Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003805.1 Hibiscus syriacus cultivar Beakdansim tig00008145_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: 2300233
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 11
Found at i:329364 original size:24 final size:24
Alignment explanation
Indices: 329337--329390 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
329327 GTATTCGAAA
329337 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
329361 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
329385 TTTGAT
1 TTTGAT
329391 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:331928 original size:20 final size:19
Alignment explanation
Indices: 331900--331954 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
331890 CAATCATCTT
*
331900 AATGTCTATCGCAACGCGGA
1 AATGACTATCGCAACGC-GA
*
331920 AATGACTATCGCAATGCGA
1 AATGACTATCGCAACGCGA
**
331939 AATGAAAATCGCAACG
1 AATGACTATCGCAACG
331955 AGAGAATCAC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (19 bp):
AATGACTATCGCAACGCGA
Found at i:331942 original size:19 final size:20
Alignment explanation
Indices: 331861--331954 Score: 68
Period size: 20 Copynumber: 4.7 Consensus size: 20
331851 GGCATTCATT
*
331861 TGACTATCGCAACACGGAAA
1 TGACTATCGCAACGCGGAAA
* **
331881 TGACGT-TCGCAATCATC-TTAA
1 TGAC-TATCGCAA-C-GCGGAAA
*
331902 TGTCTATCGCAACGCGGAAA
1 TGACTATCGCAACGCGGAAA
*
331922 TGACTATCGCAATGC-GAAA
1 TGACTATCGCAACGCGGAAA
**
331941 TGAAAATCGCAACG
1 TGACTATCGCAACG
331955 AGAGAATCAC
Statistics
Matches: 57, Mismatches: 12, Indels: 11
0.71 0.15 0.14
Matches are distributed among these distances:
19 16 0.28
20 27 0.47
21 13 0.23
22 1 0.02
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.21
Consensus pattern (20 bp):
TGACTATCGCAACGCGGAAA
Found at i:331973 original size:33 final size:33
Alignment explanation
Indices: 331931--332020 Score: 144
Period size: 33 Copynumber: 2.7 Consensus size: 33
331921 ATGACTATCG
331931 CAATGCGAAATGAAAATCGCAACGAGAGAATCA
1 CAATGCGAAATGAAAATCGCAACGAGAGAATCA
* *
331964 CAATGCGAAATGAAAATCGCAACGAGGGAATCG
1 CAATGCGAAATGAAAATCGCAACGAGAGAATCA
* *
331997 CAAAGTGAAATGAAAATCGCAACG
1 CAATGCGAAATGAAAATCGCAACG
332021 CGAATTTAGT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.47, C:0.18, G:0.23, T:0.12
Consensus pattern (33 bp):
CAATGCGAAATGAAAATCGCAACGAGAGAATCA
Found at i:332055 original size:19 final size:19
Alignment explanation
Indices: 332020--332065 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
332010 AAATCGCAAC
*
332020 GCGAATTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
332039 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
332058 GCGATTTT
1 GCGATTTT
332066 GTCATTGCGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.13, C:0.15, G:0.26, T:0.46
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:332079 original size:33 final size:33
Alignment explanation
Indices: 332037--332128 Score: 114
Period size: 33 Copynumber: 2.8 Consensus size: 33
332027 TAGTTTCGCG
* *
332037 TTGCGATTTT-AGTTTCGCGTTGCGATTTTGTCA
1 TTGCGATTTTCA-TTTCGCGTTGCGATTCTCTCA
* * *
332070 TTGCGATTTTCATTTCACGTTGTGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCA
*
332103 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
332129 AGTCATTTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
33 49 0.98
34 1 0.02
ACGTcount: A:0.13, C:0.18, G:0.21, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCA
Found at i:332255 original size:14 final size:14
Alignment explanation
Indices: 332236--332272 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
332226 CATCAATTAA
332236 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
332250 ACAAATCATCTTTT
1 ACAAATCAACTTTT
332264 ACAAATCAA
1 ACAAATCAA
332273 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:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:333690 original size:21 final size:21
Alignment explanation
Indices: 333624--333690 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
333614 GTGAATCGGG
*
333624 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
333644 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
333666 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
333687 CTCT
1 CTCT
333691 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:333709 original size:42 final size:41
Alignment explanation
Indices: 333624--333746 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
333614 GTGAATCGGG
* * * *
333624 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
333666 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
333708 CTCTTCAACGATTGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
333747 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.22, C:0.19, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:334191 original size:19 final size:19
Alignment explanation
Indices: 334167--334210 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
334157 AAAAATGACT
334167 ATCGCAACGCGAAACAAAA
1 ATCGCAACGCGAAACAAAA
*
334186 ATCGCAACGCGAAATAAAA
1 ATCGCAACGCGAAACAAAA
334205 ATCGCA
1 ATCGCA
334211 GCGAGAGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.50, C:0.25, G:0.16, T:0.09
Consensus pattern (19 bp):
ATCGCAACGCGAAACAAAA
Found at i:334280 original size:20 final size:20
Alignment explanation
Indices: 334255--334292 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
334245 CGCGATTATA
334255 GTTTCGCGTTGCGATTTTTG
1 GTTTCGCGTTGCGATTTTTG
334275 GTTTCGCGTTGCGATTTT
1 GTTTCGCGTTGCGATTTT
334293 GTCGTTGCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.05, C:0.16, G:0.29, T:0.50
Consensus pattern (20 bp):
GTTTCGCGTTGCGATTTTTG
Found at i:334318 original size:33 final size:33
Alignment explanation
Indices: 334261--334358 Score: 133
Period size: 33 Copynumber: 2.9 Consensus size: 33
334251 TATAGTTTCG
* *
334261 CGTTGCGATTTTTGGTTTCGCGTTGCGATTTTGT
1 CGTTGCGA-TTTTCGTTTCGCGTTGCGATTTTAT
* * *
334295 CGTTGCGATTTTCATTTCGCGTTGCAATTCTAT
1 CGTTGCGATTTTCGTTTCGCGTTGCGATTTTAT
*
334328 CGTTGCGATTTTCGTTTTGCGTTGCGATTTT
1 CGTTGCGATTTTCGTTTCGCGTTGCGATTTT
334359 CATTCTCTCA
Statistics
Matches: 55, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
33 47 0.85
34 8 0.15
ACGTcount: A:0.09, C:0.17, G:0.24, T:0.49
Consensus pattern (33 bp):
CGTTGCGATTTTCGTTTCGCGTTGCGATTTTAT
Found at i:334587 original size:94 final size:93
Alignment explanation
Indices: 334475--334850 Score: 580
Period size: 94 Copynumber: 4.1 Consensus size: 93
334465 ATGGATTTCA
* * *
334475 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTTAGAGTATTAAAGAATACACAGTT
1 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
* *
334540 TAACAGAATTGGCAGCAAACGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
*
334568 TTACTTTCAACCAAAAGACAAAACAAAGAAAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
334633 TTAGCAGAATTGGCAGCAACCGAACAAAT
65 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
334662 TTACTTTCAACCAAAAGATAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
334727 TTAGCAGAATTGGCAGCAACCGAATAAAT
65 TTAGCAGAATTGGCAGCAACCGAACAAAT
* *
334756 TTACTTCAACCAAAAGACAAAAAAAAAGACAAATACTAACTTCACAGTGTT----AATAAACAGT
1 TTACTTCAACCAAAAGAC-AAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* * *
334817 TTAGCAGTATTGGCAGCAACTGAATAAAT
65 TTAGCAGAATTGGCAGCAACCGAACAAAT
334846 TTACT
1 TTACT
334851 AAGCAATCTA
Statistics
Matches: 267, Mismatches: 14, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
90 41 0.15
93 17 0.06
94 209 0.78
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.22
Consensus pattern (93 bp):
TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:336601 original size:19 final size:19
Alignment explanation
Indices: 336537--336668 Score: 148
Period size: 19 Copynumber: 7.1 Consensus size: 19
336527 TCTTTTTGTT
*
336537 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
336556 GAGAATGAAAATCACAACGC
1 GA-AATGAAAATCGCAACGC
**
336576 GGAAATGACTATCGCAACGC
1 -GAAATGAAAATCGCAACGC
*
336596 GAAATGAAAATCACAACGC
1 GAAATGAAAATCGCAACGC
336615 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
336632 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
336648 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
336667 GA
1 GA
336669 TTTTGGTTTC
Statistics
Matches: 94, Mismatches: 12, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
14 10 0.11
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 47 0.50
20 29 0.31
21 2 0.02
ACGTcount: A:0.47, C:0.20, G:0.22, T:0.11
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:336712 original size:33 final size:33
Alignment explanation
Indices: 336664--336744 Score: 126
Period size: 33 Copynumber: 2.5 Consensus size: 33
336654 AAAATCGCAA
**
336664 TGCGATTTTGGTTTCGCGTTGCGATTATCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
* *
336697 TGCGATTTTCATTTCGCGTTGCGATTCTCTTGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
336730 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
336745 TCTCGTTGTG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.10, C:0.20, G:0.22, T:0.48
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
Found at i:336747 original size:21 final size:20
Alignment explanation
Indices: 336724--336799 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
336714 GTTGCGATTC
336724 TCTTGTTGCGATTTTCATTT
1 TCTTGTTGCGATTTTCATTT
* * **
336744 CTCTCGTTGTGATAGTCATTT
1 -TCTTGTTGCGATTTTCATTT
* *
336765 TCGTGTTGCGTTTTTCATTT
1 TCTTGTTGCGATTTTCATTT
* *
336785 TCATATTGCGATTTT
1 TCTTGTTGCGATTTT
336800 AAGTTTAGAA
Statistics
Matches: 42, Mismatches: 13, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
20 26 0.62
21 16 0.38
ACGTcount: A:0.12, C:0.16, G:0.17, T:0.55
Consensus pattern (20 bp):
TCTTGTTGCGATTTTCATTT
Found at i:337373 original size:20 final size:20
Alignment explanation
Indices: 337350--337443 Score: 125
Period size: 20 Copynumber: 4.7 Consensus size: 20
337340 CGATAGTCAG
*
337350 ATTCACATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * *
337370 ATTCGCATTGCGGTTTTCCT
1 ATTCGCATTGCGATTTACGT
337390 AATTCGCATTGCGATTTACGT
1 -ATTCGCATTGCGATTTACGT
* *
337411 AATCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
337431 ATTCGCATTGCGA
1 ATTCGCATTGCGA
337444 ATTAGGAAAA
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
20 45 0.73
21 17 0.27
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:337405 original size:41 final size:40
Alignment explanation
Indices: 337350--337443 Score: 125
Period size: 41 Copynumber: 2.3 Consensus size: 40
337340 CGATAGTCAG
* * * *
337350 ATTCACATTGCGATTTACGTATTCGCATTGCGGTTTTCCT
1 ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
* *
337390 AATTCGCATTGCGATTTACGTAATCGCGTTGCGATTTACGT
1 -ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
337431 ATTCGCATTGCGA
1 ATTCGCATTGCGA
337444 ATTAGGAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 13 0.28
41 34 0.72
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.38
Consensus pattern (40 bp):
ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
Found at i:337464 original size:21 final size:21
Alignment explanation
Indices: 337440--337485 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
337430 TATTCGCATT
337440 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
337461 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
337482 GCGA
1 GCGA
337486 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:338911 original size:25 final size:24
Alignment explanation
Indices: 338857--338911 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
338847 TTTAATGTTG
* *
338857 TAAATAATTAAATTAAATTTTAAA
1 TAAATAATGAAATTAAAATTTAAA
338881 TTAAATAATGAAATGATAAAATTTAAA
1 -TAAATAATGAAAT--TAAAATTTAAA
338908 -AAAT
1 TAAAT
338912 TAAATTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
25 16 0.62
27 10 0.38
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (24 bp):
TAAATAATGAAATTAAAATTTAAA
Found at i:347124 original size:21 final size:21
Alignment explanation
Indices: 347098--347153 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
347088 TTAAAGTGGA
*
347098 TGTAGGAATTTCAGCAATGGC
1 TGTAGGATTTTCAGCAATGGC
* * *
347119 TGTAGGATTTTTAGCAGTGGT
1 TGTAGGATTTTCAGCAATGGC
347140 TGTAGGATTTTCAG
1 TGTAGGATTTTCAG
347154 TAGGTTTTGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.23, C:0.09, G:0.30, T:0.38
Consensus pattern (21 bp):
TGTAGGATTTTCAGCAATGGC
Found at i:355723 original size:134 final size:134
Alignment explanation
Indices: 355544--356417 Score: 1198
Period size: 134 Copynumber: 6.5 Consensus size: 134
355534 TGAATCATTC
* *
355544 CACTGTTCTTCAGGGAAGATTGAATCGGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAAT
1 CACTATTCTTCAGGGAAGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAAT
* * * * * *
355609 ATGAAAGAATAAGAAT-CGACTCCATTACTCTTTAGGGGAGATCATACTTGAGAAAACTTTGATC
66 CTGAAAGAAGAAGAATATG-CTCCACTACTCTTTAGGGGAGATCAAACTCGAGAAAACTTTGATC
*
355673 CATTT
130 CACTT
* * * * *
355678 CACTATTCTTTAGGGAAGATTGAATCATAATCGATTTGCTTCACTGTTCTTCAGGATGACTAAAT
1 CACTATTCTTCAGGGAAGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAAT
* *** * * *
355743 TTGAAAGAAGAATTGTATGCTCCACTGCTCTTTATGGGAGATCAGACTCGAGAAAACTTTGATCC
66 CTGAAAGAAGAAGAATATGCTCCACTACTCTTTAGGGGAGATCAAACTCGAGAAAACTTTGATCC
355808 ACTT
131 ACTT
* * * * *
355812 CACTATTCTTCAAGAAATATTGAATCAGAATTGATTTGCTTCACTTCTCTTCAGGAAGACCAAAT
1 CACTATTCTTCAGGGAAGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAAT
* *
355877 CTGAAAGAAGAAAAATATGCTCCACTACTCTTTAGGGGAGATCAGACTCGAGAAAACTTTGATCC
66 CTGAAAGAAGAAGAATATGCTCCACTACTCTTTAGGGGAGATCAAACTCGAGAAAACTTTGATCC
355942 ACTT
131 ACTT
** * * *
355946 CACTGCTCTTTAGGGAAGATTGAATCAAAATCGATTTGCTTCACTTCTCTTCAGGAAGACCAAAT
1 CACTATTCTTCAGGGAAGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAAT
*
356011 CTGAAAGAAGAAGAATATGCTCCACCACTCTTTA-GGGAGATCAAACTCGAGAAAACTTTGATCC
66 CTGAAAGAAGAAGAATATGCTCCACTACTCTTTAGGGGAGATCAAACTCGAGAAAACTTTGATCC
356075 ACTT
131 ACTT
* * *
356079 CACTATTATTCAGGGAAGATTGAATCAGAATCGATTTGCTTCACTGTTCTTCTGGAAGACCAAAT
1 CACTATTCTTCAGGGAAGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAAT
* * * * * *
356144 CT-AAATGAAAAAGCATCTGCTCCACTACTCTTTAGAGGAGATCATACTCGAGAAAATTTTGATC
66 CTGAAA-GAAGAAGAATATGCTCCACTACTCTTTAGGGGAGATCAAACTCGAGAAAACTTTGATC
356208 CACTT
130 CACTT
*
356213 CACTATTCTTCAGGGAATATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAAT
1 CACTATTCTTCAGGGAAGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAAT
* * *
356278 CTGAAAGAAGAAGAATATGCTCCACTACTCTTTAGGGGAGATCAAACTCGAGAAATCTTTAATCT
66 CTGAAAGAAGAAGAATATGCTCCACTACTCTTTAGGGGAGATCAAACTCGAGAAAACTTTGATCC
356343 ACTT
131 ACTT
* * ** * * * *
356347 AAATGCTCTTCAGGAAAGATTGAAT-TGAACTTGATTTGCTTCGCTGCTCTTCAGGAAGACCAAA
1 CACTATTCTTCAGGGAAGATTGAATCAGAA-TCGATTTGCTTCACTGCTCTTCAGGAAGACCAAA
356411 TCTGAAA
65 TCTGAAA
356418 ATCAAACATT
Statistics
Matches: 652, Mismatches: 83, Indels: 10
0.88 0.11 0.01
Matches are distributed among these distances:
132 3 0.00
133 119 0.18
134 526 0.81
135 4 0.01
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.30
Consensus pattern (134 bp):
CACTATTCTTCAGGGAAGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAAT
CTGAAAGAAGAAGAATATGCTCCACTACTCTTTAGGGGAGATCAAACTCGAGAAAACTTTGATCC
ACTT
Found at i:356236 original size:401 final size:402
Alignment explanation
Indices: 355510--356417 Score: 1301
Period size: 401 Copynumber: 2.3 Consensus size: 402
355500 CTGTTTCTGC
* * *
355510 AGGGTAGATCAGA-TCGAG-AAACATTGAAT-CA-TTCCACTGTTCTTCAGGGAAGATTGAATCG
1 AGGGGAGATCAGACTCGAGAAAACTTTG-ATCCACTT-CACTGCTCTTCAGGGAAGATTGAATCG
* * * **
355571 GAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATATGAAAGAATAAGAATCGACTCCATTA
64 AAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCGACTCCACCA
* * * * *
355636 CTCTTTAGGGGAGATCATACTTGAGAAAACTTTGATCCATTTCACTATTCTTTAGGGAAGATTGA
129 CTCTTTAGGGGAGATCAAACTCGAGAAAACTTTGATCCACTTCACTATTATTCAGGGAAGATTGA
* * * * * ***
355701 ATCATAATCGATTTGCTTCACTGTTCTTCAGGATGACTAAATTTGAAAGAAGAATTGTATGCTCC
194 ATCAGAATCGATTTGCTTCACTGTTCTTCAGGAAGACCAAATCTGAAAGAAAAAGCATATGCTCC
*
355766 ACTGCTCTTTATGGGAGATCAGACTCGAGAAAACTTTGATCCACTTCACTATTCTTCAAGAAATA
259 ACTACTCTTTATGGGAGATCAGACTCGAGAAAACTTTGATCCACTTCACTATTCTTCAAGAAATA
* *
355831 TTGAATCAGAATTGATTTGCTTCACTTCTCTTCAGGAAGACCAAATCTGAAAGAAGAAAAATATG
324 TTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAAAATATG
355896 CTCCACTACTCTTT
389 CTCCACTACTCTTT
* *
355910 AGGGGAGATCAGACTCGAGAAAACTTTGATCCACTTCACTGCTCTTTAGGGAAGATTGAATCAAA
1 AGGGGAGATCAGACTCGAGAAAACTTTGATCCACTTCACTGCTCTTCAGGGAAGATTGAATCGAA
* *
355975 ATCGATTTGCTTCACTTCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATATG-CTCCACCAC
66 ATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAAT-CGACTCCACCAC
356039 TCTTTA-GGGAGATCAAACTCGAGAAAACTTTGATCCACTTCACTATTATTCAGGGAAGATTGAA
130 TCTTTAGGGGAGATCAAACTCGAGAAAACTTTGATCCACTTCACTATTATTCAGGGAAGATTGAA
* *
356103 TCAGAATCGATTTGCTTCACTGTTCTTCTGGAAGACCAAATCT-AAATGAAAAAGCATCTGCTCC
195 TCAGAATCGATTTGCTTCACTGTTCTTCAGGAAGACCAAATCTGAAA-GAAAAAGCATATGCTCC
* * * *
356167 ACTACTCTTTA-GAGGAGATCATACTCGAGAAAATTTTGATCCACTTCACTATTCTTCAGGGAAT
259 ACTACTCTTTATG-GGAGATCAGACTCGAGAAAACTTTGATCCACTTCACTATTCTTCAAGAAAT
*
356231 ATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATAT
323 ATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAAAATAT
356296 GCTCCACTACTCTTT
388 GCTCCACTACTCTTT
* * * * * * * *
356311 AGGGGAGATCAAACTCGAGAAATCTTTAATCTACTTAAATGCTCTTCAGGAAAGATTGAATTGAA
1 AGGGGAGATCAGACTCGAGAAAACTTTGATCCACTTCACTGCTCTTCAGGGAAGATTGAATCGAA
* * *
356376 CTTGATTTGCTTCGCTGCTCTTCAGGAAGACCAAATCTGAAA
66 ATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAA
356418 ATCAAACATT
Statistics
Matches: 452, Mismatches: 49, Indels: 13
0.88 0.10 0.03
Matches are distributed among these distances:
400 16 0.04
401 337 0.75
402 96 0.21
403 3 0.01
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (402 bp):
AGGGGAGATCAGACTCGAGAAAACTTTGATCCACTTCACTGCTCTTCAGGGAAGATTGAATCGAA
ATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCGACTCCACCACT
CTTTAGGGGAGATCAAACTCGAGAAAACTTTGATCCACTTCACTATTATTCAGGGAAGATTGAAT
CAGAATCGATTTGCTTCACTGTTCTTCAGGAAGACCAAATCTGAAAGAAAAAGCATATGCTCCAC
TACTCTTTATGGGAGATCAGACTCGAGAAAACTTTGATCCACTTCACTATTCTTCAAGAAATATT
GAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAAAATATGCT
CCACTACTCTTT
Found at i:356991 original size:45 final size:45
Alignment explanation
Indices: 356950--357052 Score: 134
Period size: 45 Copynumber: 2.3 Consensus size: 45
356940 ATGACAATAT
* * * * *
356950 TAAAAGATTGATTCCTCTTTACGAGAAATTCAAGGAAGACAACAC
1 TAAAAAATTGACTCCTATTCACGAGAAAATCAAGGAAGACAACAC
*
356995 TAAAAAATTGACTCCTATTCGCGAGAAAATCAAGGAAGACAACAC
1 TAAAAAATTGACTCCTATTCACGAGAAAATCAAGGAAGACAACAC
* *
357040 TATAATATTGACT
1 TAAAAAATTGACT
357053 ATCTTAGATG
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 50 1.00
ACGTcount: A:0.44, C:0.17, G:0.15, T:0.24
Consensus pattern (45 bp):
TAAAAAATTGACTCCTATTCACGAGAAAATCAAGGAAGACAACAC
Found at i:357636 original size:10 final size:10
Alignment explanation
Indices: 357617--357668 Score: 54
Period size: 10 Copynumber: 5.4 Consensus size: 10
357607 TCTGTAAAAA
357617 AAATAATAAT
1 AAATAATAAT
*
357627 AAATACTAAT
1 AAATAATAAT
357637 AAATAAT-AT
1 AAATAATAAT
**
357646 TGATAATAAT
1 AAATAATAAT
*
357656 AAAAAATAA-
1 AAATAATAAT
357665 AAAT
1 AAAT
357669 GGGTCTCCAG
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
9 10 0.30
10 23 0.70
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (10 bp):
AAATAATAAT
Found at i:359746 original size:19 final size:21
Alignment explanation
Indices: 359722--359773 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
359712 CGGCCAAGAG
*
359722 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
359741 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
359762 CATGTATTTTCA
1 CATGTATTTTCA
359774 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:360519 original size:8 final size:8
Alignment explanation
Indices: 360508--360532 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
360498 GAAAAAAATC
360508 AGAAAAGA
1 AGAAAAGA
360516 AGAAAAGA
1 AGAAAAGA
360524 AGAAAAGA
1 AGAAAAGA
360532 A
1 A
360533 AAGAAAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (8 bp):
AGAAAAGA
Found at i:363877 original size:19 final size:21
Alignment explanation
Indices: 363853--363904 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
363843 CGGCCAAGAG
*
363853 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
363872 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
363893 CATGTATTTTCA
1 CATGTATTTTCA
363905 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:365139 original size:30 final size:30
Alignment explanation
Indices: 365083--365140 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
365073 GATTTATTTA
* *
365083 GTGACCAAATTATAAATTTGGTAAAGTTTG
1 GTGACCAAAGTATAAATTTGGAAAAGTTTG
365113 GTGACCAAAGTATAAACTTT-GAAAAGTT
1 GTGACCAAAGTATAAA-TTTGGAAAAGTT
365141 CATAAAACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 22 0.88
31 3 0.12
ACGTcount: A:0.40, C:0.09, G:0.19, T:0.33
Consensus pattern (30 bp):
GTGACCAAAGTATAAATTTGGAAAAGTTTG
Found at i:380434 original size:3 final size:3
Alignment explanation
Indices: 380426--380507 Score: 98
Period size: 3 Copynumber: 27.7 Consensus size: 3
