Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007134.1 Hibiscus syriacus cultivar Beakdansim tig00018658_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: 64426
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1020 original size:13 final size:13
Alignment explanation
Indices: 1002--1027 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
992 TCTTCAACAT
1002 AAGACAAAACAAA
1 AAGACAAAACAAA
1015 AAGACAAAACAAA
1 AAGACAAAACAAA
1028 GACAATTACT
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:0.77, C:0.15, G:0.08, T:0.00
Consensus pattern (13 bp):
AAGACAAAACAAA
Found at i:1263 original size:20 final size:20
Alignment explanation
Indices: 1238--1275 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1228 TGGAGATAGA
1238 GGATTTCGTCGGAAATGGAT
1 GGATTTCGTCGGAAATGGAT
* *
1258 GGATTTTGTCGGAGATGG
1 GGATTTCGTCGGAAATGG
1276 GGACGGATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.08, G:0.39, T:0.32
Consensus pattern (20 bp):
GGATTTCGTCGGAAATGGAT
Found at i:1443 original size:41 final size:41
Alignment explanation
Indices: 1398--1484 Score: 113
Period size: 40 Copynumber: 2.1 Consensus size: 41
1388 TATTGTGTTC
* * *
1398 CGCGTAAAAGTATTTGACTTTCGCGTTGCGAATTT-GACTAT
1 CGCGT-AAAGAATTTGACTATCGCGTTGCGAATTTGGAATAT
**
1439 CGCGTTGAGAATTTGACTATCGCGTTGCGAATTTGGAATAT
1 CGCGTAAAGAATTTGACTATCGCGTTGCGAATTTGGAATAT
1480 CGCGT
1 CGCGT
1485 TGCGAAATTA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
40 25 0.62
41 15 0.38
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.34
Consensus pattern (41 bp):
CGCGTAAAGAATTTGACTATCGCGTTGCGAATTTGGAATAT
Found at i:1482 original size:21 final size:20
Alignment explanation
Indices: 1409--1490 Score: 128
Period size: 20 Copynumber: 4.0 Consensus size: 20
1399 GCGTAAAAGT
*
1409 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTATCGCGTTGCGA
*
1429 ATTTGACTATCGCGTTGAGA
1 ATTTGACTATCGCGTTGCGA
1449 ATTTGACTATCGCGTTGCGA
1 ATTTGACTATCGCGTTGCGA
*
1469 ATTTGGAATATCGCGTTGCGA
1 ATTT-GACTATCGCGTTGCGA
1490 A
1 A
1491 ATTAGAAACT
Statistics
Matches: 57, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
20 41 0.72
21 16 0.28
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.35
Consensus pattern (20 bp):
ATTTGACTATCGCGTTGCGA
Found at i:1533 original size:20 final size:21
Alignment explanation
Indices: 1483--1534 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
1473 GGAATATCGC
1483 GTTGCGAAATT-AGAAACTGG
1 GTTGCGAAATTGAGAAACTGG
*
1503 GTTGCAAAATTGA-AAACTGG
1 GTTGCGAAATTGAGAAACTGG
*
1523 GTTGCGGAATTG
1 GTTGCGAAATTG
1535 TAATTCGCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 27 0.96
21 1 0.04
ACGTcount: A:0.33, C:0.10, G:0.31, T:0.27
Consensus pattern (21 bp):
GTTGCGAAATTGAGAAACTGG
Found at i:3507 original size:2 final size:2
Alignment explanation
Indices: 3463--3488 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3453 ACCATATACA
3463 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
3489 TCATATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6840 original size:265 final size:256
Alignment explanation
Indices: 6370--6844 Score: 722
Period size: 265 Copynumber: 1.8 Consensus size: 256
6360 TTTTTATTAT
6370 TTCGGGTCGGGTCGGGTGAAACTTTATTTTTGTCAGGTCGGGTCGGTTTTTTTAAGTGTGATATT
1 TTCGGGTCGGGTCGGGTGAAACTTTATTTTTGTCAGGTCGGGTCGGTTTTTTTAAGTGTGATATT
* *
6435 CGGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAATACCCAACCCGAAAATATATATAATTTTACC
66 CGAGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAATACCCAACCCGAAAATATATATAATTATACC
* *
6500 TTATATATTTAGGAATAATTACAATAATATCCCTCTATATATAATTTTTTTCAATTAAGTCACTG
131 TTATATATTTAGGAATAATTACAATAATACCCCTCTATATATAATTTTTTTCAATTAAGTCAATG
6565 TTTCTATTGAATAAAAATAATTGTTTATTATTTCGGTCGGATCGAATTTCTAATTCATATA
196 TTTCTATTGAATAAAAATAATTGTTTATTATTTCGGTCGGATCGAATTTCTAATTCATATA
* *
6626 TTCGGGTCGGGTCGGGTGAAACTTTATTTTTTTCGGGTCGGGTCTGG-TTTTTTAAGTGTGATAT
1 TTCGGGTCGGGTCGGGTGAAACTTTATTTTTGTCAGGTCGGGTC-GGTTTTTTTAAGTGTGATA-
*
6690 TTGGGTCGAGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAA-ACCGGACCAGACCCGAATAA-ATA
64 -T---TCGAGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAATA-C---CCA-ACCCGAA-AATATA
* *
6753 TATAATTATACCTTATATATTTAGGAATAATTATAATAATACCCCTCTCTATATAATTTTTTTCA
119 TATAATTATACCTTATATATTTAGGAATAATTACAATAATACCCCTCTATATATAATTTTTTTCA
* *
6818 ATTAAGTCAATTTTTTTATTGAATAAA
184 ATTAAGTCAATGTTTCTATTGAATAAA
6845 TTTTTTATTA
Statistics
Matches: 196, Mismatches: 11, Indels: 15
0.88 0.05 0.07
Matches are distributed among these distances:
256 58 0.30
257 2 0.01
258 1 0.01
260 1 0.01
261 34 0.17
264 3 0.02
265 95 0.48
266 2 0.01
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.39
Consensus pattern (256 bp):
TTCGGGTCGGGTCGGGTGAAACTTTATTTTTGTCAGGTCGGGTCGGTTTTTTTAAGTGTGATATT
CGAGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAATACCCAACCCGAAAATATATATAATTATACC
TTATATATTTAGGAATAATTACAATAATACCCCTCTATATATAATTTTTTTCAATTAAGTCAATG
TTTCTATTGAATAAAAATAATTGTTTATTATTTCGGTCGGATCGAATTTCTAATTCATATA
Found at i:7266 original size:43 final size:43
Alignment explanation
Indices: 7209--7291 Score: 139
Period size: 43 Copynumber: 1.9 Consensus size: 43
7199 ATCTGACATG
*
7209 TCTGCGAACAAAACAGAATATGGAATTGGATTCCAATTCCATT
1 TCTGCCAACAAAACAGAATATGGAATTGGATTCCAATTCCATT
* *
7252 TCTGCCAACCAAACAGAATATGGAATTGGATTTCAATTCC
1 TCTGCCAACAAAACAGAATATGGAATTGGATTCCAATTCC
7292 TGACAGATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (43 bp):
TCTGCCAACAAAACAGAATATGGAATTGGATTCCAATTCCATT
Found at i:7306 original size:17 final size:18
Alignment explanation
Indices: 7280--7325 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
7270 TATGGAATTG
* *
7280 GATTTCAATTCC-TGACA
1 GATTTTAATTCCTTCACA
7297 GATTTTAATTCCTTCACA
1 GATTTTAATTCCTTCACA
7315 GATTTTAATTC
1 GATTTTAATTC
7326 TCTAAAAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.28, C:0.20, G:0.09, T:0.43
Consensus pattern (18 bp):
GATTTTAATTCCTTCACA
Found at i:8126 original size:20 final size:20
Alignment explanation
Indices: 8067--8126 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
8057 GCAATTTTCC
8067 TAAATCGCAATGCGATTAC-G
1 TAAATCGCAATGCGATT-CTG
*
8087 TAAATCGCAATGCGAATCTG
1 TAAATCGCAATGCGATTCTG
* *
8107 TAAATCGCAAAGAGATTCTG
1 TAAATCGCAATGCGATTCTG
8127 ACTATCGCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 1 0.03
20 34 0.97
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (20 bp):
TAAATCGCAATGCGATTCTG
Found at i:8608 original size:20 final size:20
Alignment explanation
Indices: 8583--8671 Score: 117
Period size: 20 Copynumber: 4.5 Consensus size: 20
8573 CAACGCGGAA
8583 ATCGCAACGC-GAATATGACT
1 ATCGCAACGCGGAA-ATGACT
*
8603 ATCGCAACACGGAAATGACT
1 ATCGCAACGCGGAAATGACT
* * *
8623 ATCACAATGCGGAATTGACT
1 ATCGCAACGCGGAAATGACT
*
8643 ATCGCAGCGCGGAAATGACT
1 ATCGCAACGCGGAAATGACT
8663 ATCGCAACG
1 ATCGCAACG
8672 AGAGAATCAC
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
20 55 0.95
21 3 0.05
ACGTcount: A:0.35, C:0.25, G:0.22, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:8704 original size:19 final size:19
Alignment explanation
Indices: 8676--8782 Score: 125
Period size: 19 Copynumber: 5.8 Consensus size: 19
8666 GCAACGAGAG
*
8676 AATCACAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
8695 AATCGTAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
8714 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
8733 AATCGCAA--CG-AGTG--
1 AATCGCAATGCGAAATGAA
*
8747 AATCGGAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
8767 AATCGCAACGCGAAAT
1 AATCGCAATGCGAAAT
8783 TAGTTTCGCG
Statistics
Matches: 74, Mismatches: 8, Indels: 12
0.79 0.09 0.13
Matches are distributed among these distances:
14 7 0.09
16 5 0.07
17 2 0.03
18 3 0.04
19 47 0.64
20 10 0.14
ACGTcount: A:0.47, C:0.16, G:0.21, T:0.16
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:8732 original size:38 final size:35
Alignment explanation
Indices: 8654--8782 Score: 122
Period size: 38 Copynumber: 3.7 Consensus size: 35
8644 TCGCAGCGCG
** * *
8654 GAAATGACTATCGCAA-CGAGA-GAATCACAATGC
1 GAAATGAAAATCGCAAGCGAAATGAATCGCAATGC
*
8687 GAAATGAAAATCGTAATGCGAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAA-GCGAAATG--AATCGCAATGC
* *
8725 GAAATGAAAATCGCAA-CG-AGTGAATCGGAATGC
1 GAAATGAAAATCGCAAGCGAAATGAATCGCAATGC
8758 GAAAATGAAAATCGCAACGCGAAAT
1 G-AAATGAAAATCGCAA-GCGAAAT
8783 TAGTTTCGCG
Statistics
Matches: 78, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
33 24 0.31
34 15 0.19
35 7 0.09
36 5 0.06
37 2 0.03
38 25 0.32
ACGTcount: A:0.46, C:0.16, G:0.22, T:0.16
Consensus pattern (35 bp):
GAAATGAAAATCGCAAGCGAAATGAATCGCAATGC
Found at i:8811 original size:20 final size:20
Alignment explanation
Indices: 8786--8854 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
8776 GCGAAATTAG
*
8786 TTTCGCGTTGCGATTTTCAT
1 TTTCGCATTGCGATTTTCAT
8806 TTTCGCATTGCGA--TTCA-
1 TTTCGCATTGCGATTTTCAT
*
8823 -CTCG--TTGCGATTTTCAT
1 TTTCGCATTGCGATTTTCAT
8840 TTTCGCATTGCGATT
1 TTTCGCATTGCGATT
8855 CACTCGTTGC
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
14 6 0.15
16 7 0.17
18 7 0.17
20 20 0.50
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.46
Consensus pattern (20 bp):
TTTCGCATTGCGATTTTCAT
Found at i:8887 original size:33 final size:34
Alignment explanation
Indices: 8791--8920 Score: 190
Period size: 34 Copynumber: 3.9 Consensus size: 34
8781 ATTAGTTTCG
8791 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
8825 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
* *
8859 CGTTGCGATTTTCA-TTTCACATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
* ** * *
8892 CATTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGAT
8921 AGTCTGTTTT
Statistics
Matches: 87, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
33 28 0.32
34 59 0.68
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.42
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
Found at i:8900 original size:67 final size:68
Alignment explanation
Indices: 8791--8920 Score: 190
Period size: 67 Copynumber: 1.9 Consensus size: 68
8781 ATTAGTTTCG
* * ** *
8791 CGTTGCGATTTTCATTTTCGCATTGCGATTCACTCGTTGCGATTTTCATTTTCGCATTGCGATTC
1 CGTTGCGATTTTCATTTTCACATTGCGATTCACTCATTGCGATAGTCATTTCCGCATTGCGATTC
8856 ACT
66 ACT
* *
8859 CGTTGCGATTTTCA-TTTCACATTGCGATTCTCTCATTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTTTCACATTGCGATTCACTCATTGCGATAGTCATTTCCGCATTGCGAT
8921 AGTCTGTTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
67 41 0.75
68 14 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.42
Consensus pattern (68 bp):
CGTTGCGATTTTCATTTTCACATTGCGATTCACTCATTGCGATAGTCATTTCCGCATTGCGATTC
ACT
Found at i:9145 original size:33 final size:34
Alignment explanation
Indices: 9062--9137 Score: 118
Period size: 33 Copynumber: 2.3 Consensus size: 34
9052 ATTAGTTTCG
* *
9062 CGTTGCGATTTTCATTTTCGTATTGCGATTCACT
1 CGTTGCGATTTTCATTTTCGCATTACGATTCACT
*
9096 CGTTGCGATTTTCATTTT-GCATTACGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTACGATTCACT
9129 CGTTGCGAT
1 CGTTGCGAT
9138 AGTCATTTCC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 21 0.54
34 18 0.46
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.46
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTACGATTCACT
Found at i:9240 original size:237 final size:237
Alignment explanation
Indices: 8825--9265 Score: 828
Period size: 237 Copynumber: 1.9 Consensus size: 237
8815 GCGATTCACT
*
8825 CGTTGCGATTTTCATTTTCGCATTGCGATTCACTCGTTGCGATTTTCATTTCACATTGCGATTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACTCGTTGCGATTTTCATTTCACATTACGATTCT
*
8890 CTCATTGCGATAGTCATTTCCGCGTTGCGATAGTCTGTTTTGCATTCAACATAATGCATATTGAA
66 CTCATTGCGATAGTCATTTCCGCGTTGCGATAGTCTGTTTTGCATTCAACATAATGCAGATTGAA
8955 ATCAACAAATCAACTATTACATTTCAATCAATTAAACAAGCACAAATATTATGTACACATCAATT
131 ATCAACAAATCAACTATTACATTTCAATCAATTAAACAAGCACAAATATTATGTACACATCAATT
9020 AAACAAATCGAAAATGAAAATCGCAACGCGAAATTAGTTTCG
196 AAACAAATCGAAAATGAAAATCGCAACGCGAAATTAGTTTCG
* **
9062 CGTTGCGATTTTCATTTTCGTATTGCGATTCACTCGTTGCGATTTTCATTTTGCATTACGATTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACTCGTTGCGATTTTCATTTCACATTACGATTCT
*
9127 CTCGTTGCGATAGTCATTTCCGCGTTGCGATAGTCTGTTTTGCATTCAACATAATGCAGATTGAA
66 CTCATTGCGATAGTCATTTCCGCGTTGCGATAGTCTGTTTTGCATTCAACATAATGCAGATTGAA
9192 ATCAACAAATCAACTATTACATTTCAATCAATTAAACAAGCACAAATATTATGTACACATCAATT
131 ATCAACAAATCAACTATTACATTTCAATCAATTAAACAAGCACAAATATTATGTACACATCAATT
9257 AAACAAATC
196 AAACAAATC
9266 AACATTTACA
Statistics
Matches: 198, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
237 198 1.00
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.35
Consensus pattern (237 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCACTCGTTGCGATTTTCATTTCACATTACGATTCT
CTCATTGCGATAGTCATTTCCGCGTTGCGATAGTCTGTTTTGCATTCAACATAATGCAGATTGAA
ATCAACAAATCAACTATTACATTTCAATCAATTAAACAAGCACAAATATTATGTACACATCAATT
AAACAAATCGAAAATGAAAATCGCAACGCGAAATTAGTTTCG
Found at i:9278 original size:14 final size:14
Alignment explanation
Indices: 9259--9295 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
9249 CATCAATTAA
9259 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
9273 ACAAATCATCTTTT
1 ACAAATCAACATTT
9287 ACAAATCAA
1 ACAAATCAA
9296 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:10745 original size:42 final size:42
Alignment explanation
Indices: 10638--10745 Score: 105
Period size: 42 Copynumber: 2.6 Consensus size: 42
10628 TCTAGAATGT
* * *
10638 TGGGAG-GGACCTCTTCAACGATGACAGTGGCCTCTTGAACGG
1 TGGGAGAGG-CCTCTTGAACGATGAAAGTGGCCTCTTGAACGA
* * **
10680 TGGGAGGGGACTCTTGAGGGATGATAAG-GGCCTCTTGAACGA
1 TGGGAGAGGCCTCTTGAACGATGA-AAGTGGCCTCTTGAACGA
10722 TAGGG-GAGGCCTCTTGAACGATGA
1 T-GGGAGAGGCCTCTTGAACGATGA
10746 CATGTGAGTC
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
42 46 0.87
43 7 0.13
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.21
Consensus pattern (42 bp):
TGGGAGAGGCCTCTTGAACGATGAAAGTGGCCTCTTGAACGA
Found at i:11254 original size:20 final size:20
Alignment explanation
Indices: 11229--11276 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
11219 AAACTTAAAT
11229 TCGCAACGCAAAAATGACTA
1 TCGCAACGCAAAAATGACTA
* * **
11249 TCGCAATGCGAATTTGACTA
1 TCGCAACGCAAAAATGACTA
11269 TCGCAACG
1 TCGCAACG
11277 AGAGAATCGC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (20 bp):
TCGCAACGCAAAAATGACTA
Found at i:11346 original size:20 final size:20
Alignment explanation
Indices: 11321--11370 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
11311 GATTCTTTCG
11321 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
**
11341 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCAAATTCGCA
11361 TTGCGATAGT
1 TTGCGATAGT
11371 AAACTATTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:13271 original size:20 final size:20
Alignment explanation
Indices: 13248--13301 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
13238 GAAACTTTAA
*
13248 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
13268 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
13288 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
13302 TGAAAATCGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.39, C:0.26, G:0.19, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:13350 original size:20 final size:20
Alignment explanation
Indices: 13325--13393 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
13315 GCGATTCTCT
13325 CATTGCGATAGTCAAATTCG
1 CATTGCGATAGTCAAATTCG
*
13345 CATTGCGATAGTCAAATTCC
1 CATTGCGATAGTCAAATTCG
**
13365 CATTGCGATAGTCATTTTCG
1 CATTGCGATAGTCAAATTCG
*
13385 CTTTGCGAT
1 CATTGCGAT
13394 TCACTCGTTG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.35
Consensus pattern (20 bp):
CATTGCGATAGTCAAATTCG
Found at i:13351 original size:34 final size:34
Alignment explanation
Indices: 13308--13412 Score: 102
Period size: 40 Copynumber: 2.9 Consensus size: 34
13298 GAAATGAAAA
13308 TCGCATTGCGATTCTCTCATTGCGATAGTCAAAT
1 TCGCATTGCGATTCTCTCATTGCGATAGTCAAAT
* **
13342 TCGCATTGCGATAGTCAAATTCCCATTGCGATAGTCATTT
1 TCGCATTGCGAT--TC----TCTCATTGCGATAGTCAAAT
* * *
13382 TCGCTTTGCGATTCACTCGTTGCGATAGTCA
1 TCGCATTGCGATTCTCTCATTGCGATAGTCA
13413 TTCTCGGTTT
Statistics
Matches: 58, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
34 26 0.45
36 2 0.03
38 2 0.03
40 28 0.48
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.35
Consensus pattern (34 bp):
TCGCATTGCGATTCTCTCATTGCGATAGTCAAAT
Found at i:14005 original size:20 final size:21
Alignment explanation
Indices: 13982--14038 Score: 82
Period size: 20 Copynumber: 2.8 Consensus size: 21
13972 CGATAGTCAG
*
13982 ATTCGCATTGTGATTTACGT-
1 ATTCGCATTGCGATTTACGTA
*
14002 ATTCGCATTGCGATTTATGTA
1 ATTCGCATTGCGATTTACGTA
14023 ATT-GCATTGCGATTTA
1 ATTCGCATTGCGATTTA
14039 GGAAAATCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
20 31 0.91
21 3 0.09
ACGTcount: A:0.23, C:0.14, G:0.19, T:0.44
Consensus pattern (21 bp):
ATTCGCATTGCGATTTACGTA
Found at i:14057 original size:21 final size:21
Alignment explanation
Indices: 14031--14077 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
14021 TAATTGCATT
14031 GCGATTTAGGAAAATCGCAAC
1 GCGATTTAGGAAAATCGCAAC
* * *
14052 GCGATTTTGGGAAATCGCAAT
1 GCGATTTAGGAAAATCGCAAC
14073 GCGAT
1 GCGAT
14078 AGTCAGAATC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.32, C:0.17, G:0.28, T:0.23
Consensus pattern (21 bp):
GCGATTTAGGAAAATCGCAAC
Found at i:17508 original size:14 final size:15
Alignment explanation
Indices: 17481--17509 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17471 GTTTCCCAGA
17481 TTTGATAAATTATAT
1 TTTGATAAATTATAT
17496 TTTGATAAA-TATAT
1 TTTGATAAATTATAT
17510 GTATTATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (15 bp):
TTTGATAAATTATAT
Found at i:19064 original size:13 final size:13
Alignment explanation
Indices: 19046--19073 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
19036 GTTGTTTGAC
19046 ATGGTTTTGGTTG
1 ATGGTTTTGGTTG
19059 ATGGTTTTGGTTG
1 ATGGTTTTGGTTG
19072 AT
1 AT
19074 ATTGGTGAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.11, C:0.00, G:0.36, T:0.54
Consensus pattern (13 bp):
ATGGTTTTGGTTG
Found at i:21216 original size:9 final size:9
Alignment explanation
Indices: 21202--21271 Score: 63
Period size: 9 Copynumber: 7.4 Consensus size: 9
21192 GGATCTTATA
21202 AAAAATATT
1 AAAAATATT
*
21211 AAAAATTTT
1 AAAAATATT
21220 AAGAAAT-TT
1 AA-AAATATT
*
21229 ATAAATATT
1 AAAAATATT
21238 AGAAAATTATT
1 A-AAAA-TATT
21249 -AAAATATT
1 AAAAATATT
21257 CATAAAATATT
1 -A-AAAATATT
21268 AAAA
1 AAAA
21272 TTAAAACATA
Statistics
Matches: 51, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
8 8 0.16
9 23 0.45
10 8 0.16
11 12 0.24
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.36
Consensus pattern (9 bp):
AAAAATATT
Found at i:21255 original size:19 final size:19
Alignment explanation
Indices: 21203--21272 Score: 65
Period size: 19 Copynumber: 3.7 Consensus size: 19
21193 GATCTTATAA
* *
21203 AAAATATTAAAAATTTTAAG
1 AAAATATT-AAAATATTCAG
21223 -AAAT-TTATAAATATT-AG
1 AAAATATTA-AAATATTCAG
*
21240 AAAATTATTAAAATATTCAT
1 AAAA-TATTAAAATATTCAG
21260 AAAATATTAAAAT
1 AAAATATTAAAAT
21273 TAAAACATAA
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
17 3 0.07
18 11 0.26
19 21 0.49
20 8 0.19
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (19 bp):
AAAATATTAAAATATTCAG
Found at i:23189 original size:3 final size:3
Alignment explanation
Indices: 23181--23326 Score: 247
Period size: 3 Copynumber: 48.7 Consensus size: 3
23171 TTTTTATCCA
*
23181 TAT TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
23229 TAT TAT TAT CAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
23277 TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
23325 TA
1 TA
23327 ATTTATATTA
Statistics
Matches: 133, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 133 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:23847 original size:14 final size:14
Alignment explanation
Indices: 23828--23854 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
23818 ACAGAACCGA
23828 AGAGAAAAAAAAAC
1 AGAGAAAAAAAAAC
23842 AGAGAAAAAAAAA
1 AGAGAAAAAAAAA
23855 AACAACAAAC
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:0.81, C:0.04, G:0.15, T:0.00
Consensus pattern (14 bp):
AGAGAAAAAAAAAC
Found at i:27129 original size:14 final size:14
Alignment explanation
Indices: 27092--27143 Score: 68
Period size: 14 Copynumber: 3.6 Consensus size: 14
27082 TTTTAAATAA
*
27092 TTTACATTTACATT
1 TTTACATTTGCATT
27106 TTTACATTTGCATT
1 TTTACATTTGCATT
*
27120 TTTACATTTGGCATC
1 TTTACATTT-GCATT
*
27135 TTTGCATTT
1 TTTACATTT
27144 TTTATGTCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.21, C:0.15, G:0.08, T:0.56
Consensus pattern (14 bp):
TTTACATTTGCATT
Found at i:30303 original size:16 final size:18
Alignment explanation
Indices: 30268--30311 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 18
30258 CTCATCCAGC
30268 AAAGAAAGAAGAAGAAGAA
1 AAAGAAA-AAGAAGAAGAA
30287 AAAGAAAAA-AA-AAGAA
1 AAAGAAAAAGAAGAAGAA
30303 AAAGGAAAA
1 AAA-GAAAA
30312 TCGAATAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.33
17 7 0.29
18 2 0.08
19 7 0.29
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAGAAAAAGAAGAAGAA
Found at i:32775 original size:50 final size:50
Alignment explanation
Indices: 32624--32764 Score: 282
Period size: 50 Copynumber: 2.8 Consensus size: 50
32614 TGAATTTGCC
32624 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
32674 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
32724 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
32765 GTTTGGCAGA
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 91 1.00
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.39
Consensus pattern (50 bp):
AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
Found at i:32849 original size:183 final size:183
Alignment explanation
Indices: 32541--32900 Score: 711
Period size: 183 Copynumber: 2.0 Consensus size: 183
32531 TGAATTTGCC
32541 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAACCAATCATTGAAT
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAACCAATCATTGAAT
32606 TTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGA
66 TTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGA
32671 CAGAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
131 CAGAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
*
32724 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAAT
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAACCAATCATTGAAT
32789 TTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGA
66 TTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGA
32854 CAGAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATT
131 CAGAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATT
32901 CAGTAGGAAC
Statistics
Matches: 176, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
183 176 1.00
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.38
Consensus pattern (183 bp):
AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAACCAATCATTGAAT
TTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGA
CAGAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
Found at i:35543 original size:22 final size:22
Alignment explanation
Indices: 35512--35566 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
35502 ATCTACACTC
*
35512 TTCAAAGATGATAGATTCCCTT
1 TTCAAAGATGACAGATTCCCTT
* *
35534 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCCCTT
35556 TTCAAAGATGA
1 TTCAAAGATGA
35567 AAGCTTTATC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCCCTT
Found at i:36176 original size:113 final size:113
Alignment explanation
Indices: 35973--37095 Score: 1694
Period size: 113 Copynumber: 9.9 Consensus size: 113
35963 GATTCAAATC
* *
35973 CATCACTTGATGGATTACCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCTCTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
36038 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATT
66 AGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTACCTGAATT
36086 CATCTCTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCTCTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
36151 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATT
66 AGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTACCTGAATT
36199 CATCTCTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCTCTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
36264 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATT
66 AGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTACCTGAATT
36312 CATCTCTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCTCTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
36377 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATT
66 AGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTACCTGAATT
36425 CATCTCTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCTCTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *
36490 AGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATT
66 AGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTACCTGAATT
* * * * * *
36538 CATCACTTGATAGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1 CATCTCTTGATGGATTA-TCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGG
* * **
36603 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTTCTGAATT
65 AAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTACCTGAATT
** * * * **
36652 CATCAAATTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTTATCTGAAGAATA
1 CATC-TCTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGG
* *
36717 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACCTGAATC
65 AAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTACCTGAATT
* * * * *
36766 CATCAT-TTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1 CATC-TCTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGG
* * *** *
36830 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATT
65 AAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTACCTGAATT
* * * *
36879 CATCAT-TTGATGGATCAACATTACCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1 CATC-TCTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGG
* * *** *
36943 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATT
65 AAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTACCTGAATT
* * *
36992 CATCAT-TTGATGGATCAACATTGCCAGAGAAAGTTCATGAATGAGAAGAACTCATCTGAAGAAG
1 CATC-TCTTGATGGATTATCATTGCCAGAGAAGGTTCAT-AATGAGAAGAACTCATCTGAAGAAG
* *
37056 GAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTT
64 GAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTT
37096 GTTTGATATT
Statistics
Matches: 960, Mismatches: 47, Indels: 5
0.95 0.05 0.00
Matches are distributed among these distances:
113 702 0.73
114 248 0.26
115 10 0.01
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (113 bp):
CATCTCTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTACCTGAATT
Found at i:36823 original size:454 final size:452
Alignment explanation
Indices: 35968--37095 Score: 1756
Period size: 454 Copynumber: 2.5 Consensus size: 452
35958 GCAAAGATTC
* * *
35968 AAATCCATCACTTGATGGATTACCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATTCATCTCTTGATGGATTAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAG
* * * *
36033 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCTCTTGATG
66 AAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGATG
* * *
36098 GATTATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCA
131 GATCATCATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
**
36163 TAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCTCTTGATGGATTATCATTGCCAGAG
196 TAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAATTGATGGATTATCATTGCCAGAG
* *
36228 AAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGT
261 AAGGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAATTCATAATGAGAAGAACTTGT
* * *
36293 TCAACCTTTTACCTGAATTCATCTCTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAA
326 TCAACCTTTTACCTGAATCCATCTCTTGATGGATCATCATTGCCAGAGAAAGTTCATAATGAGAA
*
36358 GAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACCT
391 GAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTACCT
* *
36420 GAATTCATCTCTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATTCATCTCTTGATGGATTAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAG
*
36485 AAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGATA
66 AAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGATG
* *
36550 GATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTC
131 GATCA-TCATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTC
** * *
36615 ATAATGAGAAGAATTTGTTCAACCTTTTTTCTGAATTCATCAAATTGATGGATTATCTTTTCCAG
195 ATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATC-AATTGATGGATTATCATTGCCAG
* * *
36680 AGAAGGTTCATAATGAGAAGAACTTATCTGAAGAATAAAGAAGAAGTTCATAATGAGAAGAACTT
259 AGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAATTCATAATGAGAAGAACTT
* * *
36745 GTTCAACCTTTTACCTGAATCCATCAT-TTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGA
324 GTTCAACCTTTTACCTGAATCCATC-TCTTGATGGATCATCATTGCCAGAGAAAGTTCATAATGA
* * ***
36809 GAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTT
388 GAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTACCT
* * *
36874 AAATTCATCAT-TTGATGGATCAACATTACCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
1 AAATTCATC-TCTTGATGGATTAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAA
* * * * *
36938 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCATTTGAT
65 GAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGAT
*
37003 GGATCAACATTGCCAGAGAAAGTTCATGAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
130 GGATCATCATTGCCAGAGAAAGTTCAT-AATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
**
37068 CATAATGAGAAGAGCTTGTTCAACCTTT
194 CATAATGAGAAGAATTTGTTCAACCTTT
37096 GTTTGATATT
Statistics
Matches: 618, Mismatches: 53, Indels: 8
0.91 0.08 0.01
Matches are distributed among these distances:
452 125 0.20
453 112 0.18
454 379 0.61
455 2 0.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (452 bp):
AAATTCATCTCTTGATGGATTAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGATG
GATCATCATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
TAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAATTGATGGATTATCATTGCCAGAG
AAGGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAATTCATAATGAGAAGAACTTGT
TCAACCTTTTACCTGAATCCATCTCTTGATGGATCATCATTGCCAGAGAAAGTTCATAATGAGAA
GAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTACCT
Found at i:37400 original size:3 final size:3
Alignment explanation
Indices: 37392--37546 Score: 256
Period size: 3 Copynumber: 51.7 Consensus size: 3
37382 TTTTTATCCA
*
37392 TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
37440 TAT CAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
37488 TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT CAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
37536 TAT TAT TAT TA
1 TAT TAT TAT TA
37547 ATTTATATTA
Statistics
Matches: 140, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 140 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:38066 original size:13 final size:13
Alignment explanation
Indices: 38048--38072 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38038 ACAGAACCGA
38048 AGAGAAAAAAAAC
1 AGAGAAAAAAAAC
38061 AGAGAAAAAAAA
1 AGAGAAAAAAAA
38073 AAACAACAAA
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:0.80, C:0.04, G:0.16, T:0.00
Consensus pattern (13 bp):
AGAGAAAAAAAAC
Found at i:42835 original size:24 final size:26
Alignment explanation
Indices: 42803--42850 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 26
42793 CAGTTCCCAC
* *
42803 TTTGCTATTATTGT-TTG-TGCTGAG
1 TTTGATATTACTGTGTTGTTGCTGAG
42827 TTTGATATTACTGTGTTGTTGCTG
1 TTTGATATTACTGTGTTGTTGCTG
42851 CAGAAATATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 12 0.60
25 3 0.15
26 5 0.25
ACGTcount: A:0.12, C:0.08, G:0.25, T:0.54
Consensus pattern (26 bp):
TTTGATATTACTGTGTTGTTGCTGAG
Found at i:47738 original size:10 final size:10
Alignment explanation
Indices: 47723--47747 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
47713 CAAAATAAGA
47723 TAAATGAAAT
1 TAAATGAAAT
47733 TAAATGAAAT
1 TAAATGAAAT
47743 TAAAT
1 TAAAT
47748 TAAACGAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (10 bp):
TAAATGAAAT
Found at i:47772 original size:15 final size:15
Alignment explanation
Indices: 47724--47773 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
47714 AAAATAAGAT
* *
47724 AAATGAAATTAAATG
1 AAATAAAATTAAACG
*
47739 AAATTAAATTAAACG
1 AAATAAAATTAAACG
47754 -AATAAAATGTAAA-G
1 AAATAAAAT-TAAACG
47768 AAATAA
1 AAATAA
47774 TAATAATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 8 0.27
15 22 0.73
ACGTcount: A:0.64, C:0.02, G:0.10, T:0.24
Consensus pattern (15 bp):
AAATAAAATTAAACG
Found at i:47786 original size:13 final size:13
Alignment explanation
Indices: 47768--47795 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
47758 AAATGTAAAG
47768 AAATAATAATAAT
1 AAATAATAATAAT
47781 AAATAATAATAAT
1 AAATAATAATAAT
47794 AA
1 AA
47796 TATAGCGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AAATAATAATAAT
Found at i:47849 original size:31 final size:31
Alignment explanation
Indices: 47803--47873 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 31
47793 TAATATAGCG
* * * *
47803 TATATAATATA-TAAAAAATATTTT-TAAAC
1 TATATATTATACTTAAAAACATTTTCAAAAC
*
47832 TATATATTATACTTAAAAACGTTTTCAAAAC
1 TATATATTATACTTAAAAACATTTTCAAAAC
47863 TATATATTATA
1 TATATATTATA
47874 TAGTTTTCAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 10 0.29
30 10 0.29
31 15 0.43
ACGTcount: A:0.49, C:0.07, G:0.01, T:0.42
Consensus pattern (31 bp):
TATATATTATACTTAAAAACATTTTCAAAAC
Found at i:48004 original size:72 final size:69
Alignment explanation
Indices: 47828--48033 Score: 217
Period size: 72 Copynumber: 2.9 Consensus size: 69
47818 AAATATTTTT
* * * * * *
47828 AAACTATATATTATA-CTTAAAAACGTTTTCAAAACTATATATTATATAGTTTTCAAAAATG-AT
1 AAACTATA-ATTATATTTTCAAAATGATTTCAAAACTATATATTATATAATTTTCAAAAATGTTT
47891 TTTAA
65 TTTAA
*
47896 AAA-TATAA-TATAAGTTTTTCAAAAT-ATTTTTTAAAACTATATATTATATAAATTTTTCAAAA
1 AAACTATAATTAT-A--TTTTCAAAATGA--TTTCAAAACTATATATTATAT-AA-TTTTCAAAA
47958 ATGTTTTTTAA
59 ATGTTTTTTAA
*
47969 AAACTATACATTATATTTTCAAAATGATTTCAAAACTATATATTATATAACTTTC-AAAATGTTT
1 AAACTATA-ATTATATTTTCAAAATGATTTCAAAACTATATATTATATAATTTTCAAAAATGTTT
48033 T
65 T
48034 AAAACTTATA
Statistics
Matches: 116, Mismatches: 9, Indels: 25
0.77 0.06 0.17
Matches are distributed among these distances:
65 3 0.03
66 2 0.02
67 4 0.03
68 3 0.03
69 16 0.14
70 24 0.21
71 3 0.03
72 32 0.28
73 19 0.16
74 5 0.04
75 2 0.02
76 3 0.03
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (69 bp):
AAACTATAATTATATTTTCAAAATGATTTCAAAACTATATATTATATAATTTTCAAAAATGTTTT
TTAA
Found at i:48008 original size:32 final size:32
Alignment explanation
Indices: 47968--48053 Score: 93
Period size: 35 Copynumber: 2.6 Consensus size: 32
47958 ATGTTTTTTA
47968 AAAACTATACATTATAT-TTTCAAAATGATTTC
1 AAAACTATACATTATATATTTCAAAATG-TTTC
* *
48000 AAAACTATATATTATATAACTTTCAAAATGTTTT
1 AAAACTATACATTATAT-A-TTTCAAAATGTTTC
* *
48034 AAAACTTATATATTGTATAT
1 AAAAC-TATACATTATATAT
48054 AAGTTTTCAA
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
32 16 0.34
33 1 0.02
34 9 0.19
35 21 0.45
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.43
Consensus pattern (32 bp):
AAAACTATACATTATATATTTCAAAATGTTTC
Found at i:48010 original size:108 final size:109
Alignment explanation
Indices: 47853--48091 Score: 262
Period size: 108 Copynumber: 2.2 Consensus size: 109
47843 CTTAAAAACG
* * * *
47853 TTTTCAAAACTATATATTATATAGTTTTCAAAAATGATTTTAAAAATATA-ATATAAGTTTTTCA
1 TTTTAAAAACTATACATTATATAGTTTTCAAAAATGATTTCAAAAATATATATATAA--CTTTC-
* * **
47917 AAATATTTTTTAAAAC-TATATATTATATA-AATTTTTCAAAAATGTT
63 AAA-ATGTTTTAAAACTTATATATTATATATAAGTTTTCAAAAACATT
47963 TTTTAAAAACTATACA-T-TATA-TTTTC-AAAATGATTTCAAAACTATATATTATATAACTTTC
1 TTTTAAAAACTATACATTATATAGTTTTCAAAAATGATTTCAAAA--ATATA-TATATAACTTTC
*
48024 AAAATGTTTTAAAACTTATATATTGTATATAAGTTTTCAAAAACATT
63 AAAATGTTTTAAAACTTATATATTATATATAAGTTTTCAAAAACATT
*
48071 TTTAAAAAACTAT--ATTATATA
1 TTTTAAAAACTATACATTATATA
48092 TATATATTCG
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
106 26 0.23
107 21 0.19
108 43 0.39
109 1 0.01
110 20 0.18
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (109 bp):
TTTTAAAAACTATACATTATATAGTTTTCAAAAATGATTTCAAAAATATATATATAACTTTCAAA
ATGTTTTAAAACTTATATATTATATATAAGTTTTCAAAAACATT
Found at i:48055 original size:37 final size:36
Alignment explanation
Indices: 47854--48065 Score: 142
Period size: 34 Copynumber: 5.9 Consensus size: 36
47844 TTAAAAACGT
*
47854 TTTCAAAACTATATATTATAT-AGTTTTCAAAAATGA
1 TTTCAAAACTATATATTATATAAGCTTTC-AAAATGA
* *
47890 TTTTAAAA--ATATA--ATATAAGTTTTTCAAAAT-A
1 TTTCAAAACTATATATTATATAAG-CTTTCAAAATGA
* ** *
47922 TTTTTTAAAACTATATATTATATAAATTTTTCAAAAATGTTT
1 --TTTCAAAACTATATATTATAT-AAGCTTTC-AAAATG--A
* *
47964 TTTAAAAACTATACATTATAT----TTTCAAAATGA
1 TTTCAAAACTATATATTATATAAGCTTTCAAAATGA
47996 TTTCAAAACTATATATTATATAA-CTTTCAAAATG-
1 TTTCAAAACTATATATTATATAAGCTTTCAAAATGA
* *
48030 TTTTAAAACTTATATATTGTATATAAGTTTTCAAAA
1 TTTCAAAAC-TATATA-T-TATATAAGCTTTCAAAA
48066 ACATTTTTAA
Statistics
Matches: 146, Mismatches: 10, Indels: 38
0.75 0.05 0.20
Matches are distributed among these distances:
32 24 0.16
33 7 0.05
34 32 0.22
35 20 0.14
36 13 0.09
37 7 0.05
38 17 0.12
39 7 0.05
40 19 0.13
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (36 bp):
TTTCAAAACTATATATTATATAAGCTTTCAAAATGA
Found at i:48092 original size:76 final size:75
Alignment explanation
Indices: 47935--48176 Score: 188
Period size: 77 Copynumber: 3.2 Consensus size: 75
47925 TTTAAAACTA
* * * * * **
47935 TATATTATATAAAT-TTTTC-AAAAATGTTTTTTAAAAACTATACATTATA-TTTTCAAAATGA-
1 TATATTATATATATATATTCGAAACATG-TTTTTGAAAACTATATATTATATTTTTCAAAAACAT
47996 TTTC--AAAAC
65 TTTCAAAAAAC
48005 TATA-TAT-TATATA-ACTTTC-AAA-ATG-TTTT-AAAACTTATATATTGTATATAAGTTTTCA
1 TATATTATATATATATA--TTCGAAACATGTTTTTGAAAAC-TATATA-T-TATAT---TTTTCA
*
48063 AAAACATTTTTAAAAAAC
58 AAAACATTTTCAAAAAAC
*
48081 TATATTATATATATATATTCGGAAACCGTGTTTTTGAAAACTATATATTATATTTTTCAAAAACA
1 TATATTATATATATATATTC-GAAA-CATGTTTTTGAAAACTATATATTATATTTTTCAAAAACA
48146 TTTTCAAAAAA-
64 TTTTCAAAAAAC
48157 TATATTATATTACTATATAT
1 TATATTATA-TA-TATATAT
48177 ATATATATAT
Statistics
Matches: 140, Mismatches: 8, Indels: 40
0.74 0.04 0.21
Matches are distributed among these distances:
66 5 0.04
67 9 0.06
68 5 0.04
69 10 0.07
70 10 0.07
73 10 0.07
74 3 0.02
76 18 0.13
77 30 0.21
78 13 0.09
79 4 0.03
80 5 0.04
81 3 0.02
82 10 0.07
83 5 0.04
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.44
Consensus pattern (75 bp):
TATATTATATATATATATTCGAAACATGTTTTTGAAAACTATATATTATATTTTTCAAAAACATT
TTCAAAAAAC
Found at i:48161 original size:2 final size:2
Alignment explanation
Indices: 48156--48195 Score: 57
Period size: 2 Copynumber: 20.5 Consensus size: 2
48146 TTTTCAAAAA
48156 AT AT AT -T AT AT -T ACT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT A
48196 GACGAAAATG
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 2 0.06
2 31 0.89
3 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48831 original size:84 final size:84
Alignment explanation
Indices: 48690--49085 Score: 318
Period size: 84 Copynumber: 4.7 Consensus size: 84
48680 GGATGTCATC
* * * * * *
48690 GAGCTGAGTGGAATCGAACTCGAAGGTCTTTGGTAGGCAGATAACCCTTCTCGACTTAAGCTATG
1 GAGCTGAGCGTAATCGAACTCAAAGGCCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
*
48755 CTGCAAATGATGTGCCTTT
66 CTGCAAATGATGTGCCTTA
* * *
48774 GAGCTGAGCGTAGTCAAACTCAAAGGCCTTTGGTTGGTAGATAACCCTTCTCGACTTAAGTTATG
1 GAGCTGAGCGTAATCGAACTCAAAGGCCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
* * * * *
48839 TTGCAAAAGATGTACCCTC
66 CTGCAAATGATGTGCCTTA
* ** * * * * * *
48858 GAAGTTGAGTATAATCGAACTCAAAGGTCTTTTGG-TGACAAATAACCCTTAT-AACCTTGAGTT
1 G-AGCTGAGCGTAATCGAACTCAAAGG-CCTTTGGTTGGCAGATAACCCTTCTCGA-CTTAAGTT
* *
48921 ATGCTGTAAATGATGTGCCCTCA
63 ATGCTGCAAATGATGTG-CCTTA
* * ** * * *
48944 AAGCTGAGTGTAATCGAACT-TGAGG-GTCT--TTGGCAGATAACCCTTCTCGACTTAAGTTATA
1 GAGCTGAGCGTAATCGAACTCAAAGGCCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
* * *
49005 CTGTAAATGATATGCCTTG
66 CTGCAAATGATGTGCCTTA
* ** * ** * *
49024 GAGCTGAGCGTAGTCGAACTTTAAGGTCTTTTTTTGGCAGACAACCCTTCTAGACTTAAGTT
1 GAGCTGAGCGTAATCGAACTCAAAGGCCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTT
49086 GTGCCCTCGA
Statistics
Matches: 245, Mismatches: 57, Indels: 20
0.76 0.18 0.06
Matches are distributed among these distances:
80 20 0.08
81 40 0.16
82 5 0.02
84 102 0.42
85 70 0.29
86 8 0.03
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (84 bp):
GAGCTGAGCGTAATCGAACTCAAAGGCCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
CTGCAAATGATGTGCCTTA
Found at i:49325 original size:84 final size:84
Alignment explanation
Indices: 49096--49335 Score: 310
Period size: 83 Copynumber: 2.9 Consensus size: 84
49086 GTGCCCTCGA
* * * * * * * * * *
49096 AGCTGAGTGTAATCAAACTCGAGGGTC-TTT-G-G-CAGATAACTCTTCTCGACTTAAGCTATGA
1 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGC
* * *
49157 TGCAAATGATGTGCCTTGG
66 TGTAAATGATATGCCTTAG
* *
49176 AGCTGAGCGTAGTCGAACTCAAAGGT-TTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGC
1 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGC
49240 TGTAAATGATATGCCTTAG
66 TGTAAATGATATGCCTTAG
49259 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGC
1 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGC
49324 TGTAAATGATAT
66 TGTAAATGATAT
49336 CTTTAAAAAA
Statistics
Matches: 138, Mismatches: 17, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
80 24 0.17
81 1 0.01
83 64 0.46
84 49 0.36
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (84 bp):
AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGC
TGTAAATGATATGCCTTAG
Found at i:55711 original size:13 final size:13
Alignment explanation
Indices: 55693--55717 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55683 AAATGAAAAG
55693 AAATAATAATAAT
1 AAATAATAATAAT
55706 AAATAATAATAA
1 AAATAATAATAA
55718 CAATAATATA
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:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAATAATAATAAT
Found at i:55935 original size:32 final size:32
Alignment explanation
Indices: 55898--55983 Score: 93
Period size: 35 Copynumber: 2.6 Consensus size: 32
55888 TGGTTTTTTA
55898 AAAACTATACATTATAT-TTTCAAAATGATTTC
1 AAAACTATACATTATATATTTCAAAATG-TTTC
* *
55930 AAAACTATATATTATATAACTTTCAAAATGTTTT
1 AAAACTATACATTATAT-A-TTTCAAAATGTTTC
* *
55964 AAAACTTATATATTGTATAT
1 AAAAC-TATACATTATATAT
55984 AAGTTTTCAA
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
32 16 0.34
33 1 0.02
34 9 0.19
35 21 0.45
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.43
Consensus pattern (32 bp):
AAAACTATACATTATATATTTCAAAATGTTTC
Found at i:55948 original size:73 final size:70
Alignment explanation
Indices: 55744--55967 Score: 200
Period size: 70 Copynumber: 3.2 Consensus size: 70
55734 ATAATATATA
** * * * *
55744 AAAAAT-ATTTTTTAAACTATATATTATA-CTTAAAAACGTTTTCAAAACTATATATTATAT--A
1 AAAAATGATTTTAAAAACTATA-ATTATATTTTCAAAATGATTTCAAAACTATATATTATATAAA
55805 GTTTTC
65 GTTTTC
*
55811 AAAAATGATTTTAAAAA-TATAA-TATAAGTTTTTCAAAAT-ATTTTTTAAAACTATATATTATA
1 AAAAATGATTTTAAAAACTATAATTAT-A--TTTTCAAAATGA--TTTCAAAACTATATATTATA
*
55873 TAAATTTTTC
61 TAAAGTTTTC
*
55883 AAAAATGGTTTTTTAAAAACTATACATTATATTTTCAAAATGATTTCAAAACTATATATTATAT-
1 AAAAAT-G-ATTTTAAAAACTATA-ATTATATTTTCAAAATGATTTCAAAACTATATATTATATA
*
55947 AA-CTTTC
63 AAGTTTTC
55954 -AAAATG-TTTTAAAA
1 AAAAATGATTTTAAAA
55968 CTTATATATT
Statistics
Matches: 131, Mismatches: 11, Indels: 30
0.76 0.06 0.17
Matches are distributed among these distances:
65 3 0.02
66 2 0.02
67 18 0.14
68 8 0.06
69 7 0.05
70 25 0.19
71 4 0.03
72 14 0.11
73 21 0.16
74 19 0.15
75 5 0.04
76 2 0.02
77 3 0.02
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.44
Consensus pattern (70 bp):
AAAAATGATTTTAAAAACTATAATTATATTTTCAAAATGATTTCAAAACTATATATTATATAAAG
TTTTC
Found at i:55954 original size:35 final size:35
Alignment explanation
Indices: 55782--56030 Score: 176
Period size: 34 Copynumber: 6.8 Consensus size: 35
55772 CTTAAAAACG
*
55782 TTTTCAAAACTATATATTATATAGTTTTCAAAAATGA
1 TTTT-AAAACTATATATTATATAATTTTC-AAAATGA
55819 TTTTAAAA--ATATA--ATATAAGTTTTTCAAAAT-A
1 TTTTAAAACTATATATTATATAA--TTTTCAAAATGA
*
55851 TTTTTTAAAACTATATATTATATAAATTTTTCAAAAATGGTT
1 --TTTTAAAACTATATATTATAT-AA-TTTTC-AAAAT-G-A
*
55893 TTTTAAAAACTATACA-T-TAT-ATTTTCAAAATGA
1 TTTT-AAAACTATATATTATATAATTTTCAAAATGA
* *
55926 TTTCAAAACTATATATTATATAACTTTCAAAATG-
1 TTTTAAAACTATATATTATATAATTTTCAAAATGA
**
55960 TTTTAAAACTTATATATTGTATATAAGTTTTCAAAAACA
1 TTTTAAAAC-TATATA-T-TATATAA-TTTTCAAAATGA
55999 TTTTTAAAAAACTATAT-TATATATATATTTTC
1 -TTTT--AAAACTATATAT-TATATA-ATTTTC
56031 GGAAGCCGTT
Statistics
Matches: 174, Mismatches: 12, Indels: 50
0.74 0.05 0.21
Matches are distributed among these distances:
32 16 0.09
33 9 0.05
34 30 0.17
35 22 0.13
36 15 0.09
37 12 0.07
38 18 0.10
39 22 0.13
40 10 0.06
41 15 0.09
42 5 0.03
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (35 bp):
TTTTAAAACTATATATTATATAATTTTCAAAATGA
Found at i:56022 original size:108 final size:107
Alignment explanation
Indices: 55794--56022 Score: 254
Period size: 108 Copynumber: 2.1 Consensus size: 107
55784 TTCAAAACTA
* * *
55794 TATATTATATAGTTTTCAAAAATGATTTTAAAAATATAATATAAGTTTTTCAAAATATTTTTTAA
1 TATATTATATA-TTTTCAAAAATGATTTCAAAAATATAATATAAG-CTTTCAAAATATGTTTTAA
* ** *
55859 AACTATATATTATATAAATTTTTCAAAAATGGTTTTTTAAAAAC
64 AACTATATATTATATAAAGTTTTCAAAAATCATTTTTAAAAAAC
*
55903 TATA-CATTATATTTTC-AAAATGATTTCAAAACTATATATTATATAA-CTTTC-AAA-ATGTTT
1 TATATTA-TATATTTTCAAAAATGATTTCAAAA--ATATA--ATATAAGCTTTCAAAATATGTTT
*
55963 TAAAACTTATATATTGTATATAAGTTTTCAAAAA-CATTTTTAAAAAAC
61 TAAAAC-TATATATTATATA-AAGTTTTCAAAAATCATTTTTAAAAAAC
56011 TATATTATATAT
1 TATATTATATAT
56023 ATATTTTCGG
Statistics
Matches: 102, Mismatches: 10, Indels: 17
0.79 0.08 0.13
Matches are distributed among these distances:
107 25 0.25
108 41 0.40
109 30 0.29
111 6 0.06
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.45
Consensus pattern (107 bp):
TATATTATATATTTTCAAAAATGATTTCAAAAATATAATATAAGCTTTCAAAATATGTTTTAAAA
CTATATATTATATAAAGTTTTCAAAAATCATTTTTAAAAAAC
Found at i:56030 original size:39 final size:40
Alignment explanation
Indices: 55972--56098 Score: 95
Period size: 39 Copynumber: 3.2 Consensus size: 40
55962 TTAAAACTTA
*
55972 TATATTGTATATA-AGTTTTC-AAAAACATTTTTAAAAAAC
1 TATATTATATATATA-TTTTCAAAAAACATTTTTAAAAAAC
** ** * **
56011 TATATTATATATATATTTTCGGAAGCCGTTTTTTTGAAAAC
1 TATATTATATATATATTTTCAAAAAAC-ATTTTTAAAAAAC
*
56052 TATA-TAT-TATAT-TTTTCAAAAAAACATTTTCAAAAAA-
1 TATATTATATATATATTTTC-AAAAAACATTTTTAAAAAAC
*
56089 TATACTATAT
1 TATATTATAT
56099 TACTATATAT
Statistics
Matches: 67, Mismatches: 15, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
37 4 0.06
38 16 0.24
39 26 0.39
40 7 0.10
41 14 0.21
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.43
Consensus pattern (40 bp):
TATATTATATATATATTTTCAAAAAACATTTTTAAAAAAC
Found at i:56107 original size:2 final size:2
Alignment explanation
Indices: 56088--56125 Score: 51
Period size: 2 Copynumber: 18.5 Consensus size: 2
56078 TTTTCAAAAA
56088 AT AT ACT AT AT -T ACT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT A-T AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT A
56126 GACGAAAATG
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 1 0.03
2 28 0.85
3 4 0.12
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:56762 original size:28 final size:29
Alignment explanation
Indices: 56725--56783 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 29
56715 TAGAATAATA
*
56725 ACTATTTTTATATATATTTTAATACTTTT
1 ACTATTTTTATATAGATTTTAATACTTTT
56754 ACTA-TTTTATATAGATTTTAATACTTTT
1 ACTATTTTTATATAGATTTTAATACTTTT
56782 AC
1 AC
56784 CGTGTATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 25 0.86
29 4 0.14
ACGTcount: A:0.32, C:0.08, G:0.02, T:0.58
Consensus pattern (29 bp):
ACTATTTTTATATAGATTTTAATACTTTT
Found at i:60718 original size:3 final size:3
Alignment explanation
Indices: 60710--60735 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
60700 AGTGAGGCAA
60710 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
60736 CAAGGAATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:60986 original size:23 final size:23
Alignment explanation
Indices: 60956--61025 Score: 106
Period size: 23 Copynumber: 3.0 Consensus size: 23
60946 CTTGTATAAA
60956 TGCACAGAAGTGCCACGTAGAAT
1 TGCACAGAAGTGCCACGTAGAAT
60979 TGCACAGAAGTGCCACGTAGAAT
1 TGCACAGAAGTGCCACGTAGAAT
* *
61002 TGCATC-GAAGTACCGCGTAGAAT
1 TGCA-CAGAAGTGCCACGTAGAAT
61025 T
1 T
61026 ACACCGTAGT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
23 43 0.98
24 1 0.02
ACGTcount: A:0.33, C:0.21, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACAGAAGTGCCACGTAGAAT
Done.