGC
1 TTGTTTCTCTTGAAACATAA-----AC-C-TTTGAGA
*
55433 TAGTTTCTCTTGAAACATAAA-CTATTGAGA
1 TTGTTTCTCTTGAAACATAAACCT-TTGAGA
*
55463 TTGTTTCTCTCGAAACA
1 TTGTTTCTCTTGAAACA
55480 AAGTTTCGTC
Statistics
Matches: 63, Mismatches: 11, Indels: 18
0.68 0.12 0.20
Matches are distributed among these distances:
29 2 0.03
30 36 0.57
34 1 0.02
35 1 0.02
36 21 0.33
37 2 0.03
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.39
Consensus pattern (30 bp):
TTGTTTCTCTTGAAACATAAACCTTTGAGA
Found at i:55447 original size:66 final size:67
Alignment explanation
Indices: 55372--55498 Score: 195
Period size: 66 Copynumber: 1.9 Consensus size: 67
55362 AAAGTTTGTC
* *
55372 TCTCCTGAAACATAAACCT-TTGAGATTGTTTCTCTTGAAACAAA-TTTTGTCTCGCTTGAGCTA
1 TCTCCTGAAACATAAA-CTATTGAGATTGTTTCTCTCGAAACAAAGTTTCGTCTCGCTTGAGCTA
55435 GTT
65 GTT
* *
55438 TCTCTTGAAACATAAACTATTGAGATTGTTTCTCTCGAAACAAAGTTTCGTCTCGTTTGAG
1 TCTCCTGAAACATAAACTATTGAGATTGTTTCTCTCGAAACAAAGTTTCGTCTCGCTTGAG
55499 ACAATTTTTC
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
65 2 0.04
66 39 0.71
67 14 0.25
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.39
Consensus pattern (67 bp):
TCTCCTGAAACATAAACTATTGAGATTGTTTCTCTCGAAACAAAGTTTCGTCTCGCTTGAGCTAG
TT
Found at i:55534 original size:66 final size:66
Alignment explanation
Indices: 55372--55534 Score: 163
Period size: 66 Copynumber: 2.5 Consensus size: 66
55362 AAAGTTTGTC
* * * * * *
55372 TCTCCTGAAACATAAACCT-TTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCGCTTGAGCTAG
1 TCTCTTGAAACACAAA-CTATTGAGAATGTTTCTCTCGAAACAAATTTCGTCTCGCTTGAGCAAG
55436 TT
65 TT
* * *
55438 TCTCTTGAAACATAAACTATTGAGATTGTTTCTCTCGAAACAAAGTTTCGTCTCGTTTGAGACAA
1 TCTCTTGAAACACAAACTATTGAGAATGTTTCTCTCGAAACAAA-TTTCGTCTCGCTTGAG-CAA
55503 -TT
64 GTT
* *
55505 TTTCCTTGAAACACAAA-TTTTGA-AATGTTT
1 TCT-CTTGAAACACAAACTATTGAGAATGTTT
55535 AACTCAAAAC
Statistics
Matches: 84, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
65 2 0.02
66 45 0.54
67 23 0.27
68 14 0.17
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (66 bp):
TCTCTTGAAACACAAACTATTGAGAATGTTTCTCTCGAAACAAATTTCGTCTCGCTTGAGCAAGT
T
Found at i:55962 original size:139 final size:139
Alignment explanation
Indices: 55707--55973 Score: 345
Period size: 139 Copynumber: 1.9 Consensus size: 139
55697 TTGGCAACCA
* * * * *
55707 ATCAGATCTCCTCAACGCGTAGAAGCAGCGTCATCTTTAGATAACCAGACTTCCTCATCACGTAA
1 ATCAGATCTCCTCAACACGAAGAAGCAGCGTCATCCTCAGACAACCAGACTTCCTCATCACGTAA
* **
55772 GAACCCTGTTATCTATAAATTATCCATAAAGACGGTTAGACGTCCTCATCACATATGAACAATAC
66 GAACCCTGTTATCTACAAATTATCCATAAAGACGACTAGACGTCCTCATCACATATGAACAATAC
55837 CGTCCACTG
131 CGTCCACTG
* * * *
55846 ATCAGATCTCCTCAACACGAAGAAGCAGTGTCATCCTCAGACAATCAGACTTCCTCATCAGGTAG