380416 CATCCATTTG
* *
380426 TTA TTA TTA TTA TTA TT- TTA TTTA TTA TTA TTG TTA TT- TTA TAA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
*
380470 TTA -TA TTA TTA TTA TTTA TTA ATA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TT
380508 TACAGACCCA
Statistics
Matches: 68, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
2 6 0.09
3 56 0.82
4 6 0.09
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:380479 original size:22 final size:23
Alignment explanation
Indices: 380426--380508 Score: 113
Period size: 21 Copynumber: 3.8 Consensus size: 23
380416 CATCCATTTG
380426 TTATTATTATTATTATTTTAT--
1 TTATTATTATTATTATTTTATAA
*
380447 TTATTATTATTGTTATTTTATAA
1 TTATTATTATTATTATTTTATAA
380470 TTA-TATTATTATTA-TTTATTAA
1 TTATTATTATTATTATTTTA-TAA
380492 -TATTATTATTATTATTT
1 TTATTATTATTATTATTT
380509 ACAGACCCAA
Statistics
Matches: 55, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
21 26 0.47
22 24 0.44
23 5 0.09
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.67
Consensus pattern (23 bp):
TTATTATTATTATTATTTTATAA
Found at i:380485 original size:38 final size:39
Alignment explanation
Indices: 380426--380506 Score: 112
Period size: 38 Copynumber: 2.1 Consensus size: 39
380416 CATCCATTTG
* * *
380426 TTATTATTATTATTATTTTATTTATTATTATTGTTATT-
1 TTATAATTATTATTATTTTATTTATTAATATTATTATTA
380464 TTATAATTA-TATTATTATTATTTATTAATATTATTATTA
1 TTATAATTATTATTATT-TTATTTATTAATATTATTATTA
380503 TTAT
1 TTAT
380507 TTACAGACCC
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
37 7 0.18
38 27 0.71
39 4 0.11
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (39 bp):
TTATAATTATTATTATTTTATTTATTAATATTATTATTA
Found at i:380509 original size:22 final size:22
Alignment explanation
Indices: 380427--380509 Score: 102
Period size: 22 Copynumber: 3.8 Consensus size: 22
380417 ATCCATTTGT
380427 TATTATTATTATTATTTTATT--
1 TATTATTATTATTA-TTTATTAA
*
380448 TATTATTATTGTTATTT-TATAA
1 TATTATTATTATTATTTAT-TAA
380470 T-TATATTATTATTATTTATTAA
1 TAT-TATTATTATTATTTATTAA
380492 TATTATTATTATTATTTA
1 TATTATTATTATTATTTA
380510 CAGACCCAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
19 1 0.02
20 4 0.07
21 14 0.26
22 33 0.61
23 2 0.04
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (22 bp):
TATTATTATTATTATTTATTAA
Found at i:381905 original size:15 final size:15
Alignment explanation
Indices: 381885--381933 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 15
381875 TTGTTTAGCC
381885 ATATTTTAATTTTAT
1 ATATTTTAATTTTAT
*
381900 ATA-TTT-ATTTTAA
1 ATATTTTAATTTTAT
381913 ATATATTTAATTATTAT
1 ATAT-TTTAATT-TTAT
381930 -TATT
1 ATATT
381934 ATTATTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
13 9 0.32
14 3 0.11
15 7 0.25
16 6 0.21
17 3 0.11
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
ATATTTTAATTTTAT
Found at i:381985 original size:49 final size:49
Alignment explanation
Indices: 381910--382007 Score: 114
Period size: 49 Copynumber: 2.0 Consensus size: 49
381900 ATATTTATTT
*
381910 TAAATATATTTAATTATTATTATTATTAT-TATT-TAATCATATATATAA
1 TAAATATATTTAATTATTATTATTATT-TCTATTAAAATCATATATATAA
*
381958 TAAATAATATTT-ATCTATTAGTT-TTATTTCTATTAAAATCATATTTATAA
1 TAAAT-ATATTTAAT-TATTA-TTATTATTTCTATTAAAATCATATATATAA
382008 ATTTAATTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
48 8 0.19
49 20 0.47
50 15 0.35
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.53
Consensus pattern (49 bp):
TAAATATATTTAATTATTATTATTATTTCTATTAAAATCATATATATAA
Found at i:391046 original size:113 final size:113
Alignment explanation
Indices: 390848--391392 Score: 824
Period size: 113 Copynumber: 4.9 Consensus size: 113
390838 TAGCAAAGAT
* * *
390848 TTGAATCCATCATTCGATGGATCAACTGTTCCAGAAGAAGTTCATAATGAGAATAACTCATATGA
1 TTGAATTCATCATTCGATGGATCAACTGTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGA
* *
390913 AGAAGGAAAAAGAAGTTCATAATAAGAAGAACTTGTTTAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGC
*
390961 TTGAATTCATCATTCGATGGATCCACTGTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGA
1 TTGAATTCATCATTCGATGGATCAACTGTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGA
* *
391026 AGAAGGAAAAAGAAGTTCATAATGAGAAGAACTTGTTTAACATTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGC
*
391074 TTAAATTCATCATTCGATGGATCAACTGTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGA
1 TTGAATTCATCATTCGATGGATCAACTGTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGA
* **
391139 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTTAT
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGC
*
391187 TTGAATCCATCATTCGAT-G-------GTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGA
1 TTGAATTCATCATTCGATGGATCAACTGTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGA
*
391244 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGC
* * * * *
391292 TCGAATTCGTCACTCAATGGATCAACT-TTCCCAG-AGAAAGTTCATAATGAGAAGAACTTATCT
1 TTGAATTCATCATTCGATGGATCAACTGTT-CCAGAAG-AAGTTCATAATGAGAAGAACTCATCT
391355 GAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
64 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
391393 CAACATTTGC
Statistics
Matches: 397, Mismatches: 25, Indels: 21
0.90 0.06 0.05
Matches are distributed among these distances:
105 95 0.24
106 1 0.00
112 39 0.10
113 262 0.66
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (113 bp):
TTGAATTCATCATTCGATGGATCAACTGTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGC
Found at i:391348 original size:218 final size:220
Alignment explanation
Indices: 390855--391392 Score: 798
Period size: 218 Copynumber: 2.4 Consensus size: 220
390845 GATTTGAATC
* * * *
390855 CATCATTCGATGGATCAACTGTTCCAGAAGAAGTTCATAATGAGAATAACTCATATGAAGAAGGA
1 CATCACTCAATGGATCAACTGTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * * *
390920 AAAAGAAGTTCATAATAAGAAGAACTTGTTTAACCTTTTGCTTGAATTCATCATTCGATGGATCC
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTACTTGAATCCATCATTCGATGG----
390985 ACTGTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAAAAGAAGTTCATAATG
127 -C-GTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAAAAGAAGTTCATAATG
* *
391050 AGAAGAACTTGTTTAACATTTTGCTTAAATT
190 AGAAGAACTTGTTCAACATTTTGCTCAAATT
* *
391081 CATCATTCGATGGATCAACTGTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCACTCAATGGATCAACTGTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *
391146 AGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTTATTTGAATCCATCATTCGAT-G-GTT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTACTTGAATCCATCATTCGATGGCGTT
*
391209 CCAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
131 CCAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAAAAGAAGTTCATAATGAGAAGA
* *
391274 ACTTGTTCAACCTTTTGCTCGAATT
196 ACTTGTTCAACATTTTGCTCAAATT
* *
391299 CGTCACTCAATGGATCAACT-TTCCCAG-AGAAAGTTCATAATGAGAAGAACTTATCTGAAG-AG
1 CATCACTCAATGGATCAACTGTT-CCAGAAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAG
391361 GAAGAAGAAGTTCATAATGAGAAGAACTTGTT
64 GAAGAAGAAGTTCATAATGAGAAGAACTTGTT
391393 CAACATTTGC
Statistics
Matches: 292, Mismatches: 18, Indels: 13
0.90 0.06 0.04
Matches are distributed among these distances:
217 37 0.13
218 138 0.47
225 1 0.00
226 116 0.40
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.28
Consensus pattern (220 bp):
CATCACTCAATGGATCAACTGTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTACTTGAATCCATCATTCGATGGCGTT
CCAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAAAAGAAGTTCATAATGAGAAGA
ACTTGTTCAACATTTTGCTCAAATT
Found at i:391393 original size:20 final size:20
Alignment explanation
Indices: 391331--391394 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
391321 CCCAGAGAAA
391331 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
* ***
391351 -ATC-TGAA-GAGGAAGAAGAA
1 GTTCAT-AATGA-GAAGAACTT
391370 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
391390 GTTCA
1 GTTCA
391395 ACATTTGCAT
Statistics
Matches: 31, Mismatches: 8, Indels: 10
0.63 0.16 0.20
Matches are distributed among these distances:
18 3 0.10
19 10 0.32
20 15 0.48
21 3 0.10
ACGTcount: A:0.42, C:0.09, G:0.23, T:0.25
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:392105 original size:3 final size:3
Alignment explanation
Indices: 392097--392181 Score: 104
Period size: 3 Copynumber: 28.7 Consensus size: 3
392087 TTTCATCCAT
*
392097 TTA TTA TTA TTA TTA TTA TT- TTA TTTA TTA CTA TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
* *
392141 TAA TTA -TA TTA TTA TTA TTTA TTA ATA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TT
392182 TACAGACCCA
Statistics
Matches: 71, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
2 6 0.08
3 59 0.83
4 6 0.08
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:392147 original size:38 final size:39
Alignment explanation
Indices: 392097--392180 Score: 127
Period size: 38 Copynumber: 2.2 Consensus size: 39
392087 TTTCATCCAT
* *
392097 TTATTATTATTATTATTATT-TTATTTATTACTATTATTA
1 TTATTATAATTA-TATTATTATTATTTATTAATATTATTA
392136 TT-TTATAATTATATTATTATTATTTATTAATATTATTA
1 TTATTATAATTATATTATTATTATTTATTAATATTATTA
392174 TTATTAT
1 TTATTAT
392181 TTACAGACCC
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
37 7 0.17
38 28 0.68
39 6 0.15
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.65
Consensus pattern (39 bp):
TTATTATAATTATATTATTATTATTTATTAATATTATTA
Found at i:392183 original size:22 final size:22
Alignment explanation
Indices: 392101--392183 Score: 102
Period size: 22 Copynumber: 3.8 Consensus size: 22
392091 ATCCATTTAT
392101 TATTATTATTATTATTTTATT--
1 TATTATTATTATTA-TTTATTAA
*
392122 TATTACTATTATTATTT-TATAA
1 TATTATTATTATTATTTAT-TAA
392144 T-TATATTATTATTATTTATTAA
1 TAT-TATTATTATTATTTATTAA
392166 TATTATTATTATTATTTA
1 TATTATTATTATTATTTA
392184 CAGACCCAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
19 1 0.02
20 4 0.07
21 14 0.26
22 33 0.61
23 2 0.04
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (22 bp):
TATTATTATTATTATTTATTAA
Found at i:393571 original size:15 final size:15
Alignment explanation
Indices: 393551--393599 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 15
393541 TTGTTTAGCC
393551 ATATTTTAATTTTAT
1 ATATTTTAATTTTAT
*
393566 ATA-TTT-ATTTTAA
1 ATATTTTAATTTTAT
393579 ATATATTTAATTATTAT
1 ATAT-TTTAATT-TTAT
393596 -TATT
1 ATATT
393600 ATTATTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
13 9 0.32
14 3 0.11
15 7 0.25
16 6 0.21
17 3 0.11
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
ATATTTTAATTTTAT
Found at i:395296 original size:21 final size:21
Alignment explanation
Indices: 395202--395289 Score: 149
Period size: 21 Copynumber: 4.2 Consensus size: 21
395192 ATTCTGACTA
*
395202 TCGCATTGCGATTTCCCAAAT
1 TCGCGTTGCGATTTCCCAAAT
395223 TCGCGTTGCGATTTCCCAAAT
1 TCGCGTTGCGATTTCCCAAAT
395244 TCGCGTTGCGATTTCCCAAAT
1 TCGCGTTGCGATTTCCCAAAT
* *
395265 TCGCGTTGCGATTTTCCTAAT
1 TCGCGTTGCGATTTCCCAAAT
395286 TCGC
1 TCGC
395290 AATGCGAATA
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 64 1.00
ACGTcount: A:0.18, C:0.28, G:0.18, T:0.35
Consensus pattern (21 bp):
TCGCGTTGCGATTTCCCAAAT
Found at i:395311 original size:20 final size:20
Alignment explanation
Indices: 395286--395432 Score: 240
Period size: 20 Copynumber: 7.3 Consensus size: 20
395276 TTTTCCTAAT
*
395286 TCGCAATGCGAATACATAAA
1 TCGCAATGCGAATACGTAAA
* **
395306 TCGCAACGCGAATTTGGTAAA
1 TCGCAATGCGAA-TACGTAAA
395327 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
395347 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
395367 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
395387 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
395407 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
395427 TCGCAA
1 TCGCAA
395433 CGAGATTCTG
Statistics
Matches: 117, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
20 101 0.86
21 16 0.14
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:395630 original size:22 final size:22
Alignment explanation
Indices: 395605--395665 Score: 97
Period size: 22 Copynumber: 2.8 Consensus size: 22
395595 TATCACTCTC
*
395605 TCCAGCGACATCCGTTCCTATA
1 TCCAACGACATCCGTTCCTATA
*
395627 TCCAACGACATTCGTTCCTATA
1 TCCAACGACATCCGTTCCTATA
395649 TCCAACGACATCC-TTCC
1 TCCAACGACATCCGTTCC
395666 CCATCCAGCA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
21 4 0.11
22 32 0.89
ACGTcount: A:0.25, C:0.38, G:0.10, T:0.28
Consensus pattern (22 bp):
TCCAACGACATCCGTTCCTATA
Found at i:398674 original size:20 final size:20
Alignment explanation
Indices: 398649--398742 Score: 145
Period size: 20 Copynumber: 4.7 Consensus size: 20
398639 GACATTCATT
398649 TGACTATCGCAACGC-GAATA
1 TGACTATCGCAACGCGGAA-A
*
398669 TGACTATCGCAACACGGAAA
1 TGACTATCGCAACGCGGAAA
* *
398689 TGACTATCGCAATGCGGAAT
1 TGACTATCGCAACGCGGAAA
398709 TGACTATCGCAACGCGGAAA
1 TGACTATCGCAACGCGGAAA
398729 TGACTATCGCAACG
1 TGACTATCGCAACG
398743 AGAGAATCGC
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
20 64 0.96
21 3 0.04
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.19
Consensus pattern (20 bp):
TGACTATCGCAACGCGGAAA
Found at i:398764 original size:33 final size:36
Alignment explanation
Indices: 398714--398803 Score: 96
Period size: 38 Copynumber: 2.5 Consensus size: 36
398704 GGAATTGACT
* ** *
398714 ATCGCAACGCGGAAATGACTATCGCAA-CG-A-GAGA
1 ATCGCAATGC-GAAATGAAAATCGCAAGCGAATGAAA
398748 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAA
398786 ATCGCAATGCGAAATGAA
1 ATCGCAATGCGAAATGAA
398804 CACGCGAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
33 14 0.30
34 9 0.19
35 2 0.04
37 1 0.02
38 21 0.45
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.14
Consensus pattern (36 bp):
ATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAA
Found at i:398771 original size:19 final size:19
Alignment explanation
Indices: 398747--398803 Score: 114
Period size: 19 Copynumber: 3.0 Consensus size: 19
398737 GCAACGAGAG
398747 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
398766 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
398785 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
398804 CACGCGAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 38 1.00
ACGTcount: A:0.47, C:0.16, G:0.21, T:0.16
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:398891 original size:33 final size:34
Alignment explanation
Indices: 398822--398897 Score: 118
Period size: 33 Copynumber: 2.3 Consensus size: 34
398812 ATTAGTTTCG
*
398822 CGTTGCGATTTTCATTTTCGCATTGCAATTCACT
1 CGTTGCGATTTCCATTTTCGCATTGCAATTCACT
* *
398856 CGTTGCGATTTCCATTTT-GCATTGCGATTCTCT
1 CGTTGCGATTTCCATTTTCGCATTGCAATTCACT
398889 CGTTGCGAT
1 CGTTGCGAT
398898 AGTCATTTCC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 22 0.56
34 17 0.44
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.43
Consensus pattern (34 bp):
CGTTGCGATTTCCATTTTCGCATTGCAATTCACT
Found at i:399038 original size:14 final size:14
Alignment explanation
Indices: 399019--399055 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
399009 CATCAATTAA
399019 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
399033 ACAAATCATCTTTT
1 ACAAATCAACATTT
399047 ACAAATCAA
1 ACAAATCAA
399056 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:401022 original size:20 final size:20
Alignment explanation
Indices: 400999--401105 Score: 178
Period size: 20 Copynumber: 5.3 Consensus size: 20
400989 GAAACTTAAA
*
400999 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
401019 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
*
401039 ATCGCAATGCGAAAATGGCT
1 ATCGCAATGCGAAAATGACT
401059 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
**
401079 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAAAATGACT
401099 ATCGCAA
1 ATCGCAA
401106 CGAGAGAATC
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 82 1.00
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:401122 original size:34 final size:34
Alignment explanation
Indices: 401079--401191 Score: 156
Period size: 34 Copynumber: 3.4 Consensus size: 34
401069 GAAAATGACT
401079 ATCGCAATGCGAATTTGACTATCGCAACGAGAGA
1 ATCGCAATGCGAATTTGACTATCGCAACGAGAGA
* ** * * *
401113 ATCGCAATGCGAA-ATGAAAATCGCAACAACAAA
1 ATCGCAATGCGAATTTGACTATCGCAACGAGAGA
*
401146 ATCGCAATGCAAATTTGACTATCGCAACGAGAGA
1 ATCGCAATGCGAATTTGACTATCGCAACGAGAGA
401180 ATCGCAATGCGA
1 ATCGCAATGCGA
401192 TTTTCATTTT
Statistics
Matches: 64, Mismatches: 14, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
33 26 0.41
34 38 0.59
ACGTcount: A:0.41, C:0.21, G:0.20, T:0.18
Consensus pattern (34 bp):
ATCGCAATGCGAATTTGACTATCGCAACGAGAGA
Found at i:401271 original size:20 final size:20
Alignment explanation
Indices: 401219--401362 Score: 165
Period size: 20 Copynumber: 7.5 Consensus size: 20
401209 GATTCTTTCG
** *
401219 TTGCGATAGTCAAATTCACA
1 TTGCGATAGTCATTTTCGCA
* *
401239 TTACGATAGTCATTTTCACA
1 TTGCGATAGTCATTTTCGCA
401259 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
401279 TTGCGTTAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
* *
401299 TTACGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
*
401313 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
401333 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
401353 TTGCGATAGT
1 TTGCGATAGT
401363 AAACTATTCT
Statistics
Matches: 106, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
14 6 0.06
16 6 0.06
18 6 0.06
20 88 0.83
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.40
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:401289 original size:40 final size:40
Alignment explanation
Indices: 401181--401362 Score: 165
Period size: 40 Copynumber: 4.9 Consensus size: 40
401171 AACGAGAGAA
* **
401181 TCGCAATGCGATTTTCATTTT-GCATTGCGAT--TC--TT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
** * *
401216 TCG--TTGCGATAGTCAAATTCACATTACGATAGTCATTT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
* *
401254 TCACATTGCGATAGTCATTTTCGCATTGCGTTAGTCATTT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
* *
401294 TCGCATTACGAT--TC--TCTCG--TTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
*
401328 TCGCGTTGCGATAGTCATTTTCGCATTGCGATAGT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGT
401363 AAACTATTCT
Statistics
Matches: 114, Mismatches: 20, Indels: 21
0.74 0.13 0.14
Matches are distributed among these distances:
33 11 0.10
34 32 0.28
35 3 0.03
36 8 0.07
38 10 0.09
40 50 0.44
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.41
Consensus pattern (40 bp):
TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
Found at i:403278 original size:20 final size:20
Alignment explanation
Indices: 403220--403289 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
403210 GAAACTTTAA
* **
403220 ATCGCAACACGAAAATGAAA
1 ATCGCAACGCGAAAATGACT
*
403240 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
403260 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
403280 ATCGCAACGC
1 ATCGCAACGC
403290 AAGAATCGCA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.41, C:0.26, G:0.17, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:403358 original size:20 final size:20
Alignment explanation
Indices: 403333--403379 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
403323 GATTTTCTCG
403333 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
** *
403353 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCA
403373 TTGCGAT
1 TTGCGAT
403380 TCACTCGTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:404024 original size:21 final size:21
Alignment explanation
Indices: 404000--404045 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
403990 TATTCGCATT
404000 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
404021 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
404042 GCGA
1 GCGA
404046 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:413254 original size:27 final size:27
Alignment explanation
Indices: 413224--413288 Score: 114
Period size: 27 Copynumber: 2.4 Consensus size: 27
413214 TTTGAATTTA
413224 TATAGTATA-AATTATATAAATATCAAC
1 TATAGTATATAA-TATATAAATATCAAC
413251 TATAGTATATAATATATAAATATCAAC
1 TATAGTATATAATATATAAATATCAAC
413278 TATAGTATATA
1 TATAGTATATA
413289 GTTTATATGT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
27 35 0.95
28 2 0.05
ACGTcount: A:0.51, C:0.06, G:0.05, T:0.38
Consensus pattern (27 bp):
TATAGTATATAATATATAAATATCAAC
Found at i:413295 original size:27 final size:27
Alignment explanation
Indices: 413224--413469 Score: 107
Period size: 27 Copynumber: 8.9 Consensus size: 27
413214 TTTGAATTTA
*
413224 TATAGTATA-AATTATATAAATATCAAC
1 TATAGTATATAGTT-TATAAATATCAAC
* *
413251 TATAGTATATAATATATAAATATCAAC
1 TATAGTATATAGTTTATAAATATCAAC
* *
413278 TATAGTATATAGTTTAT--ATGTAAAC
1 TATAGTATATAGTTTATAAATATCAAC
* *
413303 TATAGTTTATATA-TATATATATAT-ATA-
1 TATAG--TATATAGTTTATAAATATCA-AC
*
413330 TATA-TATATAGTTTTTATATGTAAT-TCATATG
1 TATAGTATATAG--TTTATA---AATATCA-A-C
* * **
413362 TAAACTATATAGTATATATAGTTTAT-ATAC
1 TATAGTATATAGT-T-TATA-AATATCA-AC
* *
413392 -ATAATATATAGTATATAAATATCAAC
1 TATAGTATATAGTTTATAAATATCAAC
* * *
413418 TATAGTATATAGTATGTAAATATAAAC
1 TATAGTATATAGTTTATAAATATCAAC
*
413445 TATAGTTTATATAGTTTATATATAT
1 TATAG--TATATAGTTTATAAATAT
413470 AGTATATAGT
Statistics
Matches: 171, Mismatches: 25, Indels: 44
0.71 0.10 0.18
Matches are distributed among these distances:
24 6 0.04
25 11 0.06
26 9 0.05
27 86 0.50
28 7 0.04
29 26 0.15
30 5 0.03
31 5 0.03
32 5 0.03
33 11 0.06
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (27 bp):
TATAGTATATAGTTTATAAATATCAAC
Found at i:413333 original size:20 final size:20
Alignment explanation
Indices: 413310--413764 Score: 94
Period size: 22 Copynumber: 21.4 Consensus size: 20
413300 AACTATAGTT
413310 TATATATATATATATATATA
1 TATATATATATATATATATA
* * *
413330 TATATATATAGTTTTTATATG
1 TATATATATA-TATATATATA
* *
413351 TA-AT-TCATATGTAAACTATA
1 TATATAT-ATATATATA-TATA
* *
413371 TAGTATATATAGTTTATATACA
1 TA-TATATATA-TATATATATA
*
413393 TA-ATATATAGTATATAAATA
1 TATATATATA-TATATATATA
*
413413 TCA-ACTATAGTATATAGTATGTA
1 T-ATA-TATA-TATATA-TATATA
* * *
413436 AATATAAACTATAGTTTATATA
1 TATATATA-TATA-TATATATA
*
413458 GTTTATATATATAGTATATAGTA
1 -TATATATATATA-TATATA-TA
*
413481 T-TCATATATATAGTATATACTT
1 TAT-ATATATATA-TATATA-TA
* * *
413503 TAAATTTATATAGTATAAAT-
1 TATATATATATA-TATATATA
*
413523 TATATA-AGTATAAACTATAT-
1 TATATATA-TATATA-TATATA
* *
413543 TATATAGTATATAAATA-ACA
1 TATATA-TATATATATATATA
413563 -AT-TATAGTATATAGTATATA
1 TATATATA-TATATA-TATATA
* *
413583 AATATCA-ACTATAGTATATAGTT
1 TATAT-ATA-TATA-TATATA-TA
* *
413606 TATATATATATATAGTTTTTA
1 TATATATATATATA-TATATA
* ** *
413627 TGTATAGT-TCATACGTAAACTA
1 TATATA-TAT-ATATATATA-TA
*
413649 TATAGTATATATAGTTTATATA
1 TATA-TATATATA-TATATATA
* *
413671 TACA-ATATATAGTATATAAA
1 TATATATATATA-TATATATA
**
413691 TATCCACTATAGTATATAGTATA
1 TATATA-TATA-TATATA-TATA
* * *
413714 TAAATATAAACTATAGTTTATA
1 TATATATATA-TATA-TATATA
*
413736 TAGTTTATATATATAGTATATA
1 TA-TATATATATATA-TATATA
413758 T-TATATA
1 TATATATA
413765 AGTAGTTTAT
Statistics
Matches: 322, Mismatches: 69, Indels: 88
0.67 0.14 0.18
Matches are distributed among these distances:
17 2 0.01
18 7 0.02
19 11 0.03
20 79 0.25
21 32 0.10
22 142 0.44
23 49 0.15
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.44
Consensus pattern (20 bp):
TATATATATATATATATATA
Found at i:413470 original size:13 final size:13
Alignment explanation
Indices: 413278--413870 Score: 111
Period size: 13 Copynumber: 43.8 Consensus size: 13
413268 AAATATCAAC
*
413278 TATAGTATATAGTT
1 TATA-TATATAGTA
* * *
413292 TATATGTAAACTA
1 TATATATATAGTA
*
413305 TAGTTTATATA-TA
1 TA-TATATATAGTA
413318 TATATATATA-TA
1 TATATATATAGTA
*
413330 TATATATATAGTT
1 TATATATATAGTA
* * *
413343 TTTATATGTAATTCA
1 TATATATAT-AGT-A
* *
413358 TATGTAAACTA-TA
1 TATATATA-TAGTA
*
413371 TAGTATATATAGTT
1 TA-TATATATAGTA
* *
413385 TATATACATAATA
1 TATATATATAGTA
*
413398 TATAGTATATA-AA
1 TATA-TATATAGTA
413411 TATCA-ACTATAGTA
1 TAT-ATA-TATAGTA
* *
413425 TATAGTATGTA-AA
1 TATA-TATATAGTA
*
413438 TATAAACTATAGTTTA
1 TATATA-TATAG--TA
*
413454 TATAGTTTATA-TA
1 TATA-TATATAGTA
413467 TATAGTATATAGTA
1 TATA-TATATAGTA
413481 TTCATATATATAGTA
1 -T-ATATATATAGTA
* * *
413496 TATACTTTAAATTTA
1 TATA-TATATA-GTA
* *
413511 TATAGTATAAATTA
1 TATA-TATATAGTA
* *
413525 TATAAGTATAAACTA
1 TAT-A-TATATAGTA
413540 TAT-TATATAGTA
1 TATATATATAGTA
* **
413552 TATAAATA-ACAA
1 TATATATATAGTA
413564 TTATAGTATATAGTA
1 -TATA-TATATAGTA
*
413579 TATAAATATCA--A
1 TATATATAT-AGTA
*
413591 CTATAGTATATAGTT
1 -TATA-TATATAGTA
413606 TATATATATA-TA
1 TATATATATAGTA
* *
413618 TAGTTTTTAT-GTA
1 TA-TATATATAGTA
*
413631 TAGT-TCATA-CGTA
1 TA-TAT-ATATAGTA
413644 -A-ACTATATAGTA
1 TATA-TATATAGTA
413656 TATATAGTTTATA-TA
1 TATATA---TATAGTA
*
413671 TACAATATATAGTA
1 TA-TATATATAGTA
* *
413685 TATAAATATCCACTA
1 TATATATAT--AGTA
413700 TAGTATATAGTA-TA
1 TA-TATATA-TAGTA
* * *
413714 TAAATATAAACTA
1 TATATATATAGTA
* *
413727 TAGTTTATATAGTT
1 TA-TATATATAGTA
413741 TATATATATAGTA
1 TATATATATAGTA
413754 TATATTATATAAGTA
1 TATA-TATAT-AGTA
* *
413769 GTTTATATA-ATTCA
1 -TATATATATAGT-A
* *
413783 T-TA-ATAAACTA
1 TATATATATAGTA
413794 TATATAT-T-GTTCA
1 TATATATATAG-T-A
* *
413807 TATGTAAACTA-TA
1 TATATATA-TAGTA
*
413820 TAGTATATATAGTT
1 TA-TATATATAGTA
*
413834 TATATATATAGTT
1 TATATATATAGTA
*
413847 TATATATGTAGTA
1 TATATATATAGTA
413860 TATATTATATA
1 TATA-TATATA
413871 AATAGTTTAT
Statistics
Matches: 428, Mismatches: 83, Indels: 136
0.66 0.13 0.21
Matches are distributed among these distances:
11 8 0.02
12 51 0.12
13 182 0.43
14 97 0.23
15 61 0.14
16 28 0.07
17 1 0.00
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (13 bp):
TATATATATAGTA
Found at i:413541 original size:27 final size:27
Alignment explanation
Indices: 413511--413750 Score: 165
Period size: 27 Copynumber: 8.9 Consensus size: 27
413501 TTTAAATTTA
* * *
413511 TATAGTATAAATTATATAAGTATAAAC
1 TATAGTATATAGTATATAAATATAAAC
* *
413538 TATATTATATAGTATATAAATA-ACAAT
1 TATAGTATATAGTATATAAATATA-AAC
*
413565 TATAGTATATAGTATATAAATATCAAC
1 TATAGTATATAGTATATAAATATAAAC
* *
413592 TATAGTATATAGT-T-TATATATATA-
1 TATAGTATATAGTATATAAATATAAAC
* * **
413616 TATAGTTTTTATGTATAGTTCATACGTAAAC
1 TATAGTATATA-GTATA-TAAATA--TAAAC
** *
413647 TATA-TAGTATA-TATAGTTTATATATAC
1 TATAGTA-TATAGTATA-TAAATATAAAC
**
413674 -A-A-TATATAGTATATAAATATCCAC
1 TATAGTATATAGTATATAAATATAAAC
413698 TATAGTATATAGTATATAAATATAAAC
1 TATAGTATATAGTATATAAATATAAAC
* *
413725 TATAGTTTATATAGTTTATATATATA
1 TATAG--TATATAGTATATAAATATA
413751 GTATATATTA
Statistics
Matches: 169, Mismatches: 28, Indels: 30
0.74 0.12 0.13
Matches are distributed among these distances:
24 20 0.12
25 17 0.10
26 5 0.03
27 85 0.50
28 4 0.02
29 27 0.16
30 4 0.02
31 7 0.04
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.42
Consensus pattern (27 bp):
TATAGTATATAGTATATAAATATAAAC
Found at i:413664 original size:29 final size:29
Alignment explanation
Indices: 413629--413688 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
413619 AGTTTTTATG
*
413629 TATAGTTCATACGTA-AACTATATAGTATA
1 TATAGTTCATACATACAA-TATATAGTATA
* *
413658 TATAGTTTATATATACAATATATAGTATA
1 TATAGTTCATACATACAATATATAGTATA
413687 TA
1 TA
413689 AATATCCACT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 25 0.93
30 2 0.07
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.42
Consensus pattern (29 bp):
TATAGTTCATACATACAATATATAGTATA
Found at i:413710 original size:280 final size:285
Alignment explanation
Indices: 413202--413757 Score: 865
Period size: 280 Copynumber: 2.0 Consensus size: 285
413192 TTTGGGGTAT
* *
413202 TATAGTATATACTTTGAATTTATATAGTATAAATTATATAAATATCAACTATAGTATATAATATA
1 TATAGTATATACTTTAAATTTATATAGTATAAATTATATAAATATAAACTATAGTATATAATATA
* **
413267 TAAATATCAACTATAGTATATAGTTTATATGTAAACTATAGTTTATATATATATATATATATATA
66 TAAATAACAACTATAGTATATAG-TTATA-GTAAACTATAGACTATATATATATATATATATATA
* * *
413332 TATATATAGTTTTTATATGTAATTCATATGTAAACTATATAGTATATATAGTTTATATACATAAT
129 TATATATAGTTTTTATATATAATTCATACGTAAACTATATAGTATATATAGTTTATATACACAAT
*
413397 ATATAGTATATAAATATCAACTATAGTATATAGTATGTAAATATAAACTATAGTTTATATAGTTT
194 ATATAGTATATAAATATCAACTATAGTATATAGTATATAAATATAAACTATAGTTTATATAGTTT
413462 ATATATATAGTATATAGTATTCATATA
259 ATATATATAGTATATAGTATTCATATA
* * *
413489 TATAGTATATACTTTAAATTTATATAGTATAAATTATATAAGTATAAACTATATTATATAGTATA
1 TATAGTATATACTTTAAATTTATATAGTATAAATTATATAAATATAAACTATAGTATATAATATA
* *
413554 TAAATAACAATTATAGTATATAG-TATA-TAAA-TATCA-ACTATAGTATATA-GT-T-TATATA
66 TAAATAACAACTATAGTATATAGTTATAGTAAACTAT-AGACTATA-TATATATATATATATATA
* * *
413612 TATATATAGTTTTTATGTATAGTTCATACGTAAACTATATAGTATATATAGTTTATATATACAAT
129 TATATATAGTTTTTATATATAATTCATACGTAAACTATATAGTATATATAGTTTATATACACAAT
*
413677 ATATAGTATATAAATATCCACTATAGTATATAGTATATAAATATAAACTATAGTTTATATAGTTT
194 ATATAGTATATAAATATCAACTATAGTATATAGTATATAAATATAAACTATAGTTTATATAGTTT
413742 ATATATATAGTATATA
259 ATATATATAGTATATA
413758 TTATATAAGT
Statistics
Matches: 249, Mismatches: 18, Indels: 11
0.90 0.06 0.04
Matches are distributed among these distances:
280 144 0.58
281 1 0.00
282 8 0.03
283 11 0.04
285 4 0.02
287 81 0.33
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (285 bp):
TATAGTATATACTTTAAATTTATATAGTATAAATTATATAAATATAAACTATAGTATATAATATA
TAAATAACAACTATAGTATATAGTTATAGTAAACTATAGACTATATATATATATATATATATATA
TATATAGTTTTTATATATAATTCATACGTAAACTATATAGTATATATAGTTTATATACACAATAT
ATAGTATATAAATATCAACTATAGTATATAGTATATAAATATAAACTATAGTTTATATAGTTTAT
ATATATAGTATATAGTATTCATATA
Found at i:413770 original size:18 final size:18
Alignment explanation
Indices: 413303--413882 Score: 95
Period size: 20 Copynumber: 31.7 Consensus size: 18
413293 ATATGTAAAC
*
413303 TATAGTTTATA-TATATA
1 TATAGTATATATTATATA
413320 TATA-TATATA-TATATA
1 TATAGTATATATTATATA
*
413336 TATAGTTTTTATATGTA-AT-
1 TATAG--TATATAT-TATATA
*
413355 TCATATGTAAACTATATAGTATA
1 T-ATA-GTATA-TAT-TA-TATA
* *
413378 TATAGTTTATATACATAATA
1 TATAGTATATAT-TAT-ATA
*
413398 TATAGTATATA-AATATCAA
1 TATAGTATATATTATAT--A
* *
413417 CTATAGTATATAGTATGTA
1 -TATAGTATATATTATATA
* * *
413436 AATA-TAAACTA-TAGTTTA
1 TATAGTATA-TATTA-TATA
413454 TATAGT-T-TA-TATATA
1 TATAGTATATATTATATA
413469 TAGTA-TATAGTATTCATATA
1 TA-TAGTATA-TATT-ATATA
*
413489 TATAGTATATACTTTAAATTTA
1 TATAGTATATA--TT--ATATA
*
413511 TATAGTATA-AAT-TATA
1 TATAGTATATATTATATA
* *
413527 TA-AGTATAAACTATATTA
1 TATAGTATATATTATA-TA
* *
413545 TATAGTATATA-AATAACAA
1 TATAGTATATATTAT-A-TA
*
413564 TTATAGTATATAGTATATA
1 -TATAGTATATATTATATA
*
413583 -A-A-TATCA-ACTATAGTA
1 TATAGTAT-ATATTATA-TA
*
413599 TATAGTTTATA-TATATA
1 TATAGTATATATTATATA
* *
413616 TATAGTTTTTATGTATAGT-
1 TATAGTATATAT-TATA-TA
*
413635 TCATACGTAAACTATATAGTATA
1 T-ATA-GTATA-TAT-TA-TATA
* *
413658 TATAGTTTATATATACAATA
1 TATAGTATATAT-TA-TATA
*
413678 TATAGTATATA-AATATCCA
1 TATAGTATATATTATAT--A
*
413697 CTATAGTATATAGTATATA
1 -TATAGTATATATTATATA
* *
413716 -A-A-TATAAACTATAGT-
1 TATAGTATATATTATA-TA
413731 T-TA-TATAGT-TTATATA
1 TATAGTATA-TATTATATA
413747 TATAGTATATATTATATA
1 TATAGTATATATTATATA
* *
413765 -AGTAGTTTATATAAT-TCA
1 TA-TAGTATATATTATAT-A
* *
413783 T-TA--ATAAACTATATA
1 TATAGTATATATTATATA
* *
413798 TATTGT-TCATATGTAAACTA
1 TATAGTAT-ATAT-TATA-TA
*
413818 TATAGTATATA-TAGTTTA
1 TATAGTATATATTA-TATA
413836 TATA-TATAGT-TTATATA
1 TATAGTATA-TATTATATA
*
413853 TGTAGTATATATTATATA
1 TATAGTATATATTATATA
* *
413871 AATAGTTTATAT
1 TATAGTATATAT
413883 ATACTAATGA
Statistics
Matches: 419, Mismatches: 66, Indels: 155
0.65 0.10 0.24
Matches are distributed among these distances:
15 37 0.09
16 47 0.11
17 49 0.12
18 84 0.20
19 41 0.10
20 106 0.25
21 24 0.06
22 27 0.06
23 4 0.01
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (18 bp):
TATAGTATATATTATATA
Found at i:413799 original size:24 final size:24
Alignment explanation
Indices: 413772--413826 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
413762 ATAAGTAGTT
413772 TATATAATTCAT-TAATAAACTATA
1 TATATAATTCATAT-ATAAACTATA
** *
413796 TATATTGTTCATATGTAAACTATA
1 TATATAATTCATATATAAACTATA
413820 TAGTATA
1 TA-TATA
413827 TATAGTTTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
24 21 0.84
25 4 0.16
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (24 bp):
TATATAATTCATATATAAACTATA
Found at i:413851 original size:31 final size:31
Alignment explanation
Indices: 413725--413915 Score: 114
Period size: 31 Copynumber: 6.1 Consensus size: 31
413715 AAATATAAAC
*
413725 TATAGTTTATATAGTTTATATATATAG--TA
1 TATAGTATATATAGTTTATATATATAGTTTA
* *
413754 TATATTATATAAGTAGTTTATATA-ATTCA-TTAA
1 TATAGTATAT-A-TAGTTTATATATA-T-AGTTTA
* * * ***
413787 TAAACTATATATA-TTGT-TCATATGTAAACTA
1 TATAGTATATATAGTT-TAT-ATATATAGTTTA
413818 TATAGTATATATAGTTTATATATATAGTTTA
1 TATAGTATATATAGTTTATATATATAGTTTA
*
413849 TATATGTAGTATATA--TTATATAAATAGTTTA
1 TATA-GTA-TATATAGTTTATATATATAGTTTA
*
413880 TATA-TACTA-ATGACTTTATAATATATAGTTTA
1 TATAGTA-TATAT-AGTTTAT-ATATATAGTTTA
413912 TATA
1 TATA
413916 TACTAATGAA
Statistics
Matches: 126, Mismatches: 18, Indels: 33
0.71 0.10 0.19
Matches are distributed among these distances:
28 2 0.02
29 13 0.10
30 6 0.05
31 67 0.53
32 23 0.18
33 15 0.12
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.48
Consensus pattern (31 bp):
TATAGTATATATAGTTTATATATATAGTTTA
Found at i:413897 original size:18 final size:18
Alignment explanation
Indices: 413876--413924 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 18
413866 ATATAAATAG
413876 TTTATATATACTAATGAC
1 TTTATATATACTAATGAC
*
413894 TTTATA-ATA-T-AT-AG
1 TTTATATATACTAATGAC
413908 TTTATATATACTAATGA
1 TTTATATATACTAATGA
413925 ACTATATAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
14 7 0.27
15 5 0.19
16 2 0.08
17 5 0.19
18 7 0.27
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (18 bp):
TTTATATATACTAATGAC
Found at i:413958 original size:30 final size:26
Alignment explanation
Indices: 413901--413980 Score: 72
Period size: 26 Copynumber: 2.9 Consensus size: 26
413891 GACTTTATAA
*
413901 TATATAGTTTATATATACTAATGAAC
1 TATATAGTTTATATATACTAATAAAC
*
413927 TATATAGTTTATTAATATAATTATATAAAC
1 TATATAGTTTA-T-ATAT-ACTA-ATAAAC
*
413957 TATATATAGTTCATATATAC-AATA
1 --TATATAGTTTATATATACTAATA
413981 CATAGTTTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
26 11 0.25
27 4 0.09
28 5 0.11
29 4 0.09
30 9 0.20
31 1 0.02
32 10 0.23
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Consensus pattern (26 bp):
TATATAGTTTATATATACTAATAAAC
Found at i:414000 original size:20 final size:20
Alignment explanation
Indices: 413962--414000 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
413952 TAAACTATAT
*
413962 ATAGTTCATATATACAATAC
1 ATAGTTCATATACACAATAC
* *
413982 ATAGTTTATATACATAATA
1 ATAGTTCATATACACAATA
414001 TAAAACTATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.38
Consensus pattern (20 bp):
ATAGTTCATATACACAATAC
Found at i:417704 original size:112 final size:112
Alignment explanation
Indices: 417503--417969 Score: 785
Period size: 112 Copynumber: 4.2 Consensus size: 112
417493 CTTATATAGT
*
417503 AAAATATGACAAAACCAGTTTCATTATGATAAAACCGGTAAAATTTACCTGATATGTTGAAAGTA
1 AAAATATGACAAAACCAGTTTCATTATGACAAAACCGGTAAAATTTACCTGATATGTTGAAAGTA
* *
417568 TCGATCATTTTTATAAAAAAGATCGATACTTTACAATATAACAAGTA
66 TCGATCATTTTTATAAAAAGGATCGATACTTTACAATATAACAGGTA
*
417615 AAAATATGACAAAACTAGTTTCATTATGACAAAACCGGTAAAATTTACCTGATATGTTGAAAGTA
1 AAAATATGACAAAACCAGTTTCATTATGACAAAACCGGTAAAATTTACCTGATATGTTGAAAGTA
* *
417680 TCGATCCTTTTTATAAAAAGGATCGTTACTTTACAATATAACAGGTA
66 TCGATCATTTTTATAAAAAGGATCGATACTTTACAATATAACAGGTA
* *
417727 AAAATATGACAAAATCAGTTTCATTATGACAAAACCGGTAAAATTTACCTAATATGTTGAAAGTA
1 AAAATATGACAAAACCAGTTTCATTATGACAAAACCGGTAAAATTTACCTGATATGTTGAAAGTA
* *
417792 TCGATCCA-TTTTATAAAAAGAATCGATACTTTATAATATAACAGGTA
66 TCGAT-CATTTTTATAAAAAGGATCGATACTTTACAATATAACAGGTA
* *
417839 AAAATATGACAAAACCAATTTTATTATGAC-AAACTCGGTAAAATTTACCTGATATGTTGAAAGT
1 AAAATATGACAAAACCAGTTTCATTATGACAAAAC-CGGTAAAATTTACCTGATATGTTGAAAGT
417903 ATCGATCATTTTTATAAAAAGGATCGATACTTTACAATATAACAGGTA
65 ATCGATCATTTTTATAAAAAGGATCGATACTTTACAATATAACAGGTA
*
417951 AAAATATGAAAAAACCAGT
1 AAAATATGACAAAACCAGT
417970 AAAATTTACC
Statistics
Matches: 331, Mismatches: 21, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
111 6 0.02
112 324 0.98
113 1 0.00
ACGTcount: A:0.44, C:0.13, G:0.12, T:0.31
Consensus pattern (112 bp):
AAAATATGACAAAACCAGTTTCATTATGACAAAACCGGTAAAATTTACCTGATATGTTGAAAGTA
TCGATCATTTTTATAAAAAGGATCGATACTTTACAATATAACAGGTA
Found at i:418446 original size:87 final size:87
Alignment explanation
Indices: 418347--418545 Score: 310
Period size: 87 Copynumber: 2.3 Consensus size: 87
418337 TTCCACGCTA
*
418347 TTTATATAATAAAATAGGTTAATTACT-GAAAACATTATCAAACACAATAACATATTAGGTATCA
1 TTTATATAATAAAATAGGTTAATTACTAG-AAACATTATCAAACACAATAACATATTAGGTAGCA
* *
418411 ATTATATAATGTAATAAGTAGTG
65 ATTATATAACGTAATAAGTAGCG
* **
418434 TTTATATAATAAAATAGGTTAATTACTAGAAACATTATCAATCACAATAACATATTAGGTAGCGC
1 TTTATATAATAAAATAGGTTAATTACTAGAAACATTATCAAACACAATAACATATTAGGTAGCAA
*
418499 TTATATAACGTAATAGGTAGCG
66 TTATATAACGTAATAAGTAGCG
*
418521 CTTATATAATAAAATAGGTTAATTA
1 TTTATATAATAAAATAGGTTAATTA
418546 TTTAATTTGT
Statistics
Matches: 103, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
87 102 0.99
88 1 0.01
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.34
Consensus pattern (87 bp):
TTTATATAATAAAATAGGTTAATTACTAGAAACATTATCAAACACAATAACATATTAGGTAGCAA
TTATATAACGTAATAAGTAGCG
Found at i:418506 original size:23 final size:23
Alignment explanation
Indices: 418480--418539 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
418470 ATCAATCACA
*
418480 ATAACATATTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
*
418503 ATAACGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
* *
418526 ATAATAAAATAGGT
1 ATAACATAATAGGT
418540 TAATTATTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.32
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:418965 original size:114 final size:112
Alignment explanation
Indices: 418765--419104 Score: 463
Period size: 114 Copynumber: 3.0 Consensus size: 112
418755 TAGCGCCTAT
*
418765 AATGTATCGATACTTTACAATATAACAGGTAAAAATATGACAAAACTAGTTTCATTATGACAAAA
1 AATGTATCGATACTTTACAATATAACA-GTAAAAATATGACAAAACCAGTTTCATTATGACAAAA
* * *
418830 -ATGGTAAAATTTACCGGATATGTTGAAAGTATCGATTTTTTTTTATAAA
65 CA-AGTAAAATTTACCTGATATGTTGAAAGTATCGA-TTATTTTTATAAA
* * *
418879 AATGTATCGATACTTTACATTATAACATGTAAAAGTATAACAAAACCAGTTTCATTATGACAAAA
1 AATGTATCGATACTTTACAATATAACA-GTAAAAATATGACAAAACCAGTTTCATTATGACAAAA
**
418944 CAAGTAAAATTTACCTGATATGTTGAAAGTATCGA-TCCTTTTATAAA
65 CAAGTAAAATTTACCTGATATGTTGAAAGTATCGATTATTTTTATAAA
** * *
418991 AA-AAATCGATACTTTATAATATAACAGATAAAAATATGACAAAA-CAGTTTCATTATGAAAAAA
1 AATGTATCGATACTTTACAATATAACAG-TAAAAATATGACAAAACCAGTTTCATTATGACAAAA
* * *
419054 CCAGTAAAATTTACCTAATATGTTGAAAGTATCGATCATTTTTATAAA
65 CAAGTAAAATTTACCTGATATGTTGAAAGTATCGATTATTTTTATAAA
419102 AAT
1 AAT
419105 ATGATAAAAT
Statistics
Matches: 201, Mismatches: 21, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
110 52 0.26
111 45 0.22
112 12 0.06
114 91 0.45
115 1 0.00
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.33
Consensus pattern (112 bp):
AATGTATCGATACTTTACAATATAACAGTAAAAATATGACAAAACCAGTTTCATTATGACAAAAC
AAGTAAAATTTACCTGATATGTTGAAAGTATCGATTATTTTTATAAA
Found at i:419155 original size:80 final size:79
Alignment explanation
Indices: 419018--419165 Score: 224
Period size: 80 Copynumber: 1.9 Consensus size: 79
419008 AATATAACAG
* *
419018 ATAAAAATATGACAAAACAGTTTCATTATGAAAAAACCAGTAAAATTTACCTAATATGTTGAAAG
1 ATAAAAATATGACAAAACAGTTTCATTATGAAAAAACCAGTAAAATTTACCTAATATGCTAAAAG
419083 TATCGATCATTTTT
66 TATCGATCATTTTT
* * * * *
419097 ATAAAAATATGATAAAATCAGTTTCATTATGACAGAACCGGTAAAATTTACCTTATATGCTAAAA
1 ATAAAAATATGACAAAA-CAGTTTCATTATGAAAAAACCAGTAAAATTTACCTAATATGCTAAAA
419162 GTAT
65 GTAT
419166 AGATACTTTT
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
79 16 0.26
80 45 0.74
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.32
Consensus pattern (79 bp):
ATAAAAATATGACAAAACAGTTTCATTATGAAAAAACCAGTAAAATTTACCTAATATGCTAAAAG
TATCGATCATTTTT
Found at i:423407 original size:36 final size:36
Alignment explanation
Indices: 423367--423436 Score: 108
Period size: 36 Copynumber: 1.9 Consensus size: 36
423357 AAATACAAAT
423367 GTGTACCGATACCCCT--ATGAGTGTATCCATACACTG
1 GTGTACCGATACCCCTGCA-G-GTGTATCCATACACTG
423403 GTGTACCGATACCCCTGCAGGTGTATCCATACAC
1 GTGTACCGATACCCCTGCAGGTGTATCCATACAC
423437 CTATGACTGC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
36 30 0.94
37 1 0.03
38 1 0.03
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (36 bp):
GTGTACCGATACCCCTGCAGGTGTATCCATACACTG
Found at i:426548 original size:18 final size:18
Alignment explanation
Indices: 426525--426582 Score: 80
Period size: 18 Copynumber: 3.1 Consensus size: 18
426515 CAACAATTGG
426525 TAACAATTGGTATCTTTT
1 TAACAATTGGTATCTTTT
*
426543 TAACAATTGATATCCTTTTGT
1 TAACAATTGGTAT-C-TTT-T
426564 TAACAATTGGTATCTTTT
1 TAACAATTGGTATCTTTT
426582 T
1 T
426583 CATTAAACAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 14 0.40
19 4 0.11
20 4 0.11
21 13 0.37
ACGTcount: A:0.28, C:0.12, G:0.10, T:0.50
Consensus pattern (18 bp):
TAACAATTGGTATCTTTT
Found at i:426568 original size:21 final size:20
Alignment explanation
Indices: 426525--426582 Score: 77
Period size: 21 Copynumber: 3.0 Consensus size: 20
426515 CAACAATTGG
426525 TAACAATTGGTAT-C-TTTT
1 TAACAATTGGTATCCTTTTT
*
426543 TAACAATTGATATCCTTTTGT
1 TAACAATTGGTATCCTTTT-T
426564 TAACAATTGGTAT-CTTTTT
1 TAACAATTGGTATCCTTTTT
426583 CATTAAACAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 12 0.34
19 2 0.06
20 8 0.23
21 13 0.37
ACGTcount: A:0.28, C:0.12, G:0.10, T:0.50
Consensus pattern (20 bp):
TAACAATTGGTATCCTTTTT
Found at i:426841 original size:35 final size:37
Alignment explanation
Indices: 426795--426863 Score: 97
Period size: 35 Copynumber: 1.9 Consensus size: 37
426785 AAATGCAAAT
* *
426795 GTGTATTGATACCCTATG-A-GTGTATCCATACATTG
1 GTGTATCGATACCCCATGCAGGTGTATCCATACATTG
*
426830 GTGTATCGATACCCCCTGCAGGTGTATCCATACA
1 GTGTATCGATACCCCATGCAGGTGTATCCATACA
426864 CCTATGACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 15 0.52
36 1 0.03
37 13 0.45
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (37 bp):
GTGTATCGATACCCCATGCAGGTGTATCCATACATTG
Found at i:429280 original size:19 final size:19
Alignment explanation
Indices: 429252--429299 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
429242 CTTTTCTATA
*
429252 ATGAATTTGTGTTATAAAG
1 ATGAAATTGTGTTATAAAG
429271 ATGAAATTGTGTTATAAAG
1 ATGAAATTGTGTTATAAAG
429290 ATGAAATTGT
1 ATGAAATTGT
429300 TGTCTTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.40, C:0.00, G:0.21, T:0.40
Consensus pattern (19 bp):
ATGAAATTGTGTTATAAAG
Found at i:432411 original size:15 final size:15
Alignment explanation
Indices: 432386--432423 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
432376 ACAAAGGCTA
432386 TGCACATTTTATGTTG
1 TGCA-ATTTTATGTTG
432402 TGCAATTTTATGTTG
1 TGCAATTTTATGTTG
432417 TGCAATT
1 TGCAATT
432424 GATCCTAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 18 0.82
16 4 0.18
ACGTcount: A:0.21, C:0.11, G:0.18, T:0.50
Consensus pattern (15 bp):
TGCAATTTTATGTTG
Found at i:436831 original size:23 final size:23
Alignment explanation
Indices: 436799--436881 Score: 91
Period size: 23 Copynumber: 3.7 Consensus size: 23
436789 TTAGTGCAGA
*
436799 GGGAATCGATACCCCCCTTGAAG
1 GGGAACCGATACCCCCCTTGAAG
* *
436822 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATACCCCCCTTGAAG
*
436845 GGGAACCGAT-TCCCCC-T-ATAG
1 GGGAACCGATACCCCCCTTGA-AG
*
436866 GGGAATCGATACCCCC
1 GGGAACCGATACCCCC
436882 TGGGGGTTCT
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
20 1 0.02
21 12 0.24
22 8 0.16
23 30 0.59
ACGTcount: A:0.24, C:0.33, G:0.25, T:0.18
Consensus pattern (23 bp):
GGGAACCGATACCCCCCTTGAAG
Found at i:439117 original size:30 final size:30
Alignment explanation
Indices: 439074--439133 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
439064 CAATTTAAGG
439074 CAAAATAGTTTTTGGACTTGAATTGAATTTA
1 CAAAATAGTTTTTGGACTT-AATTGAATTTA
439105 CAAAAT-GTTTTTGGACTTAATTGAATTTA
1 CAAAATAGTTTTTGGACTTAATTGAATTTA
439134 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (30 bp):
CAAAATAGTTTTTGGACTTAATTGAATTTA
Found at i:439239 original size:21 final size:21
Alignment explanation
Indices: 439213--439291 Score: 131
Period size: 21 Copynumber: 3.8 Consensus size: 21
439203 AAGGTGTCAA
*
439213 AGTGCATCCATGCACCCCTCC
1 AGTGCATCCATGCACCCCTGC
*
439234 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCACCCCTGC
*
439255 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCACCCCTGC
439276 AGTGCATCCATGCACC
1 AGTGCATCCATGCACC
439292 TGCACTAGTA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 55 1.00
ACGTcount: A:0.20, C:0.41, G:0.18, T:0.22
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:439279 original size:42 final size:42
Alignment explanation
Indices: 439213--439332 Score: 147
Period size: 42 Copynumber: 2.9 Consensus size: 42
439203 AAGGTGTCAA
* *
439213 AGTGCATCCATGCACCCCTCCAGTGCATCCATGCATCCCTG-C-
1 AGTGCATCCATGCATCCCTGCAGTGCATCCATGCA--CCTGACT
439255 AGTGCATCCATGCATCCCTGCAGTGCATCCATGCACCTGCACT
1 AGTGCATCCATGCATCCCTGCAGTGCATCCATGCACCTG-ACT
* * *
439298 AGTACATCGATGCAT-CATGCAGTGCATCCATGCAC
1 AGTGCATCCATGCATCCCTGCAGTGCATCCATGCAC
439333 TCAAACACCT
Statistics
Matches: 70, Mismatches: 5, Indels: 6
0.86 0.06 0.07
Matches are distributed among these distances:
40 4 0.06
42 53 0.76
43 13 0.19
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
AGTGCATCCATGCATCCCTGCAGTGCATCCATGCACCTGACT
Found at i:439319 original size:63 final size:63
Alignment explanation
Indices: 439213--439331 Score: 168
Period size: 63 Copynumber: 1.9 Consensus size: 63
439203 AAGGTGTCAA
* * *
439213 AGTGCATCCATGCACCCCTCCAGTGCATCCATGCATCCCTGCAGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCACCCCACCAGTACATCCATGCATCCATGCAGTGCATCCATGCATCCCTGC
* * *
439276 AGTGCATCCATGCACCTGCACTAGTACATCGATGCAT-CATGCAGTGCATCCATGCA
1 AGTGCATCCATGCACC-CCACCAGTACATCCATGCATCCATGCAGTGCATCCATGCA
439332 CTCAAACACC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
63 34 0.69
64 15 0.31
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (63 bp):
AGTGCATCCATGCACCCCACCAGTACATCCATGCATCCATGCAGTGCATCCATGCATCCCTGC
Found at i:442740 original size:34 final size:30
Alignment explanation
Indices: 442702--442770 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
442692 TTGATATAAC
442702 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
442736 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
442765 AATTTA
1 AATTTA
442771 TTCAAAGTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:442752 original size:30 final size:30
Alignment explanation
Indices: 442711--442770 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
442701 CAATTTAAGG
442711 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTT-AATTGAATTTA
442742 CAAAAT-GTTTTTGGACTTAATTGAATTTA
1 CAAAATGGTTTTTGGACTTAATTGAATTTA
442771 TTCAAAGTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGGTTTTTGGACTTAATTGAATTTA
Found at i:442876 original size:21 final size:21
Alignment explanation
Indices: 442850--442907 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
442840 AGGGTGTCAA
*
442850 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTAC
* *
442871 AGTGCATCCATGTATCCCTAC
1 AGTGCATCCATGCACCCCTAC
442892 AGTGCATCCATGCACC
1 AGTGCATCCATGCACC
442908 TGCACTAGTG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.22, C:0.38, G:0.17, T:0.22
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTAC
Found at i:442920 original size:22 final size:21
Alignment explanation
Indices: 442892--442948 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
442882 GTATCCCTAC
*
442892 AGTGCATCCATGCACCTGCACT
1 AGTGCATCCATGCACATGCA-T
*
442914 AGTGCATCGATGCATCATGCAT
1 AGTGCATCCATGCA-CATGCAT
442936 --TGCATCCATGCAC
1 AGTGCATCCATGCAC
442949 TCAAACACCG
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 1 0.03
20 11 0.35
22 14 0.45
23 5 0.16
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.25
Consensus pattern (21 bp):
AGTGCATCCATGCACATGCAT
Found at i:442993 original size:21 final size:21
Alignment explanation
Indices: 442969--443025 Score: 114
Period size: 21 Copynumber: 2.7 Consensus size: 21
442959 AATTCAATTA
442969 GTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATCAAGGCT
442990 GTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATCAAGGCT
443011 GTGCATCGATGCATC
1 GTGCATCGATGCATC
443026 CTGTTGTGCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.25
Consensus pattern (21 bp):
GTGCATCGATGCATCAAGGCT
Found at i:443194 original size:20 final size:22
Alignment explanation
Indices: 443156--443195 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
443146 TTTGAGTAGA
443156 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
443178 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
443196 ATATACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:443864 original size:12 final size:12
Alignment explanation
Indices: 443836--443870 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
443826 TAAGGGGGAG
443836 TAATTTC-AAAT
1 TAATTTCAAAAT
443847 TAATTTCAAAAT
1 TAATTTCAAAAT
*
443859 TGATTTCAAAAT
1 TAATTTCAAAAT
443871 CTTAAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 7 0.32
12 15 0.68
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.43
Consensus pattern (12 bp):
TAATTTCAAAAT
Found at i:450978 original size:30 final size:30
Alignment explanation
Indices: 450944--451004 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
450934 GTTAATACTT
450944 TGTATTTTATATAAGGGTAAAGTATAATAA
1 TGTATTTTATATAAGGGTAAAGTATAATAA
*
450974 TGTATTTTATATAAGGGTAAAGTATAGTAA
1 TGTATTTTATATAAGGGTAAAGTATAATAA
451004 T
1 T
451005 AGTCGCTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (30 bp):
TGTATTTTATATAAGGGTAAAGTATAATAA
Found at i:451305 original size:35 final size:35
Alignment explanation
Indices: 451254--451321 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
451244 AATACAGTCC
*
451254 TCAATTTCATTCTAAACCTCAAATTCCAAAATAAT
1 TCAATTGCATTCTAAACCTCAAATTCCAAAATAAT
* * *
451289 TCAATTGCATTTTAAACCTTAAATTCTAAAATA
1 TCAATTGCATTCTAAACCTCAAATTCCAAAATA
451322 CTTTAATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.43, C:0.19, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTGCATTCTAAACCTCAAATTCCAAAATAAT
Found at i:451372 original size:35 final size:35
Alignment explanation
Indices: 451326--451400 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
451316 AAAATACTTT
451326 AATTTAAGGTTTAGAATATAATTAAAGTATTTTGG
1 AATTTAAGGTTTAGAATATAATTAAAGTATTTTGG
* * * *
451361 AATTTAGGGTTTAGAATATAGTTGAAGTGTTTTGG
1 AATTTAAGGTTTAGAATATAATTAAAGTATTTTGG
451396 AATTT
1 AATTT
451401 TGAACATGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (35 bp):
AATTTAAGGTTTAGAATATAATTAAAGTATTTTGG
Found at i:454666 original size:10 final size:10
Alignment explanation
Indices: 454651--454675 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
454641 GACTCATACG
454651 ATAAACATAT
1 ATAAACATAT
454661 ATAAACATAT
1 ATAAACATAT
454671 ATAAA
1 ATAAA
454676 AAAAACTGTA
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:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (10 bp):
ATAAACATAT
Found at i:455099 original size:39 final size:38
Alignment explanation
Indices: 455036--455167 Score: 133
Period size: 39 Copynumber: 3.4 Consensus size: 38
455026 CATGTACACC
* *
455036 CAGTAAGGGCTTACCTTCTACACAAAGCAGAGGAGCCTG
1 CAGTAAGGACTTACCTT-TGCACAAAGCAGAGGAGCCTG
* *
455075 CAGTAAGGCCTTATCCTTTGCACAAAGTAGAGGAGCCTG
1 CAGTAAGGACTTA-CCTTTGCACAAAGCAGAGGAGCCTG
* * * *
455114 CAGTAAAGACTTACTCTGTGCACAAAGCCA-AAGAGCTTG
1 CAGTAAGGACTTAC-CTTTGCACAAAG-CAGAGGAGCCTG
455153 C-GATAAGGACTTACC
1 CAG-TAAGGACTTACC
455168 CTGAACACAA
Statistics
Matches: 79, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
38 3 0.04
39 71 0.90
40 5 0.06
ACGTcount: A:0.32, C:0.24, G:0.23, T:0.20
Consensus pattern (38 bp):
CAGTAAGGACTTACCTTTGCACAAAGCAGAGGAGCCTG
Found at i:465163 original size:12 final size:12
Alignment explanation
Indices: 465146--465172 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
465136 CTAGGAATAG
465146 GCGGATCTACAT
1 GCGGATCTACAT
465158 GCGGATCTACAT
1 GCGGATCTACAT
465170 GCG
1 GCG
465173 AAACAACATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.26, G:0.30, T:0.22
Consensus pattern (12 bp):
GCGGATCTACAT
Found at i:466071 original size:39 final size:41
Alignment explanation
Indices: 465987--466121 Score: 120
Period size: 39 Copynumber: 3.4 Consensus size: 41
465977 ACTTGTACAC
* * *
465987 CAGTAAGGGCTTACCCTGTGCACAAAGAAGATGAGCCTATG
1 CAGTAAGGACTTACCCTGTGAACAAAGAAGAGGAGCCTATG
* * *
466028 --GTAAGGTCTTATCCTGTGAACAAAGTAGAGGAG-CT-TG
1 CAGTAAGGACTTACCCTGTGAACAAAGAAGAGGAGCCTATG
* * * **
466065 CAGTAAGGACTTACCCTGAGCATAAAGCCGAGGAG-C-ATG
1 CAGTAAGGACTTACCCTGTGAACAAAGAAGAGGAGCCTATG
*
466104 CGGTAAGGACTTACCCTG
1 CAGTAAGGACTTACCCTG
466122 ACCATAAAGC
Statistics
Matches: 78, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
37 2 0.03
38 2 0.03
39 74 0.95
ACGTcount: A:0.30, C:0.21, G:0.28, T:0.21
Consensus pattern (41 bp):
CAGTAAGGACTTACCCTGTGAACAAAGAAGAGGAGCCTATG
Found at i:466122 original size:39 final size:39
Alignment explanation
Indices: 466055--466144 Score: 144
Period size: 39 Copynumber: 2.3 Consensus size: 39
466045 GAACAAAGTA
* *
466055 GAGGAGCTTGCAGTAAGGACTTACCCTGAGCATAAAGCC
1 GAGGAGCATGCAGTAAGGACTTACCCTGACCATAAAGCC
*
466094 GAGGAGCATGCGGTAAGGACTTACCCTGACCATAAAGCC
1 GAGGAGCATGCAGTAAGGACTTACCCTGACCATAAAGCC
*
466133 GAGGAGCCTGCA
1 GAGGAGCATGCA
466145 ATAACCAGTA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.30, C:0.24, G:0.30, T:0.16
Consensus pattern (39 bp):
GAGGAGCATGCAGTAAGGACTTACCCTGACCATAAAGCC
Found at i:467399 original size:30 final size:29
Alignment explanation
Indices: 467363--467421 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
467353 GAATTTGGAT
* *
467363 CCAAATTTAATCAAAAATTCACTTTGGTCC
1 CCAAATTTAAT-AAAAATTCAATTTAGTCC
*
467393 CCAAATTTAATTAAAATTCAATTTAGTCC
1 CCAAATTTAATAAAAATTCAATTTAGTCC
467422 TTAAAATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.39, C:0.20, G:0.05, T:0.36
Consensus pattern (29 bp):
CCAAATTTAATAAAAATTCAATTTAGTCC
Found at i:468150 original size:9 final size:8
Alignment explanation
Indices: 468136--468199 Score: 65
Period size: 9 Copynumber: 7.1 Consensus size: 8
468126 GTCATCCCTC
468136 CTTTCTTAT
1 CTTTCTT-T
468145 CTTTCTTT
1 CTTTCTTT
468153 CCTGTTCTTT
1 -CT-TTCTTT
468163 CTTATCTTT
1 CTT-TCTTT
468172 CTTTCCTGTT
1 CTTT-CT-TT
468182 CTTTCTTAT
1 CTTTCTT-T
468191 CTTTCTTT
1 CTTTCTTT
468199 C
1 C
468200 CTGTTCCACC
Statistics
Matches: 49, Mismatches: 0, Indels: 13
0.79 0.00 0.21
Matches are distributed among these distances:
8 6 0.12
9 31 0.63
10 12 0.24
ACGTcount: A:0.05, C:0.27, G:0.03, T:0.66
Consensus pattern (8 bp):
CTTTCTTT
Found at i:468166 original size:23 final size:23
Alignment explanation
Indices: 468136--468205 Score: 140
Period size: 23 Copynumber: 3.0 Consensus size: 23
468126 GTCATCCCTC
468136 CTTTCTTATCTTTCTTTCCTGTT
1 CTTTCTTATCTTTCTTTCCTGTT
468159 CTTTCTTATCTTTCTTTCCTGTT
1 CTTTCTTATCTTTCTTTCCTGTT
468182 CTTTCTTATCTTTCTTTCCTGTT
1 CTTTCTTATCTTTCTTTCCTGTT
468205 C
1 C
468206 CACCTTTTAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.04, C:0.27, G:0.04, T:0.64
Consensus pattern (23 bp):
CTTTCTTATCTTTCTTTCCTGTT
Found at i:472712 original size:24 final size:24
Alignment explanation
Indices: 472685--472741 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
472675 TCTTAGGGCG
*
472685 ATGTATCATCATTTATCAAGGGAA
1 ATGTATCATCATTTATCAAAGGAA
* * * *
472709 ATGTACCATCTTTTATCAAAGTAG
1 ATGTATCATCATTTATCAAAGGAA
472733 ATGTATCAT
1 ATGTATCAT
472742 ATGACTTAGG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (24 bp):
ATGTATCATCATTTATCAAAGGAA
Found at i:490423 original size:40 final size:40
Alignment explanation
Indices: 490368--490447 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
490358 TTACTCATGT
490368 AGGTTTTTGAATTGCAAGGACACAAATAGGCACAAAGATG
1 AGGTTTTTGAATTGCAAGGACACAAATAGGCACAAAGATG
490408 AGGTTTTTGAATTGCAAGGACACAAATAGGCACAAAGATG
1 AGGTTTTTGAATTGCAAGGACACAAATAGGCACAAAGATG
490448 TTACATGGGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.40, C:0.12, G:0.25, T:0.23
Consensus pattern (40 bp):
AGGTTTTTGAATTGCAAGGACACAAATAGGCACAAAGATG
Found at i:493037 original size:42 final size:42
Alignment explanation
Indices: 492978--493062 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 42
492968 CTTGTAAGAC
* *
492978 CCTTTGTTCCAAATCCCTCGACTGATCTTGAGTATTAGGGGT
1 CCTTTGTTCCAAATCCCTCGACCGATCTCGAGTATTAGGGGT
*
493020 CCTTTGTTCCAAATCCCTCGACCGTTCTCGAGTATTAGGGGT
1 CCTTTGTTCCAAATCCCTCGACCGATCTCGAGTATTAGGGGT
493062 C
1 C
493063 TCTACGAAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.18, C:0.27, G:0.21, T:0.34
Consensus pattern (42 bp):
CCTTTGTTCCAAATCCCTCGACCGATCTCGAGTATTAGGGGT
Found at i:494644 original size:19 final size:19
Alignment explanation
Indices: 494605--494644 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
494595 TCAATTTGAT
* *
494605 ATATATTTTTAATAAATTA
1 ATATATTTTTAACAAAATA
*
494624 ATATTTTTTTAACAAAATA
1 ATATATTTTTAACAAAATA
494643 AT
1 AT
494645 GATACATATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (19 bp):
ATATATTTTTAACAAAATA
Found at i:494785 original size:14 final size:15
Alignment explanation
Indices: 494762--494790 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
494752 TTTTTCAATT
494762 TAAATAATTAAAATA
1 TAAATAATTAAAATA
494777 TAAAT-ATTAAAATA
1 TAAATAATTAAAATA
494791 GTTCAATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
TAAATAATTAAAATA
Found at i:498830 original size:27 final size:28
Alignment explanation
Indices: 498789--498854 Score: 98
Period size: 27 Copynumber: 2.4 Consensus size: 28
498779 TATGCACTTA
**
498789 AAAGTGCCTTGTAGGTAATTTGCACTCG
1 AAAGTGCCTCATAGGTAATTTGCACTCG
*
498817 -AAGTGTCTCATAGGTAATTTGCACTCG
1 AAAGTGCCTCATAGGTAATTTGCACTCG
498844 AAAGTGCCTCA
1 AAAGTGCCTCA
498855 GTGATTTGCA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 24 0.73
28 9 0.27
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (28 bp):
AAAGTGCCTCATAGGTAATTTGCACTCG
Found at i:500618 original size:75 final size:75
Alignment explanation
Indices: 500495--500646 Score: 304
Period size: 75 Copynumber: 2.0 Consensus size: 75
500485 TGCAACTTTA
500495 ATCCAACGATCTCAATTTAACATGGAAAATCAATCTTAAATTCCATGTTAAATTCTACCAATTTA
1 ATCCAACGATCTCAATTTAACATGGAAAATCAATCTTAAATTCCATGTTAAATTCTACCAATTTA
500560 AAAAATGGAC
66 AAAAATGGAC
500570 ATCCAACGATCTCAATTTAACATGGAAAATCAATCTTAAATTCCATGTTAAATTCTACCAATTTA
1 ATCCAACGATCTCAATTTAACATGGAAAATCAATCTTAAATTCCATGTTAAATTCTACCAATTTA
500635 AAAAATGGAC
66 AAAAATGGAC
500645 AT
1 AT
500647 GACATTATTA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 77 1.00
ACGTcount: A:0.43, C:0.18, G:0.08, T:0.31
Consensus pattern (75 bp):
ATCCAACGATCTCAATTTAACATGGAAAATCAATCTTAAATTCCATGTTAAATTCTACCAATTTA
AAAAATGGAC
Found at i:501906 original size:75 final size:75
Alignment explanation
Indices: 501783--501934 Score: 304
Period size: 75 Copynumber: 2.0 Consensus size: 75
501773 TGCAACTTTA
501783 ATCCAACGATCTCAATTTAACATGGAAAATCAATCTTAAATTCCATGTTAAATTCTACCAATTTA
1 ATCCAACGATCTCAATTTAACATGGAAAATCAATCTTAAATTCCATGTTAAATTCTACCAATTTA
501848 AAAAATGGAC
66 AAAAATGGAC
501858 ATCCAACGATCTCAATTTAACATGGAAAATCAATCTTAAATTCCATGTTAAATTCTACCAATTTA
1 ATCCAACGATCTCAATTTAACATGGAAAATCAATCTTAAATTCCATGTTAAATTCTACCAATTTA
501923 AAAAATGGAC
66 AAAAATGGAC
501933 AT
1 AT
501935 GACATTATTA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 77 1.00
ACGTcount: A:0.43, C:0.18, G:0.08, T:0.31
Consensus pattern (75 bp):
ATCCAACGATCTCAATTTAACATGGAAAATCAATCTTAAATTCCATGTTAAATTCTACCAATTTA
AAAAATGGAC
Found at i:504305 original size:13 final size:13
Alignment explanation
Indices: 504287--504327 Score: 82
Period size: 13 Copynumber: 3.2 Consensus size: 13
504277 GAAACATTCT
504287 TTGGACTTTTCCA
1 TTGGACTTTTCCA
504300 TTGGACTTTTCCA
1 TTGGACTTTTCCA
504313 TTGGACTTTTCCA
1 TTGGACTTTTCCA
504326 TT
1 TT
504328 CAACTATAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.15, C:0.22, G:0.15, T:0.49
Consensus pattern (13 bp):
TTGGACTTTTCCA
Found at i:514729 original size:13 final size:13
Alignment explanation
Indices: 514713--514737 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
514703 TTTGTTATTG
514713 CATTTTTATTTTA
1 CATTTTTATTTTA
514726 CATTTTTATTTT
1 CATTTTTATTTT
514738 TGTATAATTT
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:0.20, C:0.08, G:0.00, T:0.72
Consensus pattern (13 bp):
CATTTTTATTTTA
Found at i:530550 original size:20 final size:21
Alignment explanation
Indices: 530527--530567 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
530517 TGATCGTTAC
*
530527 ATATAATGTTTATCATGAACA
1 ATATAATATTTATCATGAACA
530548 TATATAATATTTATCATGAA
1 -ATATAATATTTATCATGAA
530568 TGATATTTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (21 bp):
ATATAATATTTATCATGAACA
Found at i:537003 original size:17 final size:17
Alignment explanation
Indices: 536951--537003 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
536941 AAGCACTATG
536951 GTGTGTAAGGATACTTA
1 GTGTGTAAGGATACTTA
** *
536968 GTGCATATGG-TACTATA
1 GTGTGTAAGGATACT-TA
*
536985 GTGTGTAAGGACACTTA
1 GTGTGTAAGGATACTTA
537002 GT
1 GT
537004 ACATCAGTGT
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
16 4 0.15
17 20 0.74
18 3 0.11
ACGTcount: A:0.28, C:0.09, G:0.28, T:0.34
Consensus pattern (17 bp):
GTGTGTAAGGATACTTA
Found at i:537038 original size:29 final size:30
Alignment explanation
Indices: 536983--537054 Score: 128
Period size: 29 Copynumber: 2.4 Consensus size: 30
536973 TATGGTACTA
536983 TAGTGTGTAAGGACACTTAGTACATCAGTG
1 TAGTGTGTAAGGACACTTAGTACATCAGTG
*
537013 TAGTGTGTAAGTACA-TTAGTACATCAGTG
1 TAGTGTGTAAGGACACTTAGTACATCAGTG
537042 TAGTGTGTAAGGA
1 TAGTGTGTAAGGA
537055 TGCTCAGTGT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
29 26 0.65
30 14 0.35
ACGTcount: A:0.31, C:0.10, G:0.28, T:0.32
Consensus pattern (30 bp):
TAGTGTGTAAGGACACTTAGTACATCAGTG
Found at i:538401 original size:17 final size:16
Alignment explanation
Indices: 538381--538460 Score: 70
Period size: 17 Copynumber: 4.8 Consensus size: 16
538371 AATAATGCAC
538381 TTCATTTAATTAAGTAG
1 TTCA-TTAATTAAGTAG
* * *
538398 TTCATTTATGAATGTGG
1 TTCATTAATTAA-GTAG
*
538415 TTCATTAATTAAAATAG
1 TTCATTAATT-AAGTAG
* *
538432 TTCATTCATTAAACTAG
1 TTCATTAATT-AAGTAG
538449 TTCATTAATTAA
1 TTCATTAATTAA
538461 ACTAGCTCCT
Statistics
Matches: 51, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
16 8 0.16
17 41 0.80
18 2 0.04
ACGTcount: A:0.36, C:0.09, G:0.10, T:0.45
Consensus pattern (16 bp):
TTCATTAATTAAGTAG
Found at i:538461 original size:17 final size:17
Alignment explanation
Indices: 538414--538465 Score: 86
Period size: 17 Copynumber: 3.1 Consensus size: 17
538404 TATGAATGTG
*
538414 GTTCATTAATTAAAATA
1 GTTCATTAATTAAACTA
*
538431 GTTCATTCATTAAACTA
1 GTTCATTAATTAAACTA
538448 GTTCATTAATTAAACTA
1 GTTCATTAATTAAACTA
538465 G
1 G
538466 CTCCTTTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (17 bp):
GTTCATTAATTAAACTA
Found at i:544362 original size:12 final size:12
Alignment explanation
Indices: 544345--544405 Score: 54
Period size: 12 Copynumber: 4.9 Consensus size: 12
544335 TAATATATTG
544345 TTTTTGAAAACA
1 TTTTTGAAAACA
544357 TTTTTGAAAAC-
1 TTTTTGAAAACA
* *
544368 TTATAT-AATATATA
1 TT-TTTGAA-A-ACA
544382 GTTTTTGAAAACA
1 -TTTTTGAAAACA
544395 TTTTTGAAAAC
1 TTTTTGAAAAC
544406 TTATATATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 12
0.71 0.07 0.22
Matches are distributed among these distances:
11 4 0.10
12 25 0.64
13 3 0.08
14 3 0.08
15 4 0.10
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.44
Consensus pattern (12 bp):
TTTTTGAAAACA
Done.