1 ATCAGATCTCCTCAACACGAAGAAGCAGCGTCATCCTCAGACAACCAGACTTCCTCATCACGTAA
* * * * * * * * *
55911 GAACCGTGTTGTCTCCAAATTATCCCTAAAGCCGACTAGATGTCCTTATCACGTATGATCAAT
66 GAACCCTGTTATCTACAAATTATCCATAAAGACGACTAGACGTCCTCATCACATATGAACAAT
55974 TTCATCCACA
Statistics
Matches: 107, Mismatches: 21, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
139 107 1.00
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.26
Consensus pattern (139 bp):
ATCAGATCTCCTCAACACGAAGAAGCAGCGTCATCCTCAGACAACCAGACTTCCTCATCACGTAA
GAACCCTGTTATCTACAAATTATCCATAAAGACGACTAGACGTCCTCATCACATATGAACAATAC
CGTCCACTG
Found at i:55982 original size:139 final size:139
Alignment explanation
Indices: 55707--56003 Score: 342
Period size: 139 Copynumber: 2.1 Consensus size: 139
55697 TTGGCAACCA
* * * * *
55707 ATCAGATCTCCTCAACGCGTAGAAGCAGCGTCATCTTTAGATAACCAGACTTCCTCATCACGTAA
1 ATCAGATCTCCTCAACACGAAGAAGCAGCGTCATCCTCAGACAACCAGACTTCCTCATCACGTAA
* **
55772 GAACCCTGTTATCTATAAATTATCCATAAAGACGGTTAGACGTCCTCATCACATATGAACAATAC
66 GAACCCTGTTATCTACAAATTATCCATAAAGACGACTAGACGTCCTCATCACATATGAACAATAC
* *
55837 CGTCCACTG
131 CATCCACAG
* * * *
55846 ATCAGATCTCCTCAACACGAAGAAGCAGTGTCATCCTCAGACAATCAGACTTCCTCATCAGGTAG
1 ATCAGATCTCCTCAACACGAAGAAGCAGCGTCATCCTCAGACAACCAGACTTCCTCATCACGTAA
* * * * * * * * * **
55911 GAACCGTGTTGTCTCCAAATTATCCCTAAAGCCGACTAGATGTCCTTATCACGTATGATCAATTT
66 GAACCCTGTTATCTACAAATTATCCATAAAGACGACTAGACGTCCTCATCACATATGAACAATAC
55976 CATCCACAG
131 CATCCACAG
* * *
55985 ACCATATCTCATCAACACG
1 ATCAGATCTCCTCAACACG
56004 TAGGATCAAT
Statistics
Matches: 130, Mismatches: 28, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
139 130 1.00
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.26
Consensus pattern (139 bp):
ATCAGATCTCCTCAACACGAAGAAGCAGCGTCATCCTCAGACAACCAGACTTCCTCATCACGTAA
GAACCCTGTTATCTACAAATTATCCATAAAGACGACTAGACGTCCTCATCACATATGAACAATAC
CATCCACAG
Found at i:56015 original size:40 final size:40
Alignment explanation
Indices: 55960--56046 Score: 156
Period size: 40 Copynumber: 2.2 Consensus size: 40
55950 ATGTCCTTAT
*
55960 CACGTATGATCAATTTCATCCACAGACCATATCTCATCAA
1 CACGTAGGATCAATTTCATCCACAGACCATATCTCATCAA
*
56000 CACGTAGGATCAATTTCATCTACAGACCATATCTCATCAA
1 CACGTAGGATCAATTTCATCCACAGACCATATCTCATCAA
56040 CACGTAG
1 CACGTAG
56047 AAGTAACATC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.34, C:0.29, G:0.10, T:0.26
Consensus pattern (40 bp):
CACGTAGGATCAATTTCATCCACAGACCATATCTCATCAA
Found at i:56059 original size:40 final size:40
Alignment explanation
Indices: 55975--56065 Score: 121
Period size: 40 Copynumber: 2.3 Consensus size: 40
55965 ATGATCAATT
* **
55975 TCATCCACAGACCATATCTCATCAACACGTAGGATCAATT
1 TCATCCACAGACCATATCTCATCAACACGTAGAATCAACA
*
56015 TCATCTACAGACCATATCTCATCAACACGTAGAAGT-AACA
1 TCATCCACAGACCATATCTCATCAACACGTAGAA-TCAACA
*
56055 TCATCCTCAGA
1 TCATCCACAGA
56066 TAACCAAACT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
40 43 0.98
41 1 0.02
ACGTcount: A:0.36, C:0.30, G:0.10, T:0.24
Consensus pattern (40 bp):
TCATCCACAGACCATATCTCATCAACACGTAGAATCAACA
Found at i:59742 original size:77 final size:77
Alignment explanation
Indices: 59654--59796 Score: 223
Period size: 77 Copynumber: 1.9 Consensus size: 77
59644 TTGAATTTAT
* *
59654 AATAAACTATGATAATTAATATGATTATTTTTTAAAAATTAAAACAAATTGTTAGTTATGATAAT
1 AATAAACTATGATAATTAATATGATTACTCTTTAAAAATTAAAACAAATTGTTAGTTATGATAAT
59719 TTTTGTCAATTA
66 TTTTGTCAATTA
* * * * *
59731 AATAAACTATGATAGTTAATATGATTACTCTTTAAAAGTTAACATAAATTGTTAGTTATGTTAAT
1 AATAAACTATGATAATTAATATGATTACTCTTTAAAAATTAAAACAAATTGTTAGTTATGATAAT
59796 T
66 T
59797 AAATTAATAA
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
77 59 1.00
ACGTcount: A:0.43, C:0.05, G:0.09, T:0.43
Consensus pattern (77 bp):
AATAAACTATGATAATTAATATGATTACTCTTTAAAAATTAAAACAAATTGTTAGTTATGATAAT
TTTTGTCAATTA
Found at i:59844 original size:14 final size:13
Alignment explanation
Indices: 59822--59860 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
59812 ACTTTCTATA
59822 TTAATTATAATCC
1 TTAATTATAATCC
59835 TTATATTATAAAT-C
1 TTA-ATTAT-AATCC
59849 TTAATTATAATC
1 TTAATTATAATC
59861 AATAAATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
12 3 0.13
13 8 0.35
14 9 0.39
15 3 0.13
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (13 bp):
TTAATTATAATCC
Found at i:59857 original size:13 final size:14
Alignment explanation
Indices: 59822--59858 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
59812 ACTTTCTATA
59822 TTAATTAT-AATCC
1 TTAATTATAAATCC
59835 TTATATTATAAAT-C
1 TTA-ATTATAAATCC
59849 TTAATTATAA
1 TTAATTATAA
59859 TCAATAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 10 0.45
14 9 0.41
15 3 0.14
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (14 bp):
TTAATTATAAATCC
Found at i:60088 original size:2 final size:2
Alignment explanation
Indices: 60081--60134 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
60071 ATAAACAATA
60081 AT AT AT AT AT AT 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 AT AT AT AT AT AT
60123 AT AT AT AT AT AT
1 AT AT AT AT AT AT
60135 CACATGACTG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60282 original size:36 final size:33
Alignment explanation
Indices: 60233--60301 Score: 84
Period size: 33 Copynumber: 2.0 Consensus size: 33
60223 AAATTTTGAC
*
60233 AAAATGGATTTTTTTGTCAAAATTTAGAAGATGAAA
1 AAAATGGA-ATTTTTG--AAAATTTAGAAGATGAAA
* *
60269 AAAATTGAATTTTTGATAATTTAGAAGATGAAA
1 AAAATGGAATTTTTGAAAATTTAGAAGATGAAA
60302 GAGGGAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
33 17 0.57
35 6 0.20
36 7 0.23
ACGTcount: A:0.46, C:0.01, G:0.16, T:0.36
Consensus pattern (33 bp):
AAAATGGAATTTTTGAAAATTTAGAAGATGAAA
Found at i:67818 original size:23 final size:23
Alignment explanation
Indices: 67792--67861 Score: 65
Period size: 23 Copynumber: 3.1 Consensus size: 23
67782 AAGGTATGCT
67792 ATAGTTGAAATGCATATGGGTGC
1 ATAGTTGAAATGCATATGGGTGC
* * **
67815 ATAG-TCAACA-G-AAATGTATGC
1 ATAGTTGAA-ATGCATATGGGTGC
67836 TATAGTTGAAATGCATATGGGTGC
1 -ATAGTTGAAATGCATATGGGTGC
67860 AT
1 AT
67862 TGTCAACAGA
Statistics
Matches: 34, Mismatches: 8, Indels: 10
0.65 0.15 0.19
Matches are distributed among these distances:
21 7 0.21
22 9 0.26
23 11 0.32
24 7 0.21
ACGTcount: A:0.34, C:0.10, G:0.26, T:0.30
Consensus pattern (23 bp):
ATAGTTGAAATGCATATGGGTGC
Found at i:67846 original size:45 final size:44
Alignment explanation
Indices: 67754--68066 Score: 430
Period size: 45 Copynumber: 7.0 Consensus size: 44
67744 TGAAAATAAT
** *
67754 AATGCATATGGGTGCATTAACGACATGAAAGGTATGCTATAGTTGA
1 AATGCATATGGGTGCATTGTCAACA-GAAA-GTATGCTATAGTTGA
*
67800 AATGCATATGGGTGCATAGTCAACAGAAATGTATGCTATAGTTGA
1 AATGCATATGGGTGCATTGTCAACAGAAA-GTATGCTATAGTTGA
* *
67845 AATGCATATGGGTGCATTGTCAACAGAAAGATATGTTATAGTTTA
1 AATGCATATGGGTGCATTGTCAACAGAAAG-TATGCTATAGTTGA
*
67890 AATGCATATGGGTGCATTGTCAACAGAAAGGTATGCTATAGTTAA
1 AATGCATATGGGTGCATTGTCAACAGAAA-GTATGCTATAGTTGA
*
67935 AATGCATATGGGTGCATTGTCAACAGAAGAGTATGATATAGTTGA
1 AATGCATATGGGTGCATTGTCAACAGAA-AGTATGCTATAGTTGA
* * * *
67980 AATACATAT-GGTGTATTGTTAACAGAAAAATATGCTATAGTTGA
1 AATGCATATGGGTGCATTGTCAACAG-AAAGTATGCTATAGTTGA
*
68024 AATGCATATGGGTACATTGTCAACAAGAAAGTATGCTATAGTT
1 AATGCATATGGGTGCATTGTCAAC-AGAAAGTATGCTATAGTT
68067 AAAAATACAT
Statistics
Matches: 239, Mismatches: 22, Indels: 13
0.87 0.08 0.05
Matches are distributed among these distances:
44 37 0.15
45 177 0.74
46 25 0.10
ACGTcount: A:0.36, C:0.10, G:0.23, T:0.30
Consensus pattern (44 bp):
AATGCATATGGGTGCATTGTCAACAGAAAGTATGCTATAGTTGA
Found at i:74174 original size:20 final size:20
Alignment explanation
Indices: 74120--74177 Score: 62
Period size: 22 Copynumber: 2.8 Consensus size: 20
74110 TGTCGATACC
*
74120 GTAAGGGGTATCGGTACCATA
1 GTAA-GGGTATCGATACCATA
* *
74141 GTATGGTAGTATCGATACCATG
1 GTAAGG--GTATCGATACCATA
74163 GTAAGGGTATCGATA
1 GTAAGGGTATCGATA
74178 ACATCGAACC
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
20 11 0.35
21 3 0.10
22 17 0.55
ACGTcount: A:0.29, C:0.12, G:0.31, T:0.28
Consensus pattern (20 bp):
GTAAGGGTATCGATACCATA
Found at i:74767 original size:45 final size:45
Alignment explanation
Indices: 74702--74942 Score: 412
Period size: 45 Copynumber: 5.4 Consensus size: 45
74692 TTATCGGCAT
* *
74702 GAAATGTATGCTATAGTTGAAATGCATTTGGATGCATTGTCAACA
1 GAAATGTATGCTATAGTTGAAATGCATATGGGTGCATTGTCAACA
* *
74747 GAAATATATGCTATAATTGAAATGCATATGGGTGCATTGTCAACA
1 GAAATGTATGCTATAGTTGAAATGCATATGGGTGCATTGTCAACA
74792 GAAATGTATGCTATAGTTGAAATGCATATGGGTGCATTGTCAACA
1 GAAATGTATGCTATAGTTGAAATGCATATGGGTGCATTGTCAACA
74837 GAAATGTATGCTATAGTTGAAATGCATATGGGTGCATTGTCAACA
1 GAAATGTATGCTATAGTTGAAATGCATATGGGTGCATTGTCAACA
* *
74882 GAAAAGTGTGCTATAGTTGAAATGCATATGGGTGCATTGTCAACAA
1 GAAATGTATGCTATAGTTGAAATGCATATGGGTGCATTGTCAAC-A
74928 GAAA-GTATGCTATAG
1 GAAATGTATGCTATAG
74943 ATAAAAAATG
Statistics
Matches: 186, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
45 181 0.97
46 5 0.03
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.31
Consensus pattern (45 bp):
GAAATGTATGCTATAGTTGAAATGCATATGGGTGCATTGTCAACA
Found at i:75872 original size:19 final size:19
Alignment explanation
Indices: 75836--75878 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
75826 CAATGGAGAG
75836 ATAAAAGTAAAAATAAGGAA
1 ATAAAAGTAAAAATAAGG-A
75856 ATAAAA-TAAAAGA-AAGGA
1 ATAAAAGTAAAA-ATAAGGA
75874 ATAAA
1 ATAAA
75879 TCAAAAAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.27
19 9 0.41
20 7 0.32
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (19 bp):
ATAAAAGTAAAAATAAGGA
Found at i:79596 original size:77 final size:77
Alignment explanation
Indices: 79504--79654 Score: 266
Period size: 77 Copynumber: 2.0 Consensus size: 77
79494 CAATTGAACT
* *
79504 AAGATCACATAGTGCCTTTCGAATGAAGTTAGCTCCTATAGAATACGGAATAATGAAGTTGCCCG
1 AAGATCACATAGTGCCTTTCCAATGAAATTAGCTCCTATAGAATACGGAATAATGAAGTTGCCCG
79569 AATCATTTTACC
66 AATCATTTTACC
* *
79581 AAGATCACATAGTGCCTTTCCAATGAAATTAGTTCCTATAGAATATGGAATAATGAAGTTGCCCG
1 AAGATCACATAGTGCCTTTCCAATGAAATTAGCTCCTATAGAATACGGAATAATGAAGTTGCCCG
79646 AATCATTTT
66 AATCATTTT
79655 TCTTTCGTAA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
77 70 1.00
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.30
Consensus pattern (77 bp):
AAGATCACATAGTGCCTTTCCAATGAAATTAGCTCCTATAGAATACGGAATAATGAAGTTGCCCG
AATCATTTTACC
Found at i:80284 original size:21 final size:21
Alignment explanation
Indices: 80240--80284 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
80230 AGATTAGCTA
* * *
80240 TGACTTTGAAGTAAGGCGCCT
1 TGACTATGAAGTAAAGCGCAT
*
80261 TGACTATGAAGTAAAGCTCAT
1 TGACTATGAAGTAAAGCGCAT
80282 TGA
1 TGA
80285 TTCTTAATTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (21 bp):
TGACTATGAAGTAAAGCGCAT
Done